Query	CGI_ID	Hit type	PSSM-ID	From	To	E-Value	Bitscore	Accession	Short name	Incomplete	Superfamily	Definition
Q#2 - 	CGI_10000456	superfamily	241841	11	135	8.33E-46	147.279	cl00399	MoaE superfamily	 - 	 - 	"MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits."
Q#4 - 	CGI_10000774	superfamily	220249	54	121	1.85E-18	74.564	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#6 - 	CGI_10000861	superfamily	217473	50	320	1.53E-25	106.68	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#7 - 	CGI_10000994	superfamily	245612	46	539	0	645.522	cl11426	Amidase superfamily	 - 	 - 	Amidase; Amidase.  
Q#8 - 	CGI_10000643	superfamily	241600	1	181	1.26E-76	230.975	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#9 - 	CGI_10000763	superfamily	247684	57	82	0.00144517	34.6287	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10 - 	CGI_10000610	superfamily	243072	181	303	4.10E-33	120.951	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10 - 	CGI_10000610	superfamily	243072	12	131	5.08E-16	73.5718	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10 - 	CGI_10000610	superfamily	243072	278	363	2.46E-06	45.4523	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13 - 	CGI_10001333	superfamily	241739	152	460	1.49E-174	496.312	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#13 - 	CGI_10001333	superfamily	217020	2	94	2.13E-16	75.3238	cl03574	Seryl_tRNA_N superfamily	 - 	 - 	Seryl-tRNA synthetase N-terminal domain; This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Q#14 - 	CGI_10002404	superfamily	241609	45	113	8.30E-23	88.5891	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#15 - 	CGI_10002405	superfamily	216897	190	269	3.48E-15	69.2473	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#17 - 	CGI_10002407	superfamily	197676	415	437	0.000585722	38.9861	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#18 - 	CGI_10001404	superfamily	115560	136	177	0.00926158	34.0824	cl06117	MEA1 superfamily	N	 - 	"Male enhanced antigen 1 (MEA1); This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localised in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis."
Q#19 - 	CGI_10001405	superfamily	243066	30	131	1.56E-25	101.54	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19 - 	CGI_10001405	superfamily	198867	142	240	2.28E-12	63.7167	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#19 - 	CGI_10001405	superfamily	243146	381	426	3.97E-09	53.4342	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19 - 	CGI_10001405	superfamily	243146	430	472	1.66E-08	51.5082	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19 - 	CGI_10001405	superfamily	243146	331	378	3.89E-08	50.3526	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19 - 	CGI_10001405	superfamily	243146	487	538	3.32E-06	44.8567	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19 - 	CGI_10001405	superfamily	243146	528	574	9.06E-05	40.5093	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20 - 	CGI_10001406	superfamily	241581	136	234	1.17E-19	85.901	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#20 - 	CGI_10001406	superfamily	190615	338	404	2.46E-07	49.5276	cl04028	dsRNA_bind superfamily	 - 	 - 	"Double stranded RNA binding domain; This domain is a divergent double stranded RNA-binding domain. It is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules."
Q#21 - 	CGI_10001407	superfamily	243187	494	666	4.19E-103	317.205	cl02789	EFG_like_IV superfamily	 - 	 - 	"Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm."
Q#21 - 	CGI_10001407	superfamily	243185	314	407	2.30E-46	160.421	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#21 - 	CGI_10001407	superfamily	243183	662	741	3.71E-39	139.983	cl02785	Elongation_Factor_C superfamily	 - 	 - 	"Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p.  This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain.  EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown."
Q#21 - 	CGI_10001407	superfamily	247724	1	171	1.26E-67	224.033	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22 - 	CGI_10002515	superfamily	245323	530	801	2.04E-132	405.088	cl10511	Beach superfamily	 - 	 - 	"BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins."
Q#22 - 	CGI_10002515	superfamily	243092	858	1073	7.02E-33	130.148	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22 - 	CGI_10002515	superfamily	247725	421	515	1.35E-15	74.6391	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22 - 	CGI_10002515	superfamily	248312	36	187	5.01E-10	58.9041	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#23 - 	CGI_10002516	superfamily	245596	9	236	1.79E-125	357.999	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#25 - 	CGI_10001165	superfamily	241592	38	78	1.22E-21	84.6107	cl00074	H2A superfamily	NC	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#27 - 	CGI_10001233	superfamily	241563	66	97	1.80E-06	45.3559	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27 - 	CGI_10001233	superfamily	248318	14	37	0.00496026	35.4486	cl17764	FYVE superfamily	C	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#30 - 	CGI_10002446	superfamily	243179	558	636	2.50E-08	52.3501	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#32 - 	CGI_10002757	superfamily	245864	166	224	1.29E-14	71.1554	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#34 - 	CGI_10000261	superfamily	217293	1	147	1.19E-34	121.586	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#37 - 	CGI_10003755	superfamily	241572	93	138	2.62E-05	42.2257	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#37 - 	CGI_10003755	superfamily	219547	313	408	1.63E-12	63.8141	cl06669	BRF1 superfamily	 - 	 - 	Brf1-like TBP-binding domain; This region covers both the Brf homology II and III regions. This region is involved in binding TATA binding protein.
Q#37 - 	CGI_10003755	superfamily	203895	6	44	2.67E-09	53.4414	cl07036	TF_Zn_Ribbon superfamily	 - 	 - 	TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Q#37 - 	CGI_10003755	superfamily	241572	168	212	0.00318072	35.7227	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#38 - 	CGI_10003756	superfamily	243066	91	194	1.88E-21	89.2137	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#38 - 	CGI_10003756	superfamily	198867	204	307	1.09E-10	58.5068	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#40 - 	CGI_10003758	superfamily	217255	473	667	3.20E-50	174.864	cl03746	DDHD superfamily	 - 	 - 	"DDHD domain; The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3). This suggests that this region is involved in functionally important interactions in other members of this family."
Q#42 - 	CGI_10001931	superfamily	245201	694	886	1.28E-71	238.205	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#42 - 	CGI_10001931	superfamily	241584	536	616	6.04E-05	42.4835	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#43 - 	CGI_10002150	superfamily	245546	97	120	3.36E-05	39.8097	cl11198	zf-ribbon_3 superfamily	 - 	 - 	"zinc-ribbon domain; This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773."
Q#44 - 	CGI_10003110	superfamily	243054	384	610	1.85E-29	117.547	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#44 - 	CGI_10003110	superfamily	241559	135	238	2.37E-25	102.389	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#44 - 	CGI_10003110	superfamily	241559	30	124	5.74E-18	81.2031	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#44 - 	CGI_10003110	superfamily	243054	266	489	2.54E-15	75.5599	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#44 - 	CGI_10003110	superfamily	243054	502	723	1.55E-14	73.2487	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#44 - 	CGI_10003110	superfamily	247856	738	805	6.65E-12	62.5653	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#46 - 	CGI_10002840	superfamily	245202	77	165	3.58E-41	135.081	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#46 - 	CGI_10002840	superfamily	243703	1	77	7.75E-38	126.528	cl04309	RNAP_Rpb7_N_like superfamily	 - 	 - 	"RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex."
Q#47 - 	CGI_10002841	superfamily	243039	336	515	7.94E-108	322.283	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#47 - 	CGI_10002841	superfamily	247792	26	57	0.00154299	36.7182	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#48 - 	CGI_10002842	superfamily	241645	1	72	2.65E-26	95.2179	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#48 - 	CGI_10002842	superfamily	248233	73	125	8.68E-18	72.4039	cl17679	Ribosomal_S30 superfamily	 - 	 - 	Ribosomal protein S30; Ribosomal protein S30.  
Q#50 - 	CGI_10004394	superfamily	247804	809	844	4.44E-08	52.1926	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#50 - 	CGI_10004394	superfamily	212559	524	567	2.95E-07	49.9203	cl18297	SANT_MTA3_like superfamily	 - 	 - 	"Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle.  MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis."
Q#51 - 	CGI_10004395	superfamily	243176	7	526	0	876.973	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#52 - 	CGI_10004396	superfamily	244539	274	670	0	652.401	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#52 - 	CGI_10004396	superfamily	241863	79	216	7.38E-37	136.368	cl00438	Flavodoxin_2 superfamily	 - 	 - 	Flavodoxin-like fold; This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
Q#53 - 	CGI_10004397	superfamily	243490	52	299	2.78E-66	208.284	cl03656	PS_Dcarbxylase superfamily	 - 	 - 	"Phosphatidylserine decarboxylase; This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyze the reaction: Phosphatidyl-L-serine <=> phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine."
Q#55 - 	CGI_10004399	superfamily	247723	773	844	1.83E-33	124.69	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#55 - 	CGI_10004399	superfamily	247723	863	943	3.30E-37	135.617	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#59 - 	CGI_10004069	superfamily	213389	162	328	5.63E-11	62.3067	cl17092	STING_C superfamily	 - 	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#59 - 	CGI_10004069	superfamily	248012	10	90	1.23E-08	54.1209	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#60 - 	CGI_10004070	superfamily	241883	69	117	1.67E-20	79.8934	cl00466	ATP-synt_C superfamily	N	 - 	ATP synthase subunit C; ATP synthase subunit C.  
Q#62 - 	CGI_10004072	superfamily	241641	55	117	1.23E-11	58.6293	cl00150	TY superfamily	 - 	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#62 - 	CGI_10004072	superfamily	241641	141	184	7.51E-10	54.0069	cl00150	TY superfamily	N	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#64 - 	CGI_10002683	superfamily	219541	2	125	1.56E-19	79.4347	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#65 - 	CGI_10002684	superfamily	215896	20	112	4.04E-12	58.8456	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#66 - 	CGI_10003316	superfamily	222006	720	795	1.02E-09	57.2322	cl16182	Hydrolase_like2 superfamily	N	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#66 - 	CGI_10003316	superfamily	215733	319	406	2.06E-06	49.1007	cl02811	E1-E2_ATPase superfamily	C	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#71 - 	CGI_10001243	superfamily	247805	35	168	1.52E-06	44.2504	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#72 - 	CGI_10003166	superfamily	248097	1	109	1.79E-20	80.387	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#76 - 	CGI_10001588	superfamily	247745	106	447	5.10E-151	456.342	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#76 - 	CGI_10001588	superfamily	245003	442	526	4.03E-20	86.8381	cl08536	Alpha-mann_mid superfamily	 - 	 - 	"Alpha mannosidase, middle domain; Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase."
Q#77 - 	CGI_10001589	superfamily	241593	67	117	5.09E-05	41.8634	cl00075	HATPase_c superfamily	C	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#79 - 	CGI_10001648	superfamily	247724	9	179	5.59E-131	368.53	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#80 - 	CGI_10001649	superfamily	247727	53	119	6.69E-08	46.2691	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#80 - 	CGI_10001649	superfamily	247844	32	70	0.00167229	35.3629	cl17290	Methyltransf_4 superfamily	C	 - 	Putative methyltransferase; This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.
Q#82 - 	CGI_10001049	superfamily	241862	116	252	4.37E-20	85.8708	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#83 - 	CGI_10001050	superfamily	245201	286	568	3.71E-178	515.082	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#83 - 	CGI_10001050	superfamily	243040	23	118	1.60E-29	114.799	cl02447	CRD_FZ superfamily	N	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#83 - 	CGI_10001050	superfamily	241609	143	215	1.05E-21	90.9003	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#85 - 	CGI_10004307	superfamily	149284	224	370	2.32E-44	153.419	cl06952	CPL superfamily	 - 	 - 	CPL (NUC119) domain; This C terminal domain is fund in Penguin-like proteins associated with Pumilio like repeats.
Q#85 - 	CGI_10004307	superfamily	243032	126	255	9.02E-05	42.9639	cl02427	Pumilio superfamily	NC	 - 	"Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats."
Q#87 - 	CGI_10001530	superfamily	247916	114	204	5.92E-19	81.6602	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#87 - 	CGI_10001530	superfamily	216198	439	536	0.00248928	36.5229	cl08295	Transglut_C superfamily	 - 	 - 	"Transglutaminase family, C-terminal ig like domain; Transglutaminase family, C-terminal ig like domain.  "
Q#88 - 	CGI_10001531	superfamily	201479	64	188	8.04E-30	108.485	cl02994	Transglut_N superfamily	 - 	 - 	Transglutaminase family; Transglutaminase family.  
Q#89 - 	CGI_10001532	superfamily	220376	45	136	3.77E-08	48.1736	cl10729	DUF2040 superfamily	C	 - 	"Coiled-coil domain-containing protein 55 (DUF2040); This entry is a conserved domain of approximately 130 residues of proteins conserved from fungi to humans. The proteins do contain a coiled-coil domain, but the function is unknown."
Q#90 - 	CGI_10001586	superfamily	245864	2	462	8.89E-58	199.391	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#91 - 	CGI_10001587	superfamily	247856	64	124	6.39E-07	42.5349	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#91 - 	CGI_10001587	superfamily	247856	1	38	0.000681633	34.4457	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#92 - 	CGI_10005941	superfamily	241563	63	98	4.08E-05	41.504	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#92 - 	CGI_10005941	superfamily	243092	308	439	0.00139174	39.6256	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#92 - 	CGI_10005941	superfamily	241563	8	53	0.0019754	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#96 - 	CGI_10005945	superfamily	247637	63	89	0.00933949	33.2412	cl16912	MDR superfamily	N	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#97 - 	CGI_10005946	superfamily	245864	4	435	1.60E-52	184.019	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#99 - 	CGI_10005948	superfamily	247792	8	56	6.06E-07	45.8996	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#99 - 	CGI_10005948	superfamily	241563	157	188	0.00156573	36.1611	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#101 - 	CGI_10009164	superfamily	195671	13	143	1.80E-44	145.286	cl08257	Ribosomal_L11 superfamily	 - 	 - 	"Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation."
Q#102 - 	CGI_10009165	superfamily	197827	305	342	2.86E-06	44.8161	cl02725	CARP superfamily	 - 	 - 	Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product; Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product.  
Q#103 - 	CGI_10009166	superfamily	246925	52	300	2.78E-09	57.3654	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#104 - 	CGI_10009167	superfamily	241754	12	369	0	588.497	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#106 - 	CGI_10009169	superfamily	243092	88	401	4.80E-53	180.223	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#107 - 	CGI_10009170	superfamily	243072	182	277	5.35E-13	66.6382	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#107 - 	CGI_10009170	superfamily	243072	570	648	4.28E-09	55.0822	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#107 - 	CGI_10009170	superfamily	243072	444	614	9.71E-05	41.6003	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#108 - 	CGI_10009171	superfamily	241609	102	173	1.65E-15	68.1858	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#108 - 	CGI_10009171	superfamily	241629	59	84	0.000115088	39.221	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#111 - 	CGI_10009174	superfamily	219670	1	69	2.79E-06	45.4557	cl06834	zf-C3HC superfamily	N	 - 	"C3HC zinc finger-like; This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) proteins. NIPA is implicate to perform some sort of antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signaling events. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe the protein containing this domain is involved in mRNA export from the nucleus."
Q#111 - 	CGI_10009174	superfamily	219926	102	137	2.37E-05	42.416	cl07279	Rsm1 superfamily	C	 - 	Rsm1-like; Rsm1 is a protein involved in mRNA export from the nucleus
Q#112 - 	CGI_10009175	superfamily	242042	1	67	2.24E-41	131.032	cl00712	RNA_pol_N superfamily	 - 	 - 	RNA polymerases N / 8 kDa subunit; RNA polymerases N / 8 kDa subunit.  
Q#113 - 	CGI_10009176	superfamily	244265	230	508	3.95E-42	152.632	cl05973	FAM20_C_like superfamily	 - 	 - 	"C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins; Drosophila Fj is a Golgi kinase that phosphorylates Ser or Thr residues within extracellular cadherin domains of a transmembrane receptor Fat and its ligand, Dachsous (Ds). The Fat signaling pathway regulates growth, gene expression, and planar cell polarity (PCP). Defects from mutation in the Drosophila fj gene include loss of the intermediate leg joint, and a PCP defect in the eye. Fjx1, the murine homologue of Fj, has been shown to be involved in both the Fat and Hippo signaling pathways, these two pathways intersect at multiple points. The Hippo pathway is important in organ size control and in cancer. FAM20B is a xylose kinase that may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. This domain has homology to a kinase-active site, mutation of three conserved Asp residues at the Drosophila Fj putative active site abolished its ability to phosphorylate Ft and Ds cadherin domains. FAM20A may participate in enamel development and gingival homeostasis, FAM20B in proteoglycan production, and FAM20C in bone development. FAM20C, also called Dentin Matrix Protein 4, is abundant in the dentin matrix, and may participate in the differentiation of mesenchymal precursor cells into functional odontoblast-like cells. Mutations in FAM20C are associated with lethal Osteosclerotic Bone Dysplasia (Raine Syndrome), and mutations in FAM20A with Amelogenesis imperfecta (AI) and Gingival Hyperplasia Syndrome. This model includes the FAM20_C domain family, previously known as DUF1193; FAM20_C appears to be homologous to the catalytic domain of the phosphoinositide 3-kinase (PI3K)-like family."
Q#115 - 	CGI_10009178	superfamily	217962	31	79	1.02E-06	43.4032	cl09558	TPD52 superfamily	N	 - 	"Tumour protein D52 family; The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other."
Q#117 - 	CGI_10009180	superfamily	246918	741	793	5.38E-12	62.9895	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	986	1038	4.11E-11	60.2931	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	476	528	1.25E-10	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	419	471	7.89E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	930	976	5.13E-09	54.5151	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	627	678	6.11E-09	54.1299	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	1080	1133	7.20E-09	53.7447	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	684	736	5.53E-08	51.4335	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	886	925	0.000413935	39.8775	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#117 - 	CGI_10009180	superfamily	246918	544	585	0.000661586	39.1071	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#119 - 	CGI_10009182	superfamily	243066	20	124	5.63E-28	105.777	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#119 - 	CGI_10009182	superfamily	243146	232	278	6.41E-12	59.9826	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#119 - 	CGI_10009182	superfamily	243146	342	386	7.54E-11	57.1831	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#119 - 	CGI_10009182	superfamily	243146	198	243	1.84E-10	56.0275	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#119 - 	CGI_10009182	superfamily	243146	135	183	2.48E-06	44.1894	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#119 - 	CGI_10009182	superfamily	243146	294	341	1.55E-05	42.1603	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#120 - 	CGI_10000371	superfamily	245201	11	56	3.17E-25	93.5584	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#122 - 	CGI_10008750	superfamily	242893	40	140	1.75E-54	169.739	cl02121	Med31 superfamily	 - 	 - 	"SOH1; The family consists of Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes."
Q#124 - 	CGI_10008752	superfamily	147513	5	57	1.91E-14	62.2842	cl05104	UCR_UQCRX_QCR9 superfamily	 - 	 - 	"Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like; The UQCRX/QCR9 protein is the 9/10 subunit of complex III, encoding a protein of about 7-kDa. Deletion of QCR9 results in the inability of cells to grow on grow on-fermentable carbon source n yeast."
Q#125 - 	CGI_10008753	superfamily	241636	141	332	2.11E-114	338.793	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#126 - 	CGI_10008754	superfamily	247725	12	109	5.23E-60	198.728	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#126 - 	CGI_10008754	superfamily	216381	402	815	1.25E-120	370.382	cl03136	Oxysterol_BP superfamily	 - 	 - 	Oxysterol-binding protein; Oxysterol-binding protein.  
Q#127 - 	CGI_10008755	superfamily	221858	34	76	8.43E-13	59.0855	cl15169	MOZART2 superfamily	N	 - 	"Mitotic-spindle organizing gamma-tubulin ring associated; FAM128A and FAM128B proteins have been re-named MOZART2A and B. The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. The exact function of MOZART2 is not clear."
Q#129 - 	CGI_10008757	superfamily	241992	369	868	0	606.184	cl00628	Piwi-like superfamily	 - 	 - 	"Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism."
Q#129 - 	CGI_10008757	superfamily	241765	244	360	1.16E-51	177.067	cl00301	PAZ superfamily	 - 	 - 	"PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain."
Q#131 - 	CGI_10007100	superfamily	220628	323	440	3.64E-16	74.637	cl10890	Ada3 superfamily	 - 	 - 	"Histone acetyltransferases subunit 3; Ada3 is a family of proteins conserved from yeasts to humans. It is an essential component of the Ada transcriptional coactivator (alteration/deficiency in activation) complex. Ada3 plays a key role in linking histone acetyltransferase-containing complexes to p53 (tumour suppressor protein) thereby regulating p53 acetylation, stability and transcriptional activation following DNA damage."
Q#132 - 	CGI_10007101	superfamily	217951	25	220	2.08E-19	84.5076	cl18437	Mannosyl_trans2 superfamily	N	 - 	"Mannosyltransferase (PIG-V)); This is a family of eukaryotic ER membrane proteins that are involved in the synthesis of glycosylphosphatidylinositol (GPI), a glycolipid that anchors many proteins to the eukaryotic cell surface. Proteins in this family are involved in transferring the second mannose in the biosynthetic pathway of GPI."
Q#134 - 	CGI_10007103	superfamily	247725	7	129	5.05E-77	234.456	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#134 - 	CGI_10007103	superfamily	248318	155	210	2.90E-16	71.6981	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#134 - 	CGI_10007103	superfamily	248318	250	286	2.22E-09	52.8233	cl17764	FYVE superfamily	N	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#135 - 	CGI_10007104	superfamily	242165	22	209	3.10E-56	177.712	cl00880	Ribosomal_S8e_like superfamily	 - 	 - 	"Eukaryotic/archaeal ribosomal protein S8e and similar proteins; This family contains the eukaryotic/archaeal ribosomal protein S8, a component of the small ribosomal subunits, as well as the NSA2 gene product."
Q#136 - 	CGI_10007105	superfamily	245201	55	310	0	536.464	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#136 - 	CGI_10007105	superfamily	152065	487	535	1.72E-21	88.1801	cl13134	Mst1_SARAH superfamily	 - 	 - 	"C terminal SARAH domain of Mst1; This family of proteins represents the C terminal SARAH domain of Mst1. SARAH controls apoptosis and cell cycle arrest via the Ras, RASSF, MST pathway. The Mst1 SARAH domain interacts with Rassf1 and Rassf5 by forming a heterodimer which mediates the apoptosis process."
Q#137 - 	CGI_10007106	superfamily	190308	48	192	3.90E-09	55.0175	cl18163	Fringe superfamily	C	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#138 - 	CGI_10007107	superfamily	222150	376	401	7.54E-05	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#138 - 	CGI_10007107	superfamily	222150	349	372	0.00046678	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#138 - 	CGI_10007107	superfamily	246975	308	328	0.00247813	36.1709	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#140 - 	CGI_10007109	superfamily	217915	663	948	1.54E-43	166.528	cl14957	Spc97_Spc98 superfamily	N	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#140 - 	CGI_10007109	superfamily	217915	271	731	2.09E-13	72.5388	cl14957	Spc97_Spc98 superfamily	 - 	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#143 - 	CGI_10007112	superfamily	203134	392	454	8.15E-05	40.3577	cl04866	CHORD superfamily	 - 	 - 	"CHORD; CHORD represents a Zn binding domain. Silencing of the C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development."
Q#143 - 	CGI_10007112	superfamily	241701	151	195	0.00808728	36.3963	cl00223	NusB_Sun superfamily	C	 - 	"RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the N-terminal non-catalytic RNA-binding domain with NusB."
Q#144 - 	CGI_10007113	superfamily	246680	9	87	3.26E-12	62.6044	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#145 - 	CGI_10007114	superfamily	246680	9	87	3.35E-13	66.0712	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#145 - 	CGI_10007114	superfamily	246680	385	474	1.32E-09	55.9792	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#147 - 	CGI_10001026	superfamily	248020	24	356	1.06E-52	182.664	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#149 - 	CGI_10001514	superfamily	248097	265	385	1.88E-28	108.121	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#149 - 	CGI_10001514	superfamily	242406	50	113	0.00168013	37.358	cl01271	DUF1768 superfamily	C	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#151 - 	CGI_10001610	superfamily	245847	1	67	2.66E-15	66.0409	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#153 - 	CGI_10003986	superfamily	218702	76	128	3.88E-06	41.5038	cl05324	Dimer_Tnp_hAT superfamily	N	 - 	hAT family dimerisation domain; This dimerisation domain is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation domain forms extremely stable dimers in vitro.
Q#154 - 	CGI_10003987	superfamily	217926	294	430	5.50E-49	170.819	cl04418	YTH superfamily	 - 	 - 	"YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily."
Q#154 - 	CGI_10003987	superfamily	217926	734	870	5.50E-49	170.819	cl04418	YTH superfamily	 - 	 - 	"YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily."
Q#156 - 	CGI_10003989	superfamily	217643	91	253	6.69E-08	51.7745	cl04182	Solute_trans_a superfamily	N	 - 	"Organic solute transporter Ostalpha; This family is a transmembrane organic solute transport protein. In vertebrates these proteins form a complex with Ostbeta, and function as bile transporters. In plants they may transport brassinosteroid-like compounds and act as regulators of cell death."
Q#158 - 	CGI_10003991	superfamily	241597	23	86	2.30E-25	96.2133	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#159 - 	CGI_10003992	superfamily	216971	199	368	1.55E-22	92.2984	cl03532	Octopine_DH superfamily	 - 	 - 	"NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids."
Q#159 - 	CGI_10003992	superfamily	217105	51	117	0.000595319	38.755	cl18391	ApbA superfamily	NC	 - 	"Ketopantoate reductase PanE/ApbA; This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalyzed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyzes the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway. ApbA and PanE are allelic. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway."
Q#161 - 	CGI_10001640	superfamily	241758	83	130	1.20E-15	68.5506	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#164 - 	CGI_10001745	superfamily	219525	44	92	6.06E-06	40.095	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#164 - 	CGI_10001745	superfamily	219525	3	37	0.000721192	34.7022	cl06646	GCC2_GCC3 superfamily	N	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#167 - 	CGI_10004224	superfamily	193687	6	154	3.49E-59	183.681	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#168 - 	CGI_10004225	superfamily	201540	4	70	0.00378836	35.9873	cl16960	Troponin superfamily	N	 - 	"Troponin; Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin."
Q#173 - 	CGI_10003728	superfamily	245746	56	114	1.96E-17	77.2654	cl11668	Lig_chan-Glu_bd superfamily	 - 	 - 	"Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060."
Q#173 - 	CGI_10003728	superfamily	197504	311	438	7.28E-14	68.4701	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#174 - 	CGI_10003729	superfamily	244881	194	493	1.12E-140	416.209	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#174 - 	CGI_10003729	superfamily	215788	2	92	6.07E-34	125.369	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#174 - 	CGI_10003729	superfamily	203720	596	676	3.00E-20	86.4481	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#175 - 	CGI_10003336	superfamily	215647	58	176	4.24E-05	41.4401	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#177 - 	CGI_10003338	superfamily	241568	87	125	3.45E-05	40.1388	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#188 - 	CGI_10002770	superfamily	222070	7	43	0.00392058	31.8793	cl18634	DDE_3 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#190 - 	CGI_10009092	superfamily	241559	32	132	7.19E-13	66.9507	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#190 - 	CGI_10009092	superfamily	241559	141	231	2.71E-06	47.3055	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#190 - 	CGI_10009092	superfamily	216033	637	725	4.76E-16	75.8332	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	417	545	6.49E-14	69.67	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	1205	1279	9.60E-13	66.2032	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	921	992	2.41E-11	62.3512	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	728	812	4.16E-11	61.5808	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	549	634	5.74E-11	61.1956	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	819	902	4.43E-10	58.4992	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	1089	1174	1.68E-07	50.7952	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	329	413	2.03E-07	50.41	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	216033	1033	1086	3.15E-07	50.0248	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#190 - 	CGI_10009092	superfamily	241559	1	25	0.00568501	36.9051	cl00030	CH superfamily	N	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#191 - 	CGI_10009093	superfamily	216033	629	713	1.29E-18	82.3816	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#191 - 	CGI_10009093	superfamily	216033	721	810	1.82E-18	81.9964	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#191 - 	CGI_10009093	superfamily	216033	533	620	1.23E-15	73.9072	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#191 - 	CGI_10009093	superfamily	216033	358	427	1.67E-09	56.188	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#191 - 	CGI_10009093	superfamily	216033	430	524	3.45E-07	49.2544	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#192 - 	CGI_10009094	superfamily	241638	115	239	2.18E-10	55.4521	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#193 - 	CGI_10009096	superfamily	241638	148	258	2.42E-09	53.5028	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#194 - 	CGI_10009097	superfamily	241638	135	274	2.08E-10	56.5844	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#195 - 	CGI_10009098	superfamily	243555	23	215	2.02E-16	75.1202	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#196 - 	CGI_10009099	superfamily	247684	7	99	1.28E-22	89.6439	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#197 - 	CGI_10007489	superfamily	248458	47	192	1.75E-08	53.4717	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#198 - 	CGI_10007490	superfamily	246680	27	105	1.13E-07	49.6296	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#198 - 	CGI_10007490	superfamily	248012	207	306	1.15E-05	44.2364	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#200 - 	CGI_10007492	superfamily	192487	96	342	3.34E-67	216.117	cl10912	DUF2215 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2215); This entry is the central 200 residues of a family of proteins conserved from worms to humans. The function is unknown.
Q#201 - 	CGI_10007493	superfamily	198867	134	234	6.59E-39	138.06	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#201 - 	CGI_10007493	superfamily	243066	22	126	7.32E-32	118.489	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#201 - 	CGI_10007493	superfamily	243146	460	505	1.35E-14	68.8422	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#201 - 	CGI_10007493	superfamily	243146	507	551	4.92E-14	67.3014	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#201 - 	CGI_10007493	superfamily	243146	378	424	5.80E-14	67.1983	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#201 - 	CGI_10007493	superfamily	243146	413	457	8.19E-13	63.8346	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#201 - 	CGI_10007493	superfamily	243146	331	376	9.34E-13	63.7315	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#201 - 	CGI_10007493	superfamily	243146	283	330	2.92E-11	59.4943	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#203 - 	CGI_10007495	superfamily	241546	845	886	8.11E-09	54.5892	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#204 - 	CGI_10007496	superfamily	216434	434	571	3.48E-21	94.0664	cl08318	PPDK_N superfamily	C	 - 	"Pyruvate phosphate dikinase, PEP/pyruvate binding domain; This enzyme catalyzes the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP)."
Q#205 - 	CGI_10007497	superfamily	241874	9	531	0	598.696	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#207 - 	CGI_10007499	superfamily	201540	1	44	1.42E-13	62.9513	cl16960	Troponin superfamily	NC	 - 	"Troponin; Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin."
Q#212 - 	CGI_10003787	superfamily	243029	47	105	1.86E-11	60.4421	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#224 - 	CGI_10010951	superfamily	216363	239	344	9.18E-25	96.7705	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#229 - 	CGI_10010956	superfamily	245847	7	146	3.68E-14	68.3521	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#229 - 	CGI_10010956	superfamily	241619	241	287	0.000221313	38.7173	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#230 - 	CGI_10010957	superfamily	241568	187	212	0.00273195	35.5164	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#230 - 	CGI_10010957	superfamily	245847	224	369	5.63E-18	79.5229	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#230 - 	CGI_10010957	superfamily	241619	44	115	0.00160844	36.4061	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#232 - 	CGI_10010959	superfamily	222429	4	51	2.54E-07	44.1536	cl18676	Myb_DNA-bind_5 superfamily	C	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#239 - 	CGI_10006397	superfamily	246723	14	521	0	659.437	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#240 - 	CGI_10006398	superfamily	241563	64	105	4.49E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#241 - 	CGI_10006399	superfamily	243047	7	120	1.59E-43	151.233	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#244 - 	CGI_10006402	superfamily	241596	107	168	2.12E-13	62.2315	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#245 - 	CGI_10006403	superfamily	221913	1094	1284	4.46E-30	119.953	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#245 - 	CGI_10006403	superfamily	222005	788	854	2.96E-08	52.7396	cl18632	AAA_19 superfamily	 - 	 - 	Part of AAA domain; Part of AAA domain.  
Q#246 - 	CGI_10006404	superfamily	241563	68	108	3.90E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#247 - 	CGI_10006405	superfamily	241706	506	574	4.20E-22	91.0855	cl00229	eIF1_SUI1_like superfamily	 - 	 - 	"Eukaryotic initiation factor 1 and related proteins; Members of the eIF1/SUI1 (eukaryotic initiation factor 1) family are found in eukaryotes, archaea, and some bacteria; eukaryotic members are understood to play an important role in accurate initiator codon recognition during translation initiation. eIF1 interacts with 18S rRNA in the 40S ribosomal subunit during eukaryotic translation initiation. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown. The function of non-eukaryotic family members is also unclear."
Q#247 - 	CGI_10006405	superfamily	211517	6	81	1.86E-20	86.1722	cl16921	eIF2D_N_like superfamily	 - 	 - 	"N-terminal domain of eIF2D, malignant T cell-amplified sequence 1 and related proteins; This N-terminal domain of various proteins co-occurs with a PUA domain. Members of this family are: (1) MCTS-1 (malignant T cell-amplified sequence 1) or MCT-1 (multiple copies T cell malignancies), which may play roles in the regulation of the cell cycle, (2) the eukayotic translation initiation factor 2D, and (3) an uncharacterized archaeal family."
Q#247 - 	CGI_10006405	superfamily	241977	64	178	1.04E-09	56.2875	cl00607	PUA superfamily	 - 	 - 	"PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain."
Q#248 - 	CGI_10006406	superfamily	241559	5	153	2.92E-26	107.952	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#248 - 	CGI_10006406	superfamily	247744	728	910	4.51E-15	75.7362	cl17190	NK superfamily	N	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#248 - 	CGI_10006406	superfamily	247807	571	613	0.00550305	37.2746	cl17253	AAA_17 superfamily	C	 - 	AAA domain; AAA domain.  
Q#249 - 	CGI_10006407	superfamily	216056	35	135	5.36E-31	120.107	cl08279	Peptidase_M16 superfamily	 - 	 - 	Insulinase (Peptidase family M16); Insulinase (Peptidase family M16).  
Q#249 - 	CGI_10006407	superfamily	218490	181	363	6.95E-22	94.8507	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#249 - 	CGI_10006407	superfamily	218490	623	805	7.10E-09	55.1751	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#251 - 	CGI_10003515	superfamily	241636	71	257	1.44E-83	255.205	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#252 - 	CGI_10003516	superfamily	241597	69	134	1.31E-17	78.0533	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#252 - 	CGI_10003516	superfamily	222150	514	539	9.93E-05	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#252 - 	CGI_10003516	superfamily	197676	500	522	0.00397734	35.5193	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#252 - 	CGI_10003516	superfamily	220222	249	316	0.0079053	35.6567	cl09651	FadA superfamily	C	 - 	Adhesion protein FadA; FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices.
Q#253 - 	CGI_10003517	superfamily	247684	5	366	3.28E-18	84.6363	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#255 - 	CGI_10003135	superfamily	216363	129	208	1.42E-12	61.3322	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#256 - 	CGI_10003136	superfamily	222429	17	93	1.14E-07	45.3092	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#261 - 	CGI_10006311	superfamily	191128	69	109	8.14E-08	47.5336	cl04846	Ninjurin superfamily	C	 - 	Ninjurin; Ninjurin (nerve injury-induced protein) is involved in nerve regeneration and in the formation and function in some tissues.
Q#263 - 	CGI_10006313	superfamily	234167	115	180	5.21E-21	84.141	cl11877	ygfZ_signature superfamily	 - 	 - 	"folate-binding protein YgfZ; YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein [Protein synthesis, tRNA and rRNA base modification]."
Q#264 - 	CGI_10006314	superfamily	245864	122	223	9.70E-19	85.4078	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#265 - 	CGI_10006315	superfamily	247792	61	103	1.02E-06	41.6624	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#266 - 	CGI_10006316	superfamily	247856	64	124	6.39E-07	42.5349	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#266 - 	CGI_10006316	superfamily	247856	1	38	0.000681633	34.4457	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#268 - 	CGI_10006318	superfamily	198850	38	105	1.34E-15	68.3143	cl04907	L51_S25_CI-B8 superfamily	 - 	 - 	"Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain; The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins."
Q#269 - 	CGI_10006319	superfamily	243072	3	108	2.09E-22	92.8318	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#269 - 	CGI_10006319	superfamily	243072	387	451	5.23E-08	50.845	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#269 - 	CGI_10006319	superfamily	248006	178	209	0.00999194	34.0839	cl17452	TPR_10 superfamily	N	 - 	Tetratricopeptide repeat; Tetratricopeptide repeat.  
Q#270 - 	CGI_10006320	superfamily	247103	43	387	2.69E-153	441.8	cl15852	COX15-CtaA superfamily	 - 	 - 	Cytochrome oxidase assembly protein; This is a family of integral membrane proteins. CtaA is required for cytochrome aa3 oxidase assembly in Bacillus subtilis. COX15 is required for cytochrome c oxidase assembly in yeast.
Q#271 - 	CGI_10006321	superfamily	248054	35	81	1.26E-05	43.2296	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#272 - 	CGI_10006322	superfamily	247755	253	406	7.60E-93	300.716	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#272 - 	CGI_10006322	superfamily	247755	1339	1431	4.17E-53	188.238	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#272 - 	CGI_10006322	superfamily	243179	114	231	1.14E-30	119.33	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#272 - 	CGI_10006322	superfamily	244201	777	889	2.96E-27	109.243	cl05797	SMC_hinge superfamily	 - 	 - 	SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.
Q#272 - 	CGI_10006322	superfamily	248228	59	112	0.000356764	40.2357	cl17674	COG5487 superfamily	 - 	 - 	Small integral membrane protein [Function unknown]
Q#272 - 	CGI_10006322	superfamily	151039	452	591	0.000852119	39.7815	cl11115	Cenp-F_leu_zip superfamily	 - 	 - 	"Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance."
Q#273 - 	CGI_10006323	superfamily	243179	120	229	3.38E-29	108.545	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#276 - 	CGI_10003305	superfamily	246683	61	261	9.28E-89	270.146	cl14648	Aldose_epim superfamily	N	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#277 - 	CGI_10003306	superfamily	217293	68	239	4.63E-66	214.034	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#277 - 	CGI_10003306	superfamily	202474	246	472	5.58E-33	124.688	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#278 - 	CGI_10003307	superfamily	217293	5	211	1.19E-81	254.094	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#278 - 	CGI_10003307	superfamily	202474	218	450	3.58E-33	125.074	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#279 - 	CGI_10013066	superfamily	248097	61	183	1.51E-21	85.7798	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#280 - 	CGI_10013067	superfamily	241584	21	63	0.00531587	32.8535	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#282 - 	CGI_10013069	superfamily	248097	4	112	3.79E-23	87.7058	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#283 - 	CGI_10013070	superfamily	248097	93	194	3.55E-16	71.1422	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#284 - 	CGI_10013071	superfamily	248097	3	111	9.33E-18	73.4534	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#285 - 	CGI_10013072	superfamily	248097	4	59	7.32E-13	59.201	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#286 - 	CGI_10013073	superfamily	248097	81	204	4.21E-20	82.313	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#287 - 	CGI_10013074	superfamily	248054	15	69	0.000491261	38.6072	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#287 - 	CGI_10013074	superfamily	248054	213	267	0.00139816	37.4516	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#288 - 	CGI_10013075	superfamily	241832	234	349	2.12E-62	201.939	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#288 - 	CGI_10013075	superfamily	241645	438	521	8.54E-29	109.215	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#289 - 	CGI_10013076	superfamily	241832	7	78	2.83E-17	72.9896	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#289 - 	CGI_10013076	superfamily	243175	123	180	4.01E-10	53.8106	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#290 - 	CGI_10013077	superfamily	241832	7	78	2.17E-17	73.3748	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#290 - 	CGI_10013077	superfamily	243175	123	180	7.21E-10	53.0402	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#292 - 	CGI_10013079	superfamily	202715	67	167	3.11E-39	130.776	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#294 - 	CGI_10013081	superfamily	247725	95	185	2.67E-45	156.637	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#294 - 	CGI_10013081	superfamily	241647	39	68	1.97E-07	48.293	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#296 - 	CGI_10013083	superfamily	245670	676	859	3.11E-53	183.936	cl11519	DENN superfamily	 - 	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#296 - 	CGI_10013083	superfamily	243635	588	666	9.02E-14	68.5153	cl04085	uDENN superfamily	 - 	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#297 - 	CGI_10013084	superfamily	245840	24	167	2.12E-86	260.339	cl12022	Ribosomal_L18e superfamily	 - 	 - 	Ribosomal protein L18e/L15; This family includes eukaryotic L18 as well as prokaryotic L15.
Q#297 - 	CGI_10013084	superfamily	245840	240	364	2.55E-73	226.827	cl12022	Ribosomal_L18e superfamily	 - 	 - 	Ribosomal protein L18e/L15; This family includes eukaryotic L18 as well as prokaryotic L15.
Q#299 - 	CGI_10013086	superfamily	241659	90	161	3.48E-22	89.1162	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#299 - 	CGI_10013086	superfamily	241659	283	360	2.52E-21	86.805	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#301 - 	CGI_10013088	superfamily	245596	116	395	2.10E-147	434.209	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#301 - 	CGI_10013088	superfamily	222439	445	706	1.44E-44	162.023	cl16461	Glyco_transf_49 superfamily	 - 	 - 	"Glycosyl-transferase for dystroglycan; This glycosyl-transferase brings about the glycosylation of the alpha-dystroglycan subunit. Dystroglycan is an integral member of the skeletal muscular dystrophin glycoprotein complex, which links dystrophin to proteins in the extracellular matrix."
Q#302 - 	CGI_10013089	superfamily	219932	16	354	9.29E-93	283.534	cl07288	Pex16 superfamily	 - 	 - 	Peroxisomal membrane protein (Pex16); Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane.
Q#303 - 	CGI_10013090	superfamily	245874	15	79	1.60E-18	81.7037	cl12111	TNFR superfamily	C	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#304 - 	CGI_10013091	superfamily	247684	43	100	2.20E-18	78.7801	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#304 - 	CGI_10013091	superfamily	247675	3	66	0.00958995	32.5321	cl17011	Arginase_HDAC superfamily	C	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#305 - 	CGI_10009028	superfamily	241625	9	133	1.51E-27	100.092	cl00123	PROF superfamily	 - 	 - 	"Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway."
Q#307 - 	CGI_10009030	superfamily	216371	48	436	2.38E-57	196.12	cl18365	ERG4_ERG24 superfamily	 - 	 - 	Ergosterol biosynthesis ERG4/ERG24 family; Ergosterol biosynthesis ERG4/ERG24 family.  
Q#308 - 	CGI_10009031	superfamily	243066	161	251	9.16E-29	110.72	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#308 - 	CGI_10009031	superfamily	219619	504	573	1.52E-10	57.9879	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#309 - 	CGI_10009032	superfamily	243066	78	168	6.70E-23	93.7716	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#309 - 	CGI_10009032	superfamily	219619	424	499	1.03E-09	55.6767	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#309 - 	CGI_10009032	superfamily	241672	534	622	0.00463683	38.488	cl00192	ribokinase_pfkB_like superfamily	C	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#311 - 	CGI_10009034	superfamily	247875	63	233	0.00796951	35.3313	cl17321	2OG-FeII_Oxy_2 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; 2OG-Fe(II) oxygenase superfamily.  
Q#312 - 	CGI_10009035	superfamily	243092	343	585	1.55E-11	64.2784	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#312 - 	CGI_10009035	superfamily	246925	24	100	0.00450112	38.1054	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#313 - 	CGI_10009036	superfamily	243092	57	81	0.00385314	31.1286	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#314 - 	CGI_10009037	superfamily	219502	72	280	3.03E-57	186.111	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#315 - 	CGI_10009038	superfamily	219502	229	444	2.31E-52	179.563	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#315 - 	CGI_10009038	superfamily	201962	46	117	8.93E-18	78.5716	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#315 - 	CGI_10009038	superfamily	219507	126	224	1.95E-09	55.3231	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#317 - 	CGI_10009040	superfamily	243092	14	347	6.59E-45	164.815	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#317 - 	CGI_10009040	superfamily	219469	753	905	1.13E-21	95.031	cl15655	Hira superfamily	 - 	 - 	TUP1-like enhancer of split; The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain pfam00400.
Q#318 - 	CGI_10009041	superfamily	243109	2370	2524	6.08E-76	252.815	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#318 - 	CGI_10009041	superfamily	241594	3963	4328	4.90E-68	237.463	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#319 - 	CGI_10001089	superfamily	243092	305	451	5.66E-06	46.9444	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#321 - 	CGI_10014903	superfamily	243035	225	356	7.88E-28	106.145	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#323 - 	CGI_10014905	superfamily	243035	25	96	1.58E-14	64.1781	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#324 - 	CGI_10014906	superfamily	243035	22	46	0.000107247	36.4238	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#326 - 	CGI_10014908	superfamily	243034	672	767	1.44E-11	62.0124	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#326 - 	CGI_10014908	superfamily	242008	573	636	0.00687659	37.9876	cl00656	Cas1_I-II-III superfamily	N	 - 	"CRISPR/Cas system-associated protein Cas1; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain"
Q#328 - 	CGI_10014910	superfamily	245201	617	667	4.02E-09	56.776	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#328 - 	CGI_10014910	superfamily	245201	402	459	0.000408299	41.9484	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#331 - 	CGI_10014913	superfamily	220692	48	263	9.01E-05	42.1913	cl18570	7TM_GPCR_Srw superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#333 - 	CGI_10014915	superfamily	241741	60	651	0	966.323	cl00270	PEPCK_HprK superfamily	 - 	 - 	"Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP  or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity.  PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting that these two phosphotransferases have related functions."
Q#334 - 	CGI_10014916	superfamily	241741	36	626	0	948.219	cl00270	PEPCK_HprK superfamily	 - 	 - 	"Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP  or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity.  PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting that these two phosphotransferases have related functions."
Q#335 - 	CGI_10014917	superfamily	245234	15	66	1.50E-05	42.6646	cl10022	ABM superfamily	C	 - 	Antibiotic biosynthesis monooxygenase; This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. It's occurrence as a repeat in Streptomyces coelicolor SCO1909 is suggestive that the other proteins function as multimers. There is also a conserved histidine which is likely to be an active site residue.
Q#336 - 	CGI_10014918	superfamily	209898	18	40	0.000427673	38.1534	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#336 - 	CGI_10014918	superfamily	209898	65	87	0.00594323	35.0718	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#336 - 	CGI_10014918	superfamily	209898	86	103	0.00998121	34.2383	cl14787	MORN superfamily	C	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#338 - 	CGI_10014920	superfamily	243050	610	671	6.39E-37	133.285	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#338 - 	CGI_10014920	superfamily	243050	550	602	1.07E-34	126.689	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#338 - 	CGI_10014920	superfamily	243050	440	493	1.48E-29	112.526	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#340 - 	CGI_10014922	superfamily	242966	107	181	0.00260004	35.3989	cl02288	DUF1330 superfamily	C	 - 	Protein of unknown function (DUF1330); This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.
Q#340 - 	CGI_10014922	superfamily	242966	33	87	0.0033624	35.0137	cl02288	DUF1330 superfamily	NC	 - 	Protein of unknown function (DUF1330); This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.
Q#341 - 	CGI_10014923	superfamily	242966	621	688	0.000210758	39.8452	cl02288	DUF1330 superfamily	 - 	 - 	Protein of unknown function (DUF1330); This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.
Q#342 - 	CGI_10014924	superfamily	242966	81	157	0.00242903	34.6285	cl02288	DUF1330 superfamily	 - 	 - 	Protein of unknown function (DUF1330); This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.
Q#343 - 	CGI_10014925	superfamily	241578	317	478	0.000424557	40.0234	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#344 - 	CGI_10004680	superfamily	192535	18	132	0.00034405	40.657	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#346 - 	CGI_10004683	superfamily	241563	62	101	0.00054935	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#347 - 	CGI_10004684	superfamily	241953	366	424	0.0041339	37.4952	cl00567	Colicin_V superfamily	N	 - 	Colicin V production protein; Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon.
Q#350 - 	CGI_10004687	superfamily	192997	443	553	4.50E-09	55.2803	cl18184	Sterol-sensing superfamily	N	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#351 - 	CGI_10000262	superfamily	217915	14	127	2.40E-18	79.8576	cl14957	Spc97_Spc98 superfamily	N	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#352 - 	CGI_10005014	superfamily	241568	139	193	0.000841951	36.672	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#352 - 	CGI_10005014	superfamily	246918	201	253	1.24E-12	61.4487	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#352 - 	CGI_10005014	superfamily	246918	258	308	2.89E-06	43.7295	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#352 - 	CGI_10005014	superfamily	241619	27	98	0.00332274	34.862	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#353 - 	CGI_10005015	superfamily	243072	15	163	2.92E-24	93.6022	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#360 - 	CGI_10015340	superfamily	243161	4	91	5.08E-19	76.2789	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#361 - 	CGI_10015341	superfamily	220695	27	150	1.28E-06	47.9587	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#364 - 	CGI_10015344	superfamily	247803	127	298	5.20E-109	326.455	cl17249	YlqF_related_GTPase superfamily	 - 	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#365 - 	CGI_10015345	superfamily	243050	282	337	1.85E-25	97.6754	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#365 - 	CGI_10015345	superfamily	243050	219	276	2.85E-19	81.1084	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#365 - 	CGI_10015345	superfamily	243050	344	400	1.51E-15	70.8852	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#365 - 	CGI_10015345	superfamily	195146	173	211	1.14E-06	46.0883	cl05674	PET superfamily	N	 - 	"PET ((Prickle Espinas Testin) domain is involved in protein-protein interactions; PET domain is involved in protein-protein interactions and is usually found in conjunction with LIM domain, which is also a protein-protein interaction domain. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. The PET domain has been found at the N-terminal of four known groups of proteins: prickle, testin, LIMPETin/LIM-9 and overexpressed breast tumor protein (OEBT). Prickle has been implicated in regulation of cell movement through its association with the Dishevelled (Dsh) protein in the planar cell polarity (PCP) pathway. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell contact areas, and at focal adhesion plaques. It interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin, and is involved in cell motility and adhesion events. Knockout mice experiments reveal tumor repressor function of Testin.  LIMPETin/LIM-9 contains an N-terminal PET domain and 6 LIM domains at the C-terminal.  In Schistosoma mansoni, where LIMPETin was first identified, it is down regulated in sexually mature adult females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator.  In C. elegans, LIM-9 may play a role in regulating the assembly and maintenance of the muscle A-band by forming a protein complex with SCPL-1 and UNC-89 and other proteins. OEBT displays a PET domain with two LIM domains, and is predicted to be localized in the nucleus with a possible role in cancer differentiation."
Q#366 - 	CGI_10015346	superfamily	248097	93	138	8.23E-09	49.1858	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#367 - 	CGI_10015347	superfamily	248097	8	122	3.40E-16	69.6014	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#368 - 	CGI_10015348	superfamily	248097	62	188	6.19E-20	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#370 - 	CGI_10015350	superfamily	216152	3	262	1.54E-81	252.235	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#372 - 	CGI_10015352	superfamily	245206	5	245	2.24E-73	226.413	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#373 - 	CGI_10015353	superfamily	247868	288	352	8.73E-06	46.3725	cl17314	PRK07608 superfamily	N	 - 	ubiquinone biosynthesis hydroxylase family protein; Provisional
Q#373 - 	CGI_10015353	superfamily	247868	1	169	1.46E-05	45.7154	cl17314	PRK07608 superfamily	C	 - 	ubiquinone biosynthesis hydroxylase family protein; Provisional
Q#374 - 	CGI_10015354	superfamily	247755	442	683	1.08E-117	354.924	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#374 - 	CGI_10015354	superfamily	216049	141	396	4.41E-41	150.899	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#377 - 	CGI_10015357	superfamily	242274	71	359	1.18E-119	367.053	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#377 - 	CGI_10015357	superfamily	247743	627	794	6.11E-28	111.084	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#378 - 	CGI_10015358	superfamily	241607	46	92	5.88E-05	36.1182	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#380 - 	CGI_10015360	superfamily	241641	43	106	5.81E-19	82.8969	cl00150	TY superfamily	 - 	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#380 - 	CGI_10015360	superfamily	241641	292	343	8.05E-09	53.6217	cl00150	TY superfamily	N	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#380 - 	CGI_10015360	superfamily	238155	147	206	2.12E-10	58.9254	cl08547	SPARC_EC superfamily	N	 - 	"SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate cell-matrix interactions; binds to such proteins as collagen and vitronectin and binds to endothelial cells thus inhibiting cellular proliferation. The EC domain interacts with a follistatin-like (FS) domain which appears to stabilize Ca2+ binding. The two EF-hands interact canonically but their conserved disulfide bonds confer a tight association between the EF-hand pair and an acid/amphiphilic N-terminal helix. Proposed active form involves a Ca2+ dependent symmetric homodimerization of EC-FS modules."
Q#380 - 	CGI_10015360	superfamily	238155	366	449	0.000317471	40.0506	cl08547	SPARC_EC superfamily	 - 	 - 	"SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate cell-matrix interactions; binds to such proteins as collagen and vitronectin and binds to endothelial cells thus inhibiting cellular proliferation. The EC domain interacts with a follistatin-like (FS) domain which appears to stabilize Ca2+ binding. The two EF-hands interact canonically but their conserved disulfide bonds confer a tight association between the EF-hand pair and an acid/amphiphilic N-terminal helix. Proposed active form involves a Ca2+ dependent symmetric homodimerization of EC-FS modules."
Q#383 - 	CGI_10008773	superfamily	241600	82	246	3.01E-71	219.805	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#384 - 	CGI_10008774	superfamily	241570	35	92	4.01E-05	43.0834	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#384 - 	CGI_10008774	superfamily	241570	168	226	0.000151104	41.1574	cl00047	CAP_ED superfamily	N	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#384 - 	CGI_10008774	superfamily	241570	246	296	0.000728101	39.2314	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#385 - 	CGI_10008775	superfamily	248289	49	106	0.00597594	31.3324	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#388 - 	CGI_10008778	superfamily	243092	106	419	3.01E-51	175.986	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#388 - 	CGI_10008778	superfamily	219730	8	76	1.18E-19	82.5683	cl06962	NLE superfamily	 - 	 - 	NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated yeast protein YTM1.
Q#390 - 	CGI_10008780	superfamily	247725	639	751	7.07E-67	222.14	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#390 - 	CGI_10008780	superfamily	247755	5	151	2.59E-46	166.958	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#390 - 	CGI_10008780	superfamily	247789	197	356	2.05E-29	118.515	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#390 - 	CGI_10008780	superfamily	215882	559	662	1.79E-27	109.678	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#390 - 	CGI_10008780	superfamily	220215	474	550	3.35E-25	101.918	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#390 - 	CGI_10008780	superfamily	192138	764	782	7.90E-07	47.9988	cl07378	FA superfamily	C	 - 	"FERM adjacent (FA); This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates."
Q#394 - 	CGI_10009161	superfamily	243035	22	148	3.49E-23	89.2161	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#395 - 	CGI_10009162	superfamily	219079	13	70	0.00767766	32.1128	cl14967	PHA-1 superfamily	NC	 - 	Regulator protein PHA-1; This family represents the protein product of the gene pha-1 which coordinates with lin-35 Rb during animal development. The protein is expressed during embryonic development and functions in the cytoplasm. PHA-1 acts in a parallel pathway with UBC-18 to regulate the activity of a common cellular target.
Q#396 - 	CGI_10004142	superfamily	202865	37	142	6.72E-22	93.8807	cl04378	Sec8_exocyst superfamily	N	 - 	Sec8 exocyst complex component specific domain; Sec8 exocyst complex component specific domain.  
Q#397 - 	CGI_10004144	superfamily	245847	33	164	0.000900076	37.482	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#398 - 	CGI_10004145	superfamily	218609	15	66	0.00143857	34.2715	cl05189	Destabilase superfamily	C	 - 	"Destabilase; Destabilase is an endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves isopeptide bonds formed by transglutaminase (Factor XIIIa) between glutamine gamma-carboxamide and the epsilon-amino group of lysine."
Q#399 - 	CGI_10004146	superfamily	245847	3	134	0.00752483	35.1708	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#400 - 	CGI_10005018	superfamily	245213	316	352	1.04E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#400 - 	CGI_10005018	superfamily	245213	267	304	0.000187463	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#400 - 	CGI_10005018	superfamily	243061	67	156	5.98E-33	122.836	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#400 - 	CGI_10005018	superfamily	243061	158	256	5.70E-32	120.139	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#400 - 	CGI_10005018	superfamily	243068	368	591	6.40E-23	98.3864	cl02523	Zona_pellucida superfamily	 - 	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#401 - 	CGI_10005019	superfamily	243035	21	121	0.000162434	37.5994	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#402 - 	CGI_10005020	superfamily	245213	64	101	5.10E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#402 - 	CGI_10005020	superfamily	243068	125	362	5.73E-35	130.743	cl02523	Zona_pellucida superfamily	 - 	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#403 - 	CGI_10005021	superfamily	227404	391	725	3.43E-28	117.717	cl18810	ALK1 superfamily	 - 	 - 	Serine/threonine kinase of the haspin family [Cell division and chromosome partitioning]
Q#404 - 	CGI_10005022	superfamily	245206	8	262	2.22E-88	264.928	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#405 - 	CGI_10005023	superfamily	241578	1	187	5.19E-81	248.818	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#406 - 	CGI_10005024	superfamily	245226	152	329	1.63E-72	227.103	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#406 - 	CGI_10005024	superfamily	207684	97	131	0.000120176	39.2844	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#410 - 	CGI_10006746	superfamily	247792	81	118	3.74E-05	37.4252	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#412 - 	CGI_10006748	superfamily	248024	37	182	9.89E-29	110.065	cl17470	SBF superfamily	C	 - 	"Sodium Bile acid symporter family; This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae, this is a putative transmembrane protein involved in resistance to arsenic compounds."
Q#413 - 	CGI_10006749	superfamily	248024	67	204	3.97E-18	80.7901	cl17470	SBF superfamily	C	 - 	"Sodium Bile acid symporter family; This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae, this is a putative transmembrane protein involved in resistance to arsenic compounds."
Q#414 - 	CGI_10006750	superfamily	215866	6	129	1.64E-20	86.6103	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#414 - 	CGI_10006750	superfamily	243212	184	287	2.05E-08	51.5758	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#415 - 	CGI_10006751	superfamily	245205	3	47	2.22E-05	39.1433	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#416 - 	CGI_10006752	superfamily	245205	14	72	7.77E-06	38.7581	cl09930	RPA_2b-aaRSs_OBF_like superfamily	C	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#426 - 	CGI_10015168	superfamily	248458	17	87	1.38E-06	45.3825	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#427 - 	CGI_10015169	superfamily	222429	7	54	1.96E-07	43.3832	cl18676	Myb_DNA-bind_5 superfamily	C	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#428 - 	CGI_10015170	superfamily	248458	105	169	9.05E-07	46.1529	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#429 - 	CGI_10015171	superfamily	248458	13	76	5.60E-06	43.4565	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#430 - 	CGI_10015172	superfamily	248458	179	308	3.46E-09	57.3237	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#430 - 	CGI_10015172	superfamily	248458	433	541	3.02E-05	44.9973	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#431 - 	CGI_10015173	superfamily	248458	57	186	6.18E-12	65.4129	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#431 - 	CGI_10015173	superfamily	248458	273	449	1.02E-06	49.2345	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#432 - 	CGI_10015174	superfamily	245213	160	196	1.33E-07	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#432 - 	CGI_10015174	superfamily	245213	198	234	3.34E-07	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#432 - 	CGI_10015174	superfamily	245213	84	120	6.33E-06	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#432 - 	CGI_10015174	superfamily	245213	122	158	0.000202999	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#433 - 	CGI_10005525	superfamily	244906	1373	1432	5.68E-26	104.144	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#433 - 	CGI_10005525	superfamily	221593	643	757	2.34E-22	95.9038	cl13857	DUF3694 superfamily	 - 	 - 	"Kinesin protein; This domain family is found in eukaryotes, and is typically between 131 and 151 amino acids in length. The family is found in association with pfam00225, pfam00498. There is a single completely conserved residue W that may be functionally important."
Q#433 - 	CGI_10005525	superfamily	221571	233	285	1.57E-10	58.6683	cl13810	KIF1B superfamily	 - 	 - 	"Kinesin protein 1B; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00225, pfam00498. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells."
Q#434 - 	CGI_10005527	superfamily	243146	66	104	6.70E-06	42.6486	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#435 - 	CGI_10005528	superfamily	243100	169	222	4.31E-09	50.6901	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#436 - 	CGI_10005529	superfamily	241571	74	168	8.93E-07	47.0219	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#436 - 	CGI_10005529	superfamily	243035	190	245	3.98E-09	54.143	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#436 - 	CGI_10005529	superfamily	245847	264	394	0.000127152	41.003	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#438 - 	CGI_10005531	superfamily	188051	141	432	1.90E-25	105.627	cl18155	nop2p superfamily	 - 	 - 	"NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base modification]."
Q#442 - 	CGI_10012222	superfamily	248020	22	226	1.48E-06	48.6148	cl17466	Sulfatase superfamily	C	 - 	Sulfatase; Sulfatase.  
Q#445 - 	CGI_10012225	superfamily	243093	71	156	8.09E-08	50.1613	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#447 - 	CGI_10012227	superfamily	247792	16	59	7.32E-08	48.596	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#447 - 	CGI_10012227	superfamily	241563	154	189	6.01E-06	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#449 - 	CGI_10012229	superfamily	243238	38	506	4.64E-170	499.102	cl02915	Voltage_gated_ClC superfamily	 - 	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#449 - 	CGI_10012229	superfamily	246936	524	688	4.52E-19	83.8408	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#451 - 	CGI_10012231	superfamily	216033	749	837	7.91E-19	83.152	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	625	710	2.30E-15	73.1368	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	57	141	4.28E-15	72.3664	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	530	617	8.52E-15	71.596	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	245	329	1.56E-14	70.8256	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	353	428	8.12E-12	62.7364	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	460	523	9.11E-11	59.6548	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	178	236	8.59E-05	41.5504	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#451 - 	CGI_10012231	superfamily	216033	4	49	0.00231685	37.3132	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#452 - 	CGI_10012232	superfamily	245309	150	228	0.000609837	38.6292	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#452 - 	CGI_10012232	superfamily	248097	259	365	4.98E-22	92.3282	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#452 - 	CGI_10012232	superfamily	248097	503	619	8.95E-12	62.6678	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#452 - 	CGI_10012232	superfamily	248097	375	487	1.79E-06	46.4894	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#453 - 	CGI_10012233	superfamily	245309	86	164	0.00133461	37.0884	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#453 - 	CGI_10012233	superfamily	248097	193	299	2.74E-25	101.188	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#453 - 	CGI_10012233	superfamily	248097	449	556	3.47E-08	51.9193	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#453 - 	CGI_10012233	superfamily	248097	309	353	6.29E-06	44.5634	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#455 - 	CGI_10012235	superfamily	243212	356	484	3.70E-15	72.7617	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#455 - 	CGI_10012235	superfamily	215866	165	287	7.43E-12	63.1132	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#456 - 	CGI_10012236	superfamily	247725	913	1017	9.87E-34	127.508	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#456 - 	CGI_10012236	superfamily	201217	88	139	1.27E-12	64.8544	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#456 - 	CGI_10012236	superfamily	201217	582	629	1.67E-12	64.4692	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#456 - 	CGI_10012236	superfamily	205718	616	645	1.82E-07	49.411	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#456 - 	CGI_10012236	superfamily	205718	72	101	9.40E-06	44.4034	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#456 - 	CGI_10012236	superfamily	201217	143	204	2.69E-05	43.2832	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#456 - 	CGI_10012236	superfamily	201217	632	679	3.46E-05	43.2832	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#456 - 	CGI_10012236	superfamily	201217	209	253	0.000555424	39.4312	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#456 - 	CGI_10012236	superfamily	209898	1124	1142	0.00190174	37.7051	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#456 - 	CGI_10012236	superfamily	209898	1152	1169	0.00927199	35.7791	cl14787	MORN superfamily	C	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#457 - 	CGI_10012237	superfamily	128469	243	322	0.00030407	38.5904	cl17971	VPS9 superfamily	C	 - 	Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
Q#463 - 	CGI_10004485	superfamily	215866	13	147	3.41E-22	90.0771	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#463 - 	CGI_10004485	superfamily	243212	166	206	1.37E-05	42.7162	cl02844	Arrestin_C superfamily	C	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#467 - 	CGI_10007406	superfamily	245876	5	107	2.82E-50	166.693	cl12113	HSF_DNA-bind superfamily	 - 	 - 	HSF-type DNA-binding; HSF-type DNA-binding.  
Q#467 - 	CGI_10007406	superfamily	219081	251	394	0.000702796	39.6848	cl05853	Vert_HS_TF superfamily	C	 - 	"Vertebrate heat shock transcription factor; This family represents the C-terminal region of vertebrate heat shock transcription factors. Heat shock transcription factors regulate the expression of heat shock proteins - a set of proteins that protect the cell from damage caused by stress and aid the cell's recovery after the removal of stress. This C-terminal region is found with the N-terminal pfam00447, and may contain a three-stranded coiled-coil trimerisation domain and a CE2 regulatory region, the latter of which is involved in sustained heat shock response."
Q#468 - 	CGI_10007407	superfamily	241571	198	309	1.68E-24	99.7942	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#468 - 	CGI_10007407	superfamily	241571	5	99	2.36E-17	78.9934	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#468 - 	CGI_10007407	superfamily	241613	104	136	1.78E-08	51.4386	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#468 - 	CGI_10007407	superfamily	241613	399	430	1.49E-07	49.1274	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#468 - 	CGI_10007407	superfamily	241613	155	194	0.000587255	38.3418	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#469 - 	CGI_10007408	superfamily	248289	26	80	6.94E-05	37.4035	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#470 - 	CGI_10007409	superfamily	245864	97	243	3.06E-11	61.9106	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#471 - 	CGI_10007410	superfamily	238191	10	507	4.26E-130	391.31	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#473 - 	CGI_10007412	superfamily	247856	102	120	0.00526491	32.25	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#474 - 	CGI_10011934	superfamily	241782	34	429	2.93E-141	413.118	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#476 - 	CGI_10011936	superfamily	222150	243	267	1.69E-05	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#476 - 	CGI_10011936	superfamily	222150	270	295	3.08E-05	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#476 - 	CGI_10011936	superfamily	222150	298	322	0.000428054	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#476 - 	CGI_10011936	superfamily	222150	327	351	0.000867075	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#476 - 	CGI_10011936	superfamily	246975	230	250	0.00813496	33.8597	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#477 - 	CGI_10011937	superfamily	248458	18	194	7.69E-14	71.1909	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#478 - 	CGI_10011938	superfamily	241572	63	115	0.000345107	36.8329	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#479 - 	CGI_10011939	superfamily	247769	588	761	7.93E-06	45.4081	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#479 - 	CGI_10011939	superfamily	248010	343	493	2.03E-16	77.4216	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#479 - 	CGI_10011939	superfamily	248010	162	242	0.00492498	36.9756	cl17456	GAF superfamily	N	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#482 - 	CGI_10011942	superfamily	245814	606	679	1.00E-09	56.3435	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#482 - 	CGI_10011942	superfamily	245814	38	99	8.30E-08	50.5655	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#482 - 	CGI_10011942	superfamily	245814	515	571	4.33E-06	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#482 - 	CGI_10011942	superfamily	245814	134	205	4.73E-06	45.1727	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#482 - 	CGI_10011942	superfamily	245814	242	300	0.00290884	36.6983	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#482 - 	CGI_10011942	superfamily	245814	417	477	1.52E-07	49.7127	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#482 - 	CGI_10011942	superfamily	245814	310	375	2.31E-07	49.297	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#482 - 	CGI_10011942	superfamily	245814	492	532	0.00496426	36.367	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#484 - 	CGI_10011944	superfamily	241599	273	329	2.56E-06	44.9269	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#485 - 	CGI_10011945	superfamily	241563	68	109	2.61E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#487 - 	CGI_10011947	superfamily	245819	1075	1214	5.57E-51	178.927	cl11967	Nucleotidyl_cyc_III superfamily	C	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#487 - 	CGI_10011947	superfamily	245225	270	626	1.99E-51	187.455	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#487 - 	CGI_10011947	superfamily	245201	790	1003	4.26E-28	115.712	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#487 - 	CGI_10011947	superfamily	219526	1005	1062	0.000833874	40.6803	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#488 - 	CGI_10011948	superfamily	217228	204	422	3.59E-129	377.466	cl07843	G6PD_C superfamily	C	 - 	"Glucose-6-phosphate dehydrogenase, C-terminal domain; Glucose-6-phosphate dehydrogenase, C-terminal domain.  "
Q#488 - 	CGI_10011948	superfamily	215937	29	202	1.35E-84	258.971	cl02877	G6PD_N superfamily	 - 	 - 	"Glucose-6-phosphate dehydrogenase, NAD binding domain; Glucose-6-phosphate dehydrogenase, NAD binding domain.  "
Q#489 - 	CGI_10011949	superfamily	205277	121	282	1.39E-16	74.586	cl16092	ShortName superfamily	 - 	 - 	Family description; Family description.  
Q#490 - 	CGI_10011950	superfamily	242900	1	157	8.73E-27	100.423	cl02137	PRA1 superfamily	 - 	 - 	PRA1 family protein; This family includes the PRA1 (Prenylated rab acceptor) protein which is a Rab guanine dissociation inhibitor (GDI) displacement factor. This family also includes the glutamate transporter EAAC1 interacting protein GTRAP3-18.
Q#491 - 	CGI_10011951	superfamily	247750	67	363	0	525.768	cl17196	E1_enzyme_family superfamily	 - 	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#491 - 	CGI_10011951	superfamily	192164	370	457	1.54E-18	80.3472	cl07434	E2_bind superfamily	 - 	 - 	"E2 binding domain; E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains."
Q#493 - 	CGI_10008351	superfamily	241574	69	122	3.90E-17	74.5445	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#494 - 	CGI_10008352	superfamily	247724	253	427	4.18E-41	147.297	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#494 - 	CGI_10008352	superfamily	247724	106	222	2.12E-33	125.34	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#494 - 	CGI_10008352	superfamily	247724	7	62	3.24E-05	43.7528	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#495 - 	CGI_10008353	superfamily	247805	24	98	3.08E-10	54.1875	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#496 - 	CGI_10008354	superfamily	241600	132	287	2.70E-66	215.953	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#498 - 	CGI_10008356	superfamily	245208	1	55	1.98E-11	57.381	cl09933	ACAD superfamily	N	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#500 - 	CGI_10011017	superfamily	241563	38	77	1.45E-05	42.6595	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#505 - 	CGI_10011023	superfamily	246713	10	34	0.00532324	34.302	cl14786	ENDO3c superfamily	 - 	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#506 - 	CGI_10011024	superfamily	243164	103	136	3.97E-11	54.466	cl02748	zf-CDGSH superfamily	 - 	 - 	"Iron-binding zinc finger CDGSH type; The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, pfam10660. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm."
Q#506 - 	CGI_10011024	superfamily	243164	59	92	6.67E-09	47.9176	cl02748	zf-CDGSH superfamily	 - 	 - 	"Iron-binding zinc finger CDGSH type; The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, pfam10660. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm."
Q#507 - 	CGI_10011025	superfamily	243058	77	195	3.32E-21	89.2959	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#507 - 	CGI_10011025	superfamily	243058	161	279	6.81E-19	82.7475	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#507 - 	CGI_10011025	superfamily	243058	245	407	2.30E-07	48.8499	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#507 - 	CGI_10011025	superfamily	243058	28	89	0.00376149	36.1384	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#509 - 	CGI_10011027	superfamily	243035	2	107	2.90E-17	71.8821	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#510 - 	CGI_10011028	superfamily	243072	24	147	1.21E-25	97.069	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#518 - 	CGI_10006220	superfamily	242830	11	62	2.08E-27	102.628	cl02008	CAT superfamily	C	 - 	Chloramphenicol acetyltransferase; Chloramphenicol acetyltransferase.  
Q#519 - 	CGI_10006223	superfamily	248230	1	81	1.07E-38	142.016	cl17676	Rep_3 superfamily	C	 - 	Initiator Replication protein; This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene.
Q#520 - 	CGI_10006224	superfamily	221913	292	385	2.01E-08	53.6983	cl18626	AAA_12 superfamily	C	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#521 - 	CGI_10006225	superfamily	245206	4	192	1.09E-72	223.093	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#522 - 	CGI_10006226	superfamily	241600	22	159	1.91E-47	155.091	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#524 - 	CGI_10006228	superfamily	241600	281	377	1.71E-42	149.313	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#524 - 	CGI_10006228	superfamily	241600	111	192	3.08E-22	92.6886	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#524 - 	CGI_10006228	superfamily	241619	226	261	0.0011018	37.0291	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#525 - 	CGI_10006229	superfamily	241600	2	157	1.31E-49	160.869	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#529 - 	CGI_10014571	superfamily	245342	625	703	1.31E-20	88.5598	cl10594	ERCC4 superfamily	 - 	 - 	ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Q#531 - 	CGI_10014573	superfamily	220207	433	485	1.23E-17	77.6748	cl09622	Sas10_Utp3_C superfamily	C	 - 	Sas10 C-terminal domain; This family contains a C-terminal presumed domain in Sas10 which hash been identified as a regulator of chromatin silencing.
Q#531 - 	CGI_10014573	superfamily	217836	224	304	1.53E-14	69.2317	cl09556	Sas10_Utp3 superfamily	 - 	 - 	"Sas10/Utp3/C1D family; This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex. It also includes the human C1D protein and Saccharomyces cerevisiae YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs, and Sas10 which has been identified as a regulator of chromatin silencing. This family also includes the human protein Neuroguidin an initiation factor 4E (eIF4E) binding protein."
Q#532 - 	CGI_10014574	superfamily	245201	252	511	0	560.891	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#532 - 	CGI_10014574	superfamily	246908	137	232	5.80E-63	202.735	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#532 - 	CGI_10014574	superfamily	247683	78	129	8.38E-30	111.135	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#533 - 	CGI_10014575	superfamily	243072	1328	1377	7.05E-09	55.4674	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#533 - 	CGI_10014575	superfamily	152510	171	204	0.000101474	41.918	cl13504	KN_motif superfamily	 - 	 - 	"KN motif; This small motif is found at the N-terminus of Kank proteins and has been called the KN (for Kank N-terminal) motif. This protein is found in eukaryotes. Proteins in this family are typically between 413 to 1202 amino acids in length. This protein is found associated with pfam00023. This protein has two conserved sequence motifs: TPYG and LDLDF. Kank1 was obtained by positional cloning of a tumor suppressor gene in renal cell carcinoma, while the other members were found by homology search. The family is involved in the regulation of actin polymerization and cell motility through signaling pathways containing PI3K/Akt and/or unidentified modulators/effectors."
Q#534 - 	CGI_10014576	superfamily	218954	1	84	0.00194946	36.5295	cl05646	Isy1 superfamily	C	 - 	Isy1-like splicing family; Isy1 protein is important in the optimisation of splicing.
Q#535 - 	CGI_10014577	superfamily	238147	30	161	3.45E-42	148.491	cl18906	TFIIFa superfamily	N	 - 	"Transcription initiation factor IIF, alpha subunit, N-terminal region of RAP74. Subunit of transcription initiation complex involved in initiation, elongation and promoter escape.Tetramer of 2 alpha and 2 beta TFIIF subunits interacts directly with RNA polymerase II. TFIIF inhibits non-specific transcription initiation by PolII and recruits the polymerase to the preinitiation complex on promoter DNA for site-specific transcription initiation. The PolII/TFIIF-complex attaches through direct interactions of TFIIF with promoter DNA, TFIIB and the TAF250 subunit of TFIID, and provides scaffolding for addition of TFIIE and TFIIH. Together with TFIIE, TFIIF participates in DNA strand separation (open complex formation). N-terminal domains of RAP30 and RAP74 co-fold to form a single core structure, a triple barrel heterodimer, and has pseudo-2-fold symmetry."
Q#536 - 	CGI_10014578	superfamily	212555	135	348	9.73E-37	133.386	cl17024	FBX4_GTPase_like superfamily	 - 	 - 	"C-terminal GTPase-like domain of F-Box Only Protein 4; F-box proteins are involved in substrate recognition as part of SCF (Skp1-Cul1-Rbx1-F-box protein) ubiquitin ligase complexes. Fbx4 (or Fbxo4) binds to the telomere repeat binding factor 1 (TRF1), whose activity at telomeres is regulated in part by selective ubiquitination and degradation. This ubiquitination of TRF1 is mediated by Fbx4, which binds to the TRFH domain of TRF1, via the C-terminal domain characterized by this model, a module resembling a small GTPase domain that lacks the GTP-binding site. When bound to telomeres, TIN2 acts to protect TRF1 from SCF-Fbx4 mediated ubiquitination. Tankyrase-mediated ADP-ribosylation releases TRF1 from telomeres, rendering them susceptible to ubiquitination and degradation, which in turn promotes telomere elongation. Fbx4 has also been reported to target cyclin D1 for degradation by the proteasome, a mechanism ensuring the fidelity of DNA replication. More recently, these findings have been disputed."
Q#536 - 	CGI_10014578	superfamily	243074	37	83	1.73E-13	64.0649	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#537 - 	CGI_10014579	superfamily	242200	1	91	4.29E-28	99.0852	cl00932	Ribosomal_L37e superfamily	 - 	 - 	Ribosomal protein L37e; This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc.
Q#540 - 	CGI_10014582	superfamily	246902	22	84	1.25E-31	109.236	cl15239	PLDc_SF superfamily	N	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#541 - 	CGI_10014583	superfamily	218768	21	164	5.47E-43	143.549	cl05419	DUF846 superfamily	 - 	 - 	Eukaryotic protein of unknown function (DUF846); This family consists of several of unknown function from a variety of eukaryotic organisms.
Q#543 - 	CGI_10014585	superfamily	243555	25	211	4.03E-21	88.6022	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#545 - 	CGI_10014587	superfamily	245595	29	352	8.06E-158	453.588	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#545 - 	CGI_10014587	superfamily	248053	356	438	2.49E-20	85.2684	cl17499	Peptidase_M14NE-CP-C_like superfamily	 - 	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#548 - 	CGI_10014590	superfamily	248279	588	652	1.90E-12	63.9247	cl17725	zf-HC5HC2H superfamily	C	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#549 - 	CGI_10007841	superfamily	242903	23	97	7.53E-48	152.327	cl02148	APC10-like superfamily	C	 - 	"APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An  APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here."
Q#554 - 	CGI_10007847	superfamily	245847	9	156	6.65E-17	72.9745	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#557 - 	CGI_10007850	superfamily	243104	14	55	6.89E-05	37.9097	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#557 - 	CGI_10007850	superfamily	245205	99	156	0.00379233	33.3653	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#560 - 	CGI_10000417	superfamily	242240	9	151	1.14E-34	123.941	cl00997	DUF297 superfamily	N	 - 	TM1410 hypothetical-related protein; TM1410 hypothetical-related protein.  
Q#561 - 	CGI_10000522	superfamily	216901	28	229	0.000264258	39.4913	cl03466	Rap_GAP superfamily	 - 	 - 	Rap/ran-GAP; Rap/ran-GAP.  
Q#562 - 	CGI_10000553	superfamily	247724	17	93	3.05E-21	88.3611	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#563 - 	CGI_10013033	superfamily	241611	1293	1451	3.33E-16	80.1252	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#563 - 	CGI_10013033	superfamily	207627	232	294	1.25E-08	56.1039	cl02522	Calx-beta superfamily	N	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	1529	1616	3.90E-08	54.5631	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	2049	2136	2.03E-07	52.2519	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	976	1044	3.86E-07	51.4815	cl02522	Calx-beta superfamily	N	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	4302	4392	9.12E-07	50.3307	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	2531	2603	1.02E-06	50.3259	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	3926	4017	1.42E-06	49.9455	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	4933	5012	1.42E-06	49.9407	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	325	417	3.38E-06	48.7899	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	2752	2852	2.98E-05	45.7083	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	2919	3014	3.40E-05	45.7083	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	3544	3635	0.000106299	44.1627	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	1908	2010	0.000254021	43.0071	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	4168	4257	0.000412536	42.2367	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	814	916	0.000535749	41.8563	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	103	173	0.000750086	41.4711	cl02522	Calx-beta superfamily	N	 - 	Calx-beta domain; Calx-beta domain.  
Q#563 - 	CGI_10013033	superfamily	207627	2629	2717	0.000956225	41.0859	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#564 - 	CGI_10013034	superfamily	248302	661	776	2.05E-22	93.7279	cl17748	VRR_NUC superfamily	 - 	 - 	VRR-NUC domain; VRR-NUC domain.  
Q#565 - 	CGI_10013035	superfamily	243088	2	112	1.82E-34	119.301	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#566 - 	CGI_10013036	superfamily	246908	39	139	4.64E-48	158.458	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#566 - 	CGI_10013036	superfamily	246908	225	300	2.41E-25	97.1086	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#566 - 	CGI_10013036	superfamily	247683	156	214	2.29E-23	90.9008	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#567 - 	CGI_10013037	superfamily	241546	1369	1488	2.73E-53	185.557	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#567 - 	CGI_10013037	superfamily	248011	134	208	1.13E-09	57.8917	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#567 - 	CGI_10013037	superfamily	248011	41	112	2.46E-05	44.7106	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#567 - 	CGI_10013037	superfamily	248011	3	33	0.000797984	40.127	cl17457	PKD superfamily	N	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#567 - 	CGI_10013037	superfamily	243086	1288	1321	0.00898446	36.9694	cl02559	GPS superfamily	C	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#567 - 	CGI_10013037	superfamily	219520	1727	1780	0.00942925	37.9716	cl18515	5TM-5TMR_LYT superfamily	NC	 - 	5TMR of 5TMR-LYT; This entry represents the transmembrane region of the 5TM-LYT (5TM Receptors of the LytS-YhcK type).
Q#568 - 	CGI_10013038	superfamily	241636	1	149	5.89E-44	149.275	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#570 - 	CGI_10013040	superfamily	216033	235	285	0.00147918	36.928	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#570 - 	CGI_10013040	superfamily	128778	25	150	0.00208976	36.8591	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#571 - 	CGI_10013041	superfamily	241758	229	466	3.98E-55	188.397	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#571 - 	CGI_10013041	superfamily	241780	2	198	8.46E-53	180.446	cl00319	Gn_AT_II superfamily	 - 	 - 	"Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate.  Asparagine synthetase B  synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the formation of the beta-lactam ring in the beta-lactamase inhibitor clavulanic acid. GltS synthesizes L-glutamate from 2-oxoglutarate and L-glutamine. These enzymes are generally dimers, but GPATase also exists as a homotetramer."
Q#572 - 	CGI_10013042	superfamily	247856	35	96	1.77E-07	45.6165	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#572 - 	CGI_10013042	superfamily	247856	70	138	9.25E-07	43.6905	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#575 - 	CGI_10013045	superfamily	214781	216	316	1.02E-14	71.2192	cl02747	NRF superfamily	 - 	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#576 - 	CGI_10013046	superfamily	216316	1278	1718	6.79E-164	509.093	cl10574	CD36 superfamily	 - 	 - 	CD36 family; The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion.
Q#581 - 	CGI_10001052	superfamily	246723	226	610	2.92E-40	151.816	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#582 - 	CGI_10001053	superfamily	243092	25	131	3.38E-13	63.8932	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#583 - 	CGI_10011092	superfamily	241546	1	63	0.000576447	34.9637	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#584 - 	CGI_10011093	superfamily	246751	214	435	7.94E-89	274.891	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#584 - 	CGI_10011093	superfamily	246751	56	199	2.62E-42	152.012	cl14883	Lipase superfamily	C	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#585 - 	CGI_10011094	superfamily	246751	47	332	2.36E-96	293.766	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#585 - 	CGI_10011094	superfamily	241546	342	435	5.69E-05	41.5121	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#587 - 	CGI_10011096	superfamily	245201	222	514	0	583.404	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#587 - 	CGI_10011096	superfamily	241620	61	106	7.87E-20	83.4735	cl00113	CRIB superfamily	 - 	 - 	"PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules."
Q#588 - 	CGI_10011097	superfamily	217740	65	245	1.77E-23	95.1209	cl18427	Scramblase superfamily	 - 	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#589 - 	CGI_10011098	superfamily	217311	69	504	2.19E-119	365.891	cl18402	DUF229 superfamily	 - 	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#590 - 	CGI_10011099	superfamily	248338	15	275	9.38E-07	49.1369	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#590 - 	CGI_10011099	superfamily	247999	291	330	8.22E-06	42.5842	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#592 - 	CGI_10011101	superfamily	215502	84	301	9.62E-16	76.2292	cl18335	PLN02929 superfamily	C	 - 	NADH kinase
Q#594 - 	CGI_10011103	superfamily	241563	157	194	1.37E-05	43.0447	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#594 - 	CGI_10011103	superfamily	128778	201	318	0.00133317	38.0147	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#595 - 	CGI_10011104	superfamily	247792	72	114	0.00070665	38.5808	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#595 - 	CGI_10011104	superfamily	241563	217	245	6.91E-05	41.696	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#596 - 	CGI_10011105	superfamily	241767	64	170	2.80E-42	144.332	cl00304	TP_methylase superfamily	N	 - 	"S-AdoMet dependent tetrapyrrole methylases; This family uses S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared by both pathways and a few enzymes are pathway-specific. Diphthine synthase and Ribosomal RNA small subunit methyltransferase I (RsmI) are two superfamily members that are not involved in cobalamin biosynthesis. Diphthine synthase participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. RsmI catalyzes the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA using S-adenosylmethionine (Ado-Met) as the methyl donor."
Q#597 - 	CGI_10011106	superfamily	241594	710	1067	9.89E-138	421.588	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#598 - 	CGI_10011108	superfamily	215821	13	95	5.99E-35	116.571	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#599 - 	CGI_10011109	superfamily	215821	228	304	9.87E-36	126.586	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#599 - 	CGI_10011109	superfamily	215821	30	91	3.29E-11	59.1763	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#600 - 	CGI_10011110	superfamily	215821	32	106	1.71E-17	72.273	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#601 - 	CGI_10011111	superfamily	215821	84	161	4.38E-32	111.949	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#602 - 	CGI_10011112	superfamily	241565	1037	1102	4.96E-06	45.7755	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#602 - 	CGI_10011112	superfamily	241565	1139	1212	0.006362	36.5846	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#605 - 	CGI_10001286	superfamily	243362	354	395	0.00022821	40.4863	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#605 - 	CGI_10001286	superfamily	241563	60	96	0.000739732	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#605 - 	CGI_10001286	superfamily	128778	121	216	0.00142486	37.6295	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#608 - 	CGI_10005120	superfamily	110440	91	117	0.000977636	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#609 - 	CGI_10005121	superfamily	247755	1026	1246	2.75E-127	393.012	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#609 - 	CGI_10005121	superfamily	247755	458	681	3.13E-104	329.815	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#609 - 	CGI_10005121	superfamily	216049	168	415	1.11E-10	62.3034	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#609 - 	CGI_10005121	superfamily	216049	778	970	4.93E-05	45.3546	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#613 - 	CGI_10001940	superfamily	247792	10	69	4.66E-05	45.4616	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#614 - 	CGI_10001839	superfamily	220253	53	129	1.33E-07	48.8287	cl09706	Cobl superfamily	C	 - 	"Cordon-bleu domain; The Cordon-bleu protein domain is highly conserved among vertebrates. The sequence contains three repeated lysine, arginine, and proline-rich regions, the KKRAP motif. The exact function of the protein is unknown but it is thought to be involved in mid-brain neural tube closure. It is expressed specifically in the node."
Q#616 - 	CGI_10011442	superfamily	243072	332	454	5.75E-23	94.3726	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#616 - 	CGI_10011442	superfamily	243072	404	519	9.44E-20	85.513	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#616 - 	CGI_10011442	superfamily	243072	311	335	0.000154551	39.4596	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#618 - 	CGI_10011444	superfamily	245847	21	161	9.22E-16	69.8929	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#624 - 	CGI_10011450	superfamily	248097	76	194	1.92E-22	88.4762	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#626 - 	CGI_10011453	superfamily	217473	11	33	0.00692743	33.8778	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#628 - 	CGI_10002181	superfamily	243110	135	356	8.98E-19	85.5589	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#630 - 	CGI_10001384	superfamily	204434	14	39	7.86E-10	54.5081	cl10963	zf-CCHH superfamily	 - 	 - 	"Zinc-finger (CX5CX6HX5H) motif; This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism."
Q#630 - 	CGI_10001384	superfamily	241752	245	394	3.14E-09	55.4143	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#630 - 	CGI_10001384	superfamily	204434	71	94	1.52E-07	47.9597	cl10963	zf-CCHH superfamily	 - 	 - 	"Zinc-finger (CX5CX6HX5H) motif; This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism."
Q#632 - 	CGI_10012121	superfamily	241743	255	344	1.80E-14	69.9094	cl00274	ML superfamily	C	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#633 - 	CGI_10012122	superfamily	241743	30	161	9.05E-24	92.251	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#634 - 	CGI_10012123	superfamily	241743	83	138	3.81E-09	50.6494	cl00274	ML superfamily	C	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#635 - 	CGI_10012124	superfamily	202367	1	137	1.75E-21	88.3656	cl18226	3HCDH_N superfamily	 - 	 - 	"3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda crystallin."
Q#635 - 	CGI_10012124	superfamily	216084	142	214	3.60E-15	68.7725	cl08285	3HCDH superfamily	C	 - 	"3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; This family also includes lambda crystallin. Some proteins include two copies of this domain."
Q#636 - 	CGI_10012125	superfamily	245201	19	335	0	598.579	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#637 - 	CGI_10012126	superfamily	221377	1506	1672	9.36E-63	213.484	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#637 - 	CGI_10012126	superfamily	242184	826	864	0.00137507	38.512	cl00909	Ribosomal_L24e_L24 superfamily	 - 	 - 	"Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site.  L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination.  L24 may be an important protein in eukaryotic reproduction:  in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identified in bacteria, but a functionally equivalent protein may exist.  Bacterial L19 forms an interprotein beta sheet with L14 that is similar to the L24e/L14 interprotein beta sheet observed in the archaeal L24e structures. Some eukaryotic L24 proteins were initially identified as L30, and this alignment model contains several sequences called L30."
Q#638 - 	CGI_10012127	superfamily	244551	286	375	1.15E-34	125.819	cl06904	eNOPS_SF superfamily	 - 	 - 	"NOPS domain, including C-terminal helical extension region, in the p54nrb/PSF/PSP1 family; All members in this family contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRM1 and RRM2), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain with a long helical C-terminal extension. The NOPS domain specifically binds to RRM2 domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. PSF has an additional large N-terminal domain that differentiates it from other family members. The p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and DNA-binding protein (p54nrb), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and paraspeckle protein 1 (PSP1), which are ubiquitously expressed and are well conserved in vertebrates. p54nrb, also termed NONO or NMT55, is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF, also termed POMp100, is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1, also termed PSPC1, is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species. For instance, the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore."
Q#638 - 	CGI_10012127	superfamily	247723	140	210	4.63E-29	110.059	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#638 - 	CGI_10012127	superfamily	247723	216	295	2.42E-28	108.162	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#640 - 	CGI_10012129	superfamily	248458	231	382	6.97E-25	108.94	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#640 - 	CGI_10012129	superfamily	247743	772	848	0.00231575	39.8756	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#641 - 	CGI_10012130	superfamily	247727	70	185	4.53E-14	67.455	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#643 - 	CGI_10012132	superfamily	243035	283	382	3.26E-06	45.6886	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#643 - 	CGI_10012132	superfamily	243035	5	111	4.67E-06	45.3034	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#643 - 	CGI_10012132	superfamily	243035	433	553	0.00452061	36.0586	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#644 - 	CGI_10012133	superfamily	243035	5	92	3.87E-08	47.7686	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#646 - 	CGI_10012135	superfamily	243035	198	317	3.39E-11	59.9409	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#647 - 	CGI_10002104	superfamily	243092	1	163	7.50E-07	47.3296	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#651 - 	CGI_10004233	superfamily	247725	401	528	1.22E-72	231.031	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#651 - 	CGI_10004233	superfamily	241631	5	180	2.08E-63	208.616	cl00136	Sec7 superfamily	 - 	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#655 - 	CGI_10011430	superfamily	245201	9	252	4.22E-144	425.16	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#656 - 	CGI_10011431	superfamily	247740	241	493	1.19E-129	384.562	cl17186	TIM_phosphate_binding superfamily	N	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#656 - 	CGI_10011431	superfamily	246936	115	230	1.67E-52	175.854	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#656 - 	CGI_10011431	superfamily	247740	29	109	1.26E-34	132.641	cl17186	TIM_phosphate_binding superfamily	C	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#659 - 	CGI_10011434	superfamily	243072	1	40	9.10E-06	44.6819	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#659 - 	CGI_10011434	superfamily	241832	662	722	1.24E-05	44.2214	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#661 - 	CGI_10011436	superfamily	220651	23	203	1.03E-42	144.593	cl10932	Mlf1IP superfamily	 - 	 - 	"Myelodysplasia-myeloid leukemia factor 1-interacting protein; This entry is the conserved central region of a group of proteins that are putative transcriptional repressors. The structure contains a putative 14-3-3 binding motif involved in the subcellular localisation of various regulatory molecules, and it may be that interaction with the transcription factor DREF could be regulated through this motif. DREF regulates proliferation-related genes in Drosophila. Mlf1IP is expressed in both the nuclei and the cytoplasm and thus may have multi-functions."
Q#662 - 	CGI_10011437	superfamily	217473	794	960	3.22E-21	95.5097	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#665 - 	CGI_10011440	superfamily	242849	40	113	1.59E-27	99.5856	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#666 - 	CGI_10011441	superfamily	247999	533	580	1.59E-10	57.5004	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#666 - 	CGI_10011441	superfamily	247999	421	456	2.58E-07	48.2556	cl17445	PHD superfamily	C	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#666 - 	CGI_10011441	superfamily	247999	363	421	7.82E-05	40.9368	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#666 - 	CGI_10011441	superfamily	247999	475	533	7.82E-05	40.9368	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#668 - 	CGI_10008204	superfamily	241610	2707	2759	1.53E-20	89.2314	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#668 - 	CGI_10008204	superfamily	246671	2058	2180	3.75E-11	63.596	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#668 - 	CGI_10008204	superfamily	243034	1647	1738	0.000140192	43.1376	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#668 - 	CGI_10008204	superfamily	219042	2308	2498	4.32E-71	239.967	cl05795	Spond_N superfamily	 - 	 - 	Spondin_N; This conserved region is found at the in the N-terminal half of several Spondin proteins. Spondins are involved in patterning axonal growth trajectory through either inhibiting or promoting adhesion of embryonic nerve cells.
Q#668 - 	CGI_10008204	superfamily	246918	2849	2900	2.86E-12	65.3007	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#668 - 	CGI_10008204	superfamily	246918	2566	2612	2.68E-08	53.3595	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#668 - 	CGI_10008204	superfamily	246918	2647	2693	7.78E-06	46.4259	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#668 - 	CGI_10008204	superfamily	246918	2905	2956	0.000373574	41.4183	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#669 - 	CGI_10008205	superfamily	246669	271	407	1.19E-79	244.315	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#669 - 	CGI_10008205	superfamily	246669	140	264	3.01E-30	113.129	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#671 - 	CGI_10008207	superfamily	221176	79	401	9.89E-32	128.977	cl13202	Npa1 superfamily	 - 	 - 	"Ribosome 60S biogenesis N-terminal; Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length."
Q#672 - 	CGI_10008208	superfamily	227778	45	161	9.43E-12	59.8219	cl17122	VPS24 superfamily	C	 - 	Conserved protein implicated in secretion [Cell motility and secretion]
Q#673 - 	CGI_10008209	superfamily	241563	13	44	1.55E-06	45.3559	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#673 - 	CGI_10008209	superfamily	192987	81	187	0.00561351	35.6259	cl13724	TMF_TATA_bd superfamily	N	 - 	"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family."
Q#674 - 	CGI_10008210	superfamily	245610	6	287	2.64E-94	299	cl11424	nitrilase superfamily	 - 	 - 	"Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy."
Q#674 - 	CGI_10008210	superfamily	241758	326	649	5.86E-83	268.262	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#675 - 	CGI_10008211	superfamily	243082	826	1045	3.68E-58	202.231	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#675 - 	CGI_10008211	superfamily	243082	313	431	4.22E-26	109.784	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#675 - 	CGI_10008211	superfamily	245220	116	173	4.57E-15	72.0522	cl09957	zf-UBP superfamily	 - 	 - 	Zn-finger in ubiquitin-hydrolases and other protein; Zn-finger in ubiquitin-hydrolases and other protein.  
Q#675 - 	CGI_10008211	superfamily	243082	214	247	8.28E-09	56.626	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#676 - 	CGI_10008212	superfamily	241581	206	319	4.98E-25	97.0718	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#677 - 	CGI_10008213	superfamily	248458	93	270	4.50E-07	51.1605	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#677 - 	CGI_10008213	superfamily	248458	414	493	0.000601914	41.1453	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#687 - 	CGI_10007559	superfamily	247684	73	160	2.48E-05	43.7316	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#687 - 	CGI_10007559	superfamily	202746	212	442	1.10E-80	252.216	cl08402	Hexokinase_2 superfamily	 - 	 - 	Hexokinase; Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains.
Q#688 - 	CGI_10007560	superfamily	247896	21	505	1.66E-162	473.725	cl17342	Pyruvate_Kinase superfamily	 - 	 - 	"Pyruvate kinase (PK):  Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors.  Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state.  PK exists as several different isozymes, depending on organism and tissue type.  In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung.  PK forms a homotetramer, with each subunit containing three domains.  The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer."
Q#689 - 	CGI_10007561	superfamily	219909	3	279	1.20E-133	384.656	cl07252	Mo25 superfamily	 - 	 - 	Mo25-like; Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localised alternately to the spindle pole body and to the site cell division in a cell cycle dependent manner.
Q#690 - 	CGI_10007562	superfamily	248054	13	235	2.99E-12	64.6311	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#691 - 	CGI_10007563	superfamily	243077	348	404	1.51E-14	68.3409	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#691 - 	CGI_10007563	superfamily	243034	17	95	8.52E-12	61.6272	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#691 - 	CGI_10007563	superfamily	243034	226	325	1.58E-09	55.0788	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#691 - 	CGI_10007563	superfamily	243034	114	208	1.55E-08	51.9972	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#692 - 	CGI_10016397	superfamily	241597	2829	2867	6.76E-06	47.2374	cl00082	HMG-box superfamily	C	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#692 - 	CGI_10016397	superfamily	243250	4731	4984	7.75E-78	269.518	cl02959	Glyco_hydro_9 superfamily	C	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#692 - 	CGI_10016397	superfamily	215827	336	512	7.86E-37	142.222	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#692 - 	CGI_10016397	superfamily	248279	1738	1817	1.75E-17	82.0291	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#692 - 	CGI_10016397	superfamily	215827	824	908	1.96E-15	78.6643	cl02830	Tyrosinase superfamily	N	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#692 - 	CGI_10016397	superfamily	247999	1878	1926	1.19E-12	66.7452	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#692 - 	CGI_10016397	superfamily	247999	2196	2244	1.37E-12	66.7452	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#692 - 	CGI_10016397	superfamily	247999	1829	1879	5.55E-09	56.3448	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#692 - 	CGI_10016397	superfamily	247999	2146	2194	6.00E-08	52.9846	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#692 - 	CGI_10016397	superfamily	247999	2274	2326	7.41E-06	47.1	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#692 - 	CGI_10016397	superfamily	247999	1962	2016	0.00261936	39.5026	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#693 - 	CGI_10016398	superfamily	245206	157	367	1.23E-83	256.068	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#694 - 	CGI_10016399	superfamily	247829	23	405	8.86E-180	512.504	cl17275	PRTase_typeII superfamily	 - 	 - 	"Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate phosphoribosyltransferase (NAPRTase), to be used in the synthesis of NAD. QAPRTase catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide, an important step in the de novo synthesis of NAD. NAPRTase catalyses a similar reaction leading to NAMN and pyrophosphate, using nicotinic acid an PPRP as substrates, used in the NAD salvage pathway."
Q#695 - 	CGI_10016400	superfamily	248312	73	167	0.000636771	37.3329	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#696 - 	CGI_10016401	superfamily	243051	190	318	1.16E-31	124.798	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	2303	2453	6.34E-30	119.79	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	2	158	7.75E-25	105.152	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	321	448	1.62E-23	101.3	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	624	790	2.13E-23	100.915	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	463	615	1.01E-19	90.1297	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	2136	2294	5.79E-19	87.8185	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	2857	3003	1.18E-18	86.6629	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	2470	2614	1.10E-15	78.1885	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	241613	1297	1332	6.13E-09	55.2906	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#696 - 	CGI_10016401	superfamily	241613	3204	3238	1.98E-08	53.7498	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#696 - 	CGI_10016401	superfamily	241613	2817	2851	1.49E-07	51.4386	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#696 - 	CGI_10016401	superfamily	241613	3010	3042	7.96E-05	43.3494	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#696 - 	CGI_10016401	superfamily	241613	2619	2653	0.00409589	38.3418	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#696 - 	CGI_10016401	superfamily	241613	3163	3201	0.0042323	37.9566	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#696 - 	CGI_10016401	superfamily	243061	1916	2017	1.19E-44	160.2	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#696 - 	CGI_10016401	superfamily	241640	3346	3410	1.14E-19	91.569	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#696 - 	CGI_10016401	superfamily	243051	2659	2814	4.86E-11	63.9089	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243061	3063	3159	6.45E-10	59.4026	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#696 - 	CGI_10016401	superfamily	241640	3410	3462	9.41E-09	57.2862	cl00149	Tryp_SPc superfamily	N	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#696 - 	CGI_10016401	superfamily	243061	1673	1718	1.10E-06	49.6478	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#696 - 	CGI_10016401	superfamily	243051	2007	2131	0.000162468	43.4933	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	1339	1485	0.00020441	43.1009	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#696 - 	CGI_10016401	superfamily	243051	799	984	0.000571423	41.9798	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#697 - 	CGI_10016402	superfamily	243051	151	289	3.94E-14	68.9165	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#697 - 	CGI_10016402	superfamily	241571	322	381	1.92E-06	45.4811	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#697 - 	CGI_10016402	superfamily	243060	24	79	0.000160123	39.6696	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#698 - 	CGI_10016403	superfamily	243060	240	303	1.06E-09	55.0776	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#698 - 	CGI_10016403	superfamily	243060	118	180	5.61E-06	43.9068	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#700 - 	CGI_10016405	superfamily	248458	121	500	5.80E-39	146.305	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#701 - 	CGI_10016406	superfamily	247856	151	213	2.58E-15	70.6545	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#701 - 	CGI_10016406	superfamily	247856	377	441	1.73E-10	56.7873	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#701 - 	CGI_10016406	superfamily	247856	300	366	4.65E-07	47.1573	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#701 - 	CGI_10016406	superfamily	247856	187	242	0.000550105	37.9125	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#703 - 	CGI_10016408	superfamily	245206	28	299	4.51E-151	428.538	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#706 - 	CGI_10016411	superfamily	241563	59	99	7.97E-06	43.4799	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#706 - 	CGI_10016411	superfamily	110440	484	510	0.000302119	38.9281	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#707 - 	CGI_10016412	superfamily	243092	170	280	0.000430797	40.396	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#707 - 	CGI_10016412	superfamily	110440	357	383	0.00145818	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#709 - 	CGI_10001189	superfamily	243035	101	230	3.83E-14	67.2597	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#709 - 	CGI_10001189	superfamily	243035	29	77	2.63E-06	44.533	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#711 - 	CGI_10004174	superfamily	245309	59	134	1.87E-05	41.7108	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#711 - 	CGI_10004174	superfamily	243035	219	323	2.97E-05	41.4514	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#712 - 	CGI_10004175	superfamily	217658	24	114	2.79E-25	94.8872	cl04196	UPF0041 superfamily	 - 	 - 	Uncharacterized protein family (UPF0041); Uncharacterized protein family (UPF0041).  
Q#713 - 	CGI_10004176	superfamily	247723	53	125	2.11E-45	154.319	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#713 - 	CGI_10004176	superfamily	222683	144	228	2.59E-31	115.39	cl16803	CSTF2_hinge superfamily	 - 	 - 	"Hinge domain of cleavage stimulation factor subunit 2; The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localisation. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex."
Q#713 - 	CGI_10004176	superfamily	206472	437	479	5.23E-08	49.4189	cl16788	CSTF_C superfamily	 - 	 - 	"Transcription termination and cleavage factor C-terminal; The C-terminal section of CSTF proteins is a discreet structure is crucial for mRNA 3'-end processing. This domain interacts with Pcf11 and possibly PC4, thus linking CstF2 to transcription, transcriptional termination, and cell growth."
Q#714 - 	CGI_10004177	superfamily	248097	330	453	9.21E-17	76.1498	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#715 - 	CGI_10004178	superfamily	247743	121	233	0.000172117	40.646	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#716 - 	CGI_10004179	superfamily	243088	29	153	2.26E-69	208.466	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#717 - 	CGI_10004180	superfamily	219918	12	102	2.14E-23	95.8336	cl07265	DUF1767 superfamily	 - 	 - 	Domain of unknown function (DUF1767); Eukaryotic domain of unknown function. This domain is found to the N-terminus of the nucleic acid binding domain.
Q#718 - 	CGI_10004181	superfamily	242611	63	410	1.49E-127	374.139	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#721 - 	CGI_10002999	superfamily	245008	814	880	3.00E-14	69.1392	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#721 - 	CGI_10002999	superfamily	207794	372	794	0	560.372	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#721 - 	CGI_10002999	superfamily	243574	65	223	5.22E-15	73.7005	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#722 - 	CGI_10003000	superfamily	248097	606	720	4.60E-26	104.269	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#723 - 	CGI_10003001	superfamily	241574	170	316	1.67E-33	126.546	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#723 - 	CGI_10003001	superfamily	241574	366	511	2.76E-14	71.4629	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#724 - 	CGI_10004794	superfamily	247905	4	117	1.26E-25	104.242	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#724 - 	CGI_10004794	superfamily	248281	605	667	0.000542173	39.5611	cl17727	GT1 superfamily	C	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#726 - 	CGI_10005632	superfamily	241815	5	241	2.31E-40	140.272	cl00361	Transcrip_reg superfamily	 - 	 - 	"Transcriptional regulator; This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region."
Q#727 - 	CGI_10005633	superfamily	247856	308	367	2.60E-11	58.7133	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#727 - 	CGI_10005633	superfamily	247856	271	330	0.00291279	35.2161	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#732 - 	CGI_10005638	superfamily	246921	8	53	2.98E-10	56.6149	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#733 - 	CGI_10005639	superfamily	246921	186	226	0.00499747	33.8881	cl15299	FG-GAP superfamily	C	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#734 - 	CGI_10005640	superfamily	207627	132	189	0.00363857	34.9227	cl02522	Calx-beta superfamily	N	 - 	Calx-beta domain; Calx-beta domain.  
Q#741 - 	CGI_10003432	superfamily	110440	378	404	5.90E-05	40.4689	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#742 - 	CGI_10003880	superfamily	217900	2	34	2.23E-12	63.7551	cl04403	APG9 superfamily	N	 - 	"Autophagy protein Apg9; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways."
Q#745 - 	CGI_10003883	superfamily	241613	301	335	1.11E-11	60.6833	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#745 - 	CGI_10003883	superfamily	241613	223	257	5.13E-11	58.7574	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#745 - 	CGI_10003883	superfamily	241613	262	296	2.65E-10	56.4462	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#747 - 	CGI_10007918	superfamily	241592	100	211	2.76E-71	215.539	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#748 - 	CGI_10007919	superfamily	247792	536	574	1.04E-05	43.5224	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#749 - 	CGI_10007920	superfamily	241688	39	157	7.78E-30	112.645	cl00210	Isoprenoid_Biosyn_C1 superfamily	NC	 - 	"Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD."
Q#750 - 	CGI_10007921	superfamily	243109	319	511	2.63E-70	224.323	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#750 - 	CGI_10007921	superfamily	247999	54	89	0.00130508	37.1914	cl17445	PHD superfamily	N	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#751 - 	CGI_10007922	superfamily	248304	421	513	2.19E-05	43.2792	cl17750	CTD superfamily	 - 	 - 	"Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif."
Q#752 - 	CGI_10007923	superfamily	245201	31	289	2.47E-44	163.053	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#753 - 	CGI_10007924	superfamily	243540	85	308	2.85E-21	89.2292	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#754 - 	CGI_10007925	superfamily	114591	4	153	1.58E-07	48.3083	cl05445	Mt_ATP-synt_D superfamily	 - 	 - 	"ATP synthase D chain, mitochondrial (ATP5H); This family consists of several ATP synthase D chain, mitochondrial (ATP5H) proteins. Subunit d has no extensive hydrophobic sequences, and is not apparently related to any subunit described in the simpler ATP synthases in bacteria and chloroplasts."
Q#755 - 	CGI_10007926	superfamily	243066	26	112	1.61E-25	96.468	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#756 - 	CGI_10007927	superfamily	245201	17	277	9.37E-149	425.839	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#756 - 	CGI_10007927	superfamily	247725	340	395	2.96E-10	56.8396	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#757 - 	CGI_10007928	superfamily	207684	638	672	2.65E-10	57.0035	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#757 - 	CGI_10007928	superfamily	210068	153	177	1.24E-05	43.4274	cl15286	RPEL superfamily	 - 	 - 	RPEL repeat; The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that the Drosophila myocardin-related transcription factor contains a pfam02037 domain that is also implicated in DNA binding.
Q#757 - 	CGI_10007928	superfamily	210068	197	222	0.000512995	38.805	cl15286	RPEL superfamily	 - 	 - 	RPEL repeat; The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that the Drosophila myocardin-related transcription factor contains a pfam02037 domain that is also implicated in DNA binding.
Q#759 - 	CGI_10007930	superfamily	218390	644	763	3.72E-30	122.039	cl04895	PARG_cat superfamily	C	 - 	"Poly (ADP-ribose) glycohydrolase (PARG); Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death."
Q#760 - 	CGI_10007931	superfamily	242164	36	133	1.59E-28	104.726	cl00878	Ribosomal_S24e superfamily	C	 - 	Ribosomal protein S24e; Ribosomal protein S24e.  
Q#761 - 	CGI_10015876	superfamily	218118	1357	1437	1.18E-13	68.7948	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#761 - 	CGI_10015876	superfamily	247792	1267	1292	0.00319407	37.3724	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#762 - 	CGI_10015877	superfamily	217293	62	195	6.22E-13	66.8875	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#762 - 	CGI_10015877	superfamily	202474	270	350	6.84E-08	51.8857	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#763 - 	CGI_10015878	superfamily	202474	1	119	1.73E-12	62.6713	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#765 - 	CGI_10015880	superfamily	243035	108	222	3.30E-22	88.4457	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#766 - 	CGI_10015881	superfamily	247856	110	168	2.44E-05	39.4533	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#766 - 	CGI_10015881	superfamily	247856	39	100	0.000329702	36.3717	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#767 - 	CGI_10015882	superfamily	241575	461	527	8.52E-17	76.1571	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#767 - 	CGI_10015882	superfamily	241575	356	405	2.69E-07	48.8079	cl00054	DSRM superfamily	C	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#767 - 	CGI_10015882	superfamily	241575	137	188	3.57E-07	48.4227	cl00054	DSRM superfamily	C	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#767 - 	CGI_10015882	superfamily	241575	279	318	2.19E-06	46.1115	cl00054	DSRM superfamily	N	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#768 - 	CGI_10015883	superfamily	241568	42	92	1.67E-05	38.2128	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#769 - 	CGI_10015884	superfamily	245206	2	237	1.36E-81	248.462	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#771 - 	CGI_10015886	superfamily	191913	32	129	2.74E-16	71.2098	cl07876	NIPSNAP superfamily	 - 	 - 	NIPSNAP; Members of this family include many hypothetical proteins. It also includes members of the NIPSNAP family which have putative roles in vesicular transport. This domain is often found in duplicate.
Q#774 - 	CGI_10015889	superfamily	243859	255	327	1.90E-05	41.9318	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#775 - 	CGI_10015890	superfamily	219525	495	533	0.00114672	37.3986	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#775 - 	CGI_10015890	superfamily	219525	344	384	0.00230787	36.6282	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#775 - 	CGI_10015890	superfamily	219525	415	452	0.00411758	35.8578	cl06646	GCC2_GCC3 superfamily	N	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#775 - 	CGI_10015890	superfamily	219525	455	503	0.00859334	34.7022	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#779 - 	CGI_10015896	superfamily	247913	161	531	6.47E-37	140.91	cl17359	PTR2 superfamily	 - 	 - 	POT family; The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters.
Q#779 - 	CGI_10015896	superfamily	247913	31	250	3.47E-05	45.3243	cl17359	PTR2 superfamily	C	 - 	POT family; The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters.
Q#781 - 	CGI_10015898	superfamily	243072	137	220	5.77E-16	75.1126	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#781 - 	CGI_10015898	superfamily	243047	10	126	4.78E-40	142.48	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#781 - 	CGI_10015898	superfamily	209407	330	360	4.44E-08	50.2716	cl11983	GIT_SHD superfamily	 - 	 - 	"Spa2 homology domain (SHD) of GIT; GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase."
Q#781 - 	CGI_10015898	superfamily	209407	274	295	9.21E-06	43.338	cl11983	GIT_SHD superfamily	N	 - 	"Spa2 homology domain (SHD) of GIT; GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase."
Q#782 - 	CGI_10015899	superfamily	243072	11	101	3.94E-18	80.8906	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#782 - 	CGI_10015899	superfamily	221304	155	437	8.87E-94	291.627	cl13359	GPCR_chapero_1 superfamily	 - 	 - 	"GPCR-chaperone; This domain, and the associated ANK family repeat pfam00023 domain, together act as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2."
Q#783 - 	CGI_10015900	superfamily	152787	151	216	5.29E-13	61.4597	cl18053	V-SNARE_C superfamily	 - 	 - 	Snare region anchored in the vesicle membrane C-terminus; Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle pfam05008.
Q#786 - 	CGI_10015903	superfamily	113482	2	50	1.83E-18	74.7139	cl04700	BCL_N superfamily	 - 	 - 	"BCL7, N-terminal conserver region; Members of the BCL family have significant sequence similarity at their N-terminus, represented in this family. The function of BCL7 proteins is unknown. They may be involved in early development. In addition, BCL7B is commonly hemizygously deleted in patients with Williams syndrome."
Q#787 - 	CGI_10015904	superfamily	241703	5	304	8.41E-121	352.332	cl00226	nuc_hydro superfamily	 - 	 - 	"nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity.  This group contains eukaryotic, bacterial and archeal proteins similar to the inosine-uridine preferring nucleoside hydrolase from Crithidia fasciculata,  the xanthosine-inosine-uridine-adenosine-preferring nucleoside hydrolase RihC from Salmonella enterica serovar Typhimurium, the purine-specific  inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax and, pyrimidine-specific uridine-cytidine preferring nucleoside hydrolases such as URH1 from Saccharomyces cerevisiae, RihA and RihB from Escherichia coli. Nucleoside hydrolases are of interest as a target for antiprotozoan drugs as, no nucleoside hydrolase activity or genes encoding these enzymes have been detected in humans and, parasitic protozoans lack de novo purine synthesis relying on nucleoside hydrolase to scavenge purine and/or pyrimidines from the environment."
Q#788 - 	CGI_10015905	superfamily	238191	20	461	4.12E-117	356.642	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#789 - 	CGI_10015906	superfamily	241619	51	105	5.30E-05	37.9469	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#791 - 	CGI_10008711	superfamily	219541	88	140	1.03E-18	78.6643	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#792 - 	CGI_10008712	superfamily	241644	95	252	2.00E-23	92.6505	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#793 - 	CGI_10008713	superfamily	190534	608	698	3.34E-28	109.42	cl18165	bZIP_Maf superfamily	 - 	 - 	"bZIP Maf transcription factor; Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerisation and DNA binding property. Thus, this family is probably related to pfam00170."
Q#793 - 	CGI_10008713	superfamily	245716	182	207	0.001905	36.8385	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#793 - 	CGI_10008713	superfamily	245716	134	155	0.00278718	36.3823	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#794 - 	CGI_10008714	superfamily	241647	15	44	1.14E-13	64.8566	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#794 - 	CGI_10008714	superfamily	241647	56	86	1.50E-06	44.8262	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#794 - 	CGI_10008714	superfamily	245206	120	401	3.64E-132	384.256	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#795 - 	CGI_10008715	superfamily	243082	622	890	8.49E-39	145.704	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#795 - 	CGI_10008715	superfamily	243082	521	640	6.90E-07	50.7844	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#796 - 	CGI_10008716	superfamily	241739	224	413	5.49E-95	297.965	cl00268	class_II_aaRS-like_core superfamily	N	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#796 - 	CGI_10008716	superfamily	241738	541	650	1.17E-47	164.653	cl00266	HGTP_anticodon superfamily	 - 	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#796 - 	CGI_10008716	superfamily	241805	9	57	2.26E-19	83.3046	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#796 - 	CGI_10008716	superfamily	241739	68	140	4.18E-25	105.365	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#796 - 	CGI_10008716	superfamily	241738	651	722	1.87E-12	64.532	cl00266	HGTP_anticodon superfamily	N	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#797 - 	CGI_10008717	superfamily	241754	1	546	0	956.267	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#799 - 	CGI_10008719	superfamily	247684	52	474	7.41E-89	284.17	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#802 - 	CGI_10008722	superfamily	243352	39	315	9.63E-112	328.014	cl03224	Porin3 superfamily	 - 	 - 	"Eukaryotic porin family that forms channels in the mitochondrial outer membrane; The porin family 3 contains two sub-families that play vital roles in the mitochondrial outer membrane, a translocase for unfolded pre-proteins (Tom40) and the voltage-dependent anion channel (VDAC) that regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane."
Q#803 - 	CGI_10002489	superfamily	243035	30	139	1.12E-05	40.681	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#804 - 	CGI_10002490	superfamily	243035	50	118	1.88E-06	42.9922	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#805 - 	CGI_10005003	superfamily	246908	107	255	7.14E-13	65.2982	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#806 - 	CGI_10005004	superfamily	247723	62	141	1.74E-37	128.548	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#807 - 	CGI_10005005	superfamily	241659	130	207	7.86E-28	102.213	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#808 - 	CGI_10005006	superfamily	241717	152	311	7.12E-29	109.508	cl00240	RRF superfamily	 - 	 - 	"Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation.  Thus ribosomes are "recycled" and ready for another round of protein synthesis.  RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear.  RRF is essential for bacterial growth.  It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species."
Q#809 - 	CGI_10005007	superfamily	243563	69	334	2.22E-158	447.367	cl03888	PTPA superfamily	 - 	 - 	"Phosphotyrosyl phosphatase activator (PTPA) is also known as protein phosphatase 2A (PP2A) phosphatase activator. PTPA is an essential, well conserved protein that stimulates the tyrosyl phosphatase activity of PP2A. It also reactivates the serine/threonine phosphatase activity of an inactive form of PP2A. Together, PTPA and PP2A constitute an ATPase. It has been suggested that PTPA alters the relative specificity of PP2A from phosphoserine/phosphothreonine substrates to phosphotyrosine substrates in an ATP-hydrolysis-dependent manner. Basal expression of PTPA is controlled by the transcription factor Yin Yang1 (YY1). PTPA has been suggested to play a role in the insertion of metals to the PP2A catalytic subunit (PP2Ac) active site, to act as a chaperone, and more recently, to have peptidyl prolyl cis/trans isomerase activity that specifically targets human PP2Ac."
Q#811 - 	CGI_10005009	superfamily	247684	1	256	4.88E-57	194.033	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#814 - 	CGI_10002737	superfamily	243088	12	130	2.43E-30	113.274	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#817 - 	CGI_10004590	superfamily	219525	326	373	2.84E-07	49.3397	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	111397	26	94	1.23E-06	48.1063	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#817 - 	CGI_10004590	superfamily	205157	1196	1231	9.47E-06	44.4507	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#817 - 	CGI_10004590	superfamily	219525	927	972	1.48E-05	44.3322	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	219525	820	867	1.49E-05	44.3322	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	219525	600	647	1.51E-05	44.3322	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	219525	1037	1084	8.17E-05	42.021	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	219525	711	758	0.000332292	40.095	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	219525	547	592	0.000605073	39.3246	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	219525	1144	1192	0.000693415	39.3246	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#817 - 	CGI_10004590	superfamily	219525	979	1028	0.00124553	38.5542	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#819 - 	CGI_10004592	superfamily	207794	9	146	1.15E-54	179.716	cl02948	GH20_hexosaminidase superfamily	N	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#820 - 	CGI_10002678	superfamily	246723	70	154	1.56E-41	146.179	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#821 - 	CGI_10002679	superfamily	217473	92	314	3.14E-27	111.688	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#823 - 	CGI_10002967	superfamily	243035	102	128	0.000460011	36.4238	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#824 - 	CGI_10007233	superfamily	243091	58	106	1.37E-05	42.094	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#825 - 	CGI_10007234	superfamily	222150	347	366	0.000440805	39.2973	cl16282	zf-H2C2_2 superfamily	C	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#825 - 	CGI_10007234	superfamily	246975	334	355	0.00176589	37.7117	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#825 - 	CGI_10007234	superfamily	246975	829	850	0.00239389	37.3265	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#825 - 	CGI_10007234	superfamily	222150	814	839	0.00290206	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#825 - 	CGI_10007234	superfamily	222150	317	343	0.00709273	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#827 - 	CGI_10007236	superfamily	241613	654	690	8.27E-10	55.6758	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#827 - 	CGI_10007236	superfamily	193258	86	194	0.000795128	40.7901	cl15087	Innate_immun superfamily	NC	 - 	"Invertebrate innate immunity transcript family; The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge."
Q#828 - 	CGI_10007237	superfamily	247856	757	801	1.54E-08	52.5501	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#828 - 	CGI_10007237	superfamily	248020	15	346	3.57E-44	163.404	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#828 - 	CGI_10007237	superfamily	221634	535	592	3.56E-12	65.0984	cl13923	DUF3740 superfamily	N	 - 	"Sulfatase protein; This domain family is found in eukaryotes, and is typically between 144 and 173 amino acids in length. The family is found in association with pfam00884."
Q#828 - 	CGI_10007237	superfamily	247856	827	884	0.00353179	36.7569	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#829 - 	CGI_10007238	superfamily	220388	98	457	2.93E-118	360.525	cl12372	FimP superfamily	 - 	 - 	"Fms-interacting protein; This entry carries part of the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C-terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes."
Q#830 - 	CGI_10007239	superfamily	218267	32	101	2.52E-12	60.9112	cl04754	LMBR1 superfamily	C	 - 	"LMBR1-like membrane protein; Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought. Vertebrate members of this family may play a role in limb development. A member of this family has been shown to be a lipocalin membrane receptor"
Q#831 - 	CGI_10001051	superfamily	241563	62	98	2.62E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#831 - 	CGI_10001051	superfamily	110440	492	518	0.000272142	38.9281	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#831 - 	CGI_10001051	superfamily	241563	8	53	0.000685283	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#834 - 	CGI_10012802	superfamily	222150	753	777	0.000429555	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#835 - 	CGI_10012803	superfamily	218079	108	194	0.00739043	34.5657	cl04507	CHD5 superfamily	C	 - 	CHD5-like protein; Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. In Saccharomyces cerevisiae this protein localises to the ER and is thought to play a homeostatic role.
Q#836 - 	CGI_10012804	superfamily	241599	1159	1215	2.19E-17	79.5948	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#836 - 	CGI_10012804	superfamily	241599	1402	1460	8.56E-14	69.1944	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#836 - 	CGI_10012804	superfamily	241599	1683	1741	1.11E-13	68.8092	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#836 - 	CGI_10012804	superfamily	241599	1052	1110	4.38E-11	61.4904	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#838 - 	CGI_10012806	superfamily	245816	239	405	1.77E-40	143.671	cl11964	CYTH-like_Pase superfamily	 - 	 - 	"CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; CYTH-like superfamily enzymes hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB), and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions."
Q#840 - 	CGI_10012808	superfamily	241810	14	86	1.64E-26	96.3906	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#840 - 	CGI_10012808	superfamily	190164	54	126	7.34E-27	97.2503	cl03394	Ribosomal_L14e superfamily	 - 	 - 	Ribosomal protein L14; This family includes the eukaryotic ribosomal protein L14.
Q#841 - 	CGI_10012809	superfamily	216574	19	155	2.98E-34	125.013	cl14794	FAD_binding_4 superfamily	 - 	 - 	"FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan."
Q#842 - 	CGI_10012811	superfamily	243555	55	148	0.000281496	38.141	cl03871	Chitin_bind_3 superfamily	N	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#843 - 	CGI_10012812	superfamily	247907	58	140	2.60E-09	51.6501	cl17353	LamG superfamily	C	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#844 - 	CGI_10012813	superfamily	218427	222	299	3.10E-28	105.551	cl18456	CIAPIN1 superfamily	 - 	 - 	"Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis; Anamorsin, subsequently named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1, in humans is the homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS). CIAPIN1 is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis. Dre2 has been found to interact with the yeast reductase Tah18, forming a tight cytosolic complex implicated in the response to high levels of oxidative stress."
Q#844 - 	CGI_10012813	superfamily	247727	36	98	3.03E-06	44.1844	cl17173	AdoMet_MTases superfamily	N	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#845 - 	CGI_10012814	superfamily	192955	439	572	7.99E-15	73.3483	cl13625	TPX2_importin superfamily	C	 - 	Cell cycle regulated microtubule associated protein; This domain is found in eukaryotes. This domain is typically between 127 to 182 amino acids in length. This domain is found associated with pfam06886. This domain is found in the protein TPX2 (a.k.a p100) which is involved in cell cycling. It is only expressed between the start of the S phase and completion of cytokinesis. The microtubule-associated protein TPX2 has been reported to be crucial for mitotic spindle formation. This domain is close to the C terminal of TPX2. The protein importin alpha regulates the activity of TPX2 by binding to the nuclear localisation signal in this domain.
Q#847 - 	CGI_10014134	superfamily	241584	1	92	1.14E-19	81.7739	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#847 - 	CGI_10014134	superfamily	241584	104	187	1.66E-14	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#847 - 	CGI_10014134	superfamily	241584	213	293	2.54E-13	64.4399	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#848 - 	CGI_10014135	superfamily	110440	284	311	0.00140971	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#849 - 	CGI_10014136	superfamily	241574	1531	1758	6.79E-108	344.569	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#849 - 	CGI_10014136	superfamily	241584	1154	1241	1.16E-10	60.5879	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	422	511	5.49E-07	49.8023	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	602	690	5.62E-07	49.8023	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	795	877	1.41E-06	48.2615	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	513	585	2.13E-05	44.7947	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	148	230	0.000216971	41.7131	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	885	970	0.000398145	40.9427	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	692	770	0.00425243	37.4759	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	241584	991	1058	0.00622876	37.0907	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#849 - 	CGI_10014136	superfamily	197431	1274	1428	0.000800033	40.8704	cl06408	UP_III_II superfamily	 - 	 - 	"Uroplakin IIIb, IIIa and II; Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb,  UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains separating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers; six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis."
Q#853 - 	CGI_10014141	superfamily	247736	12	45	0.000131603	35.5883	cl17182	NAT_SF superfamily	N	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#854 - 	CGI_10014142	superfamily	247736	4	69	2.43E-08	46.2365	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#855 - 	CGI_10014143	superfamily	241818	7	212	1.27E-143	402.712	cl00366	PMSR superfamily	 - 	 - 	Peptide methionine sulfoxide reductase; This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine.
Q#857 - 	CGI_10014145	superfamily	248019	83	135	3.47E-05	41.7943	cl17465	DAGK_cat superfamily	NC	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#858 - 	CGI_10007636	superfamily	245882	25	407	3.11E-162	488.724	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#858 - 	CGI_10007636	superfamily	219542	526	636	2.09E-40	146.618	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#858 - 	CGI_10007636	superfamily	219541	884	1025	1.23E-24	101.776	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#858 - 	CGI_10007636	superfamily	215896	644	824	1.63E-14	72.3276	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#862 - 	CGI_10007640	superfamily	220070	335	536	1.83E-37	139.468	cl18542	SF3b1 superfamily	 - 	 - 	"Splicing factor 3B subunit 1; This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly."
Q#863 - 	CGI_10007641	superfamily	111646	256	392	1.72E-76	235.764	cl03707	S-AdoMet_synt_C superfamily	 - 	 - 	"S-adenosylmethionine synthetase, C-terminal domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#863 - 	CGI_10007641	superfamily	217221	132	254	6.24E-70	218.059	cl03706	S-AdoMet_synt_M superfamily	 - 	 - 	"S-adenosylmethionine synthetase, central domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#863 - 	CGI_10007641	superfamily	201226	20	119	2.08E-62	198.077	cl02868	S-AdoMet_synt_N superfamily	 - 	 - 	"S-adenosylmethionine synthetase, N-terminal domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#864 - 	CGI_10007642	superfamily	111646	30	166	2.91E-78	231.912	cl03707	S-AdoMet_synt_C superfamily	 - 	 - 	"S-adenosylmethionine synthetase, C-terminal domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#864 - 	CGI_10007642	superfamily	217221	1	28	1.04E-07	46.6455	cl03706	S-AdoMet_synt_M superfamily	N	 - 	"S-adenosylmethionine synthetase, central domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#865 - 	CGI_10007643	superfamily	111646	268	404	2.82E-75	233.068	cl03707	S-AdoMet_synt_C superfamily	 - 	 - 	"S-adenosylmethionine synthetase, C-terminal domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#865 - 	CGI_10007643	superfamily	217221	144	266	2.53E-68	214.207	cl03706	S-AdoMet_synt_M superfamily	 - 	 - 	"S-adenosylmethionine synthetase, central domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#865 - 	CGI_10007643	superfamily	201226	32	131	4.09E-63	200.003	cl02868	S-AdoMet_synt_N superfamily	 - 	 - 	"S-adenosylmethionine synthetase, N-terminal domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#867 - 	CGI_10007645	superfamily	241600	2	153	1.44E-58	183.596	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#868 - 	CGI_10007646	superfamily	203136	138	267	4.15E-12	61.5915	cl04867	LRAT superfamily	 - 	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#869 - 	CGI_10007647	superfamily	245206	1	126	5.49E-30	108.927	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#874 - 	CGI_10006086	superfamily	247905	294	349	2.66E-09	58.7885	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#874 - 	CGI_10006086	superfamily	247805	19	179	2.20E-05	46.8687	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#876 - 	CGI_10011579	superfamily	215847	20	155	9.41E-19	82.4942	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#879 - 	CGI_10011582	superfamily	247057	15	63	1.47E-05	41.3869	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#879 - 	CGI_10011582	superfamily	245595	214	255	0.00240682	37.2145	cl11393	Peptidase_M14_like superfamily	NC	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#881 - 	CGI_10011584	superfamily	221377	19	86	4.12E-06	44.3819	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#882 - 	CGI_10011585	superfamily	241568	425	478	0.000298676	39.3684	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#883 - 	CGI_10011586	superfamily	243099	414	524	1.68E-13	68.5136	cl02575	Bcl-2_like superfamily	N	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#884 - 	CGI_10011587	superfamily	213465	89	247	1.50E-08	52.0653	cl17074	PRK03963 superfamily	N	 - 	V-type ATP synthase subunit E; Provisional
Q#892 - 	CGI_10010319	superfamily	241578	44	195	9.39E-31	115.852	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#897 - 	CGI_10010325	superfamily	241592	14	74	2.01E-08	46.8362	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#898 - 	CGI_10010326	superfamily	241568	146	184	9.38E-05	39.3684	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#901 - 	CGI_10014457	superfamily	241889	149	280	6.49E-33	120.428	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#902 - 	CGI_10014458	superfamily	246671	1	91	6.06E-08	47.0325	cl14606	Reeler_cohesin_like superfamily	N	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#903 - 	CGI_10014459	superfamily	243047	18	132	4.72E-54	177.427	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#904 - 	CGI_10014460	superfamily	142634	1488	1681	1.08E-89	295.641	cl11429	RNAP_largest_subunit_C superfamily	N	 - 	"Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria."
Q#904 - 	CGI_10014460	superfamily	245715	410	655	5.52E-91	299.049	cl11591	RNA_pol_Rpb1_2 superfamily	N	 - 	"RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion."
Q#904 - 	CGI_10014460	superfamily	142634	1198	1325	3.35E-53	191.252	cl11429	RNAP_largest_subunit_C superfamily	C	 - 	"Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria."
Q#904 - 	CGI_10014460	superfamily	218361	633	815	2.22E-36	137.367	cl04873	RNA_pol_Rpb1_3 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking."
Q#904 - 	CGI_10014460	superfamily	218372	899	964	2.05E-19	86.6554	cl04881	RNA_pol_Rpb1_4 superfamily	N	 - 	"RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors."
Q#904 - 	CGI_10014460	superfamily	218370	27	123	6.61E-17	82.7329	cl04880	RNA_pol_Rpb1_1 superfamily	C	 - 	"RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand."
Q#905 - 	CGI_10014461	superfamily	241563	67	99	0.00361497	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#907 - 	CGI_10014463	superfamily	216686	71	260	1.01E-39	139.766	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#908 - 	CGI_10014464	superfamily	219958	1	162	1.25E-55	177.057	cl18536	Alg14 superfamily	 - 	 - 	Oligosaccharide biosynthesis protein Alg14 like; Alg14 is involved dolichol-linked oligosaccharide biosynthesis and anchors the catalytic subunit Alg13 to the ER membrane.
Q#909 - 	CGI_10014465	superfamily	241832	57	232	1.54E-84	252.426	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#910 - 	CGI_10014466	superfamily	243166	67	213	2.08E-22	96.1906	cl02759	TRAM_LAG1_CLN8 superfamily	N	 - 	TLC domain; TLC domain.  
Q#910 - 	CGI_10014466	superfamily	193049	414	499	0.000396475	39.9611	cl13867	DUF3702 superfamily	N	 - 	ImpA domain protein; This family of proteins is found in bacteria. Proteins in this family are typically between 207 and 469 amino acids in length. The family is found in association with pfam06812.
Q#910 - 	CGI_10014466	superfamily	150420	331	429	0.000419972	40.1039	cl18042	Jnk-SapK_ap_N superfamily	N	 - 	JNK_SAPK-associated protein-1; This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end.
Q#911 - 	CGI_10014467	superfamily	242793	148	372	8.07E-26	102.131	cl01947	MT-A70 superfamily	 - 	 - 	"MT-A70; MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A methyl-transferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs."
Q#911 - 	CGI_10014467	superfamily	247727	101	180	0.0025093	36.8914	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#912 - 	CGI_10014468	superfamily	243065	970	1112	5.49E-20	89.7685	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#913 - 	CGI_10014469	superfamily	220131	494	774	7.60E-62	215.988	cl11721	DUF1943 superfamily	 - 	 - 	"Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined."
Q#913 - 	CGI_10014469	superfamily	219034	805	895	1.91E-06	48.4866	cl05778	DUF1081 superfamily	 - 	 - 	Domain of Unknown Function (DUF1081); This region is found in Apolipophorin proteins.
Q#914 - 	CGI_10014470	superfamily	243065	568	710	1.20E-20	90.9241	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#914 - 	CGI_10014470	superfamily	248070	1	23	0.00455485	36.7711	cl17516	AAA_29 superfamily	NC	 - 	P-loop containing region of AAA domain; P-loop containing region of AAA domain.  
Q#915 - 	CGI_10014471	superfamily	245864	52	461	5.85E-107	328.084	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#916 - 	CGI_10014472	superfamily	245864	13	402	7.18E-108	329.239	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#917 - 	CGI_10014473	superfamily	247805	129	334	1.20E-99	306.333	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#917 - 	CGI_10014473	superfamily	247905	371	477	1.92E-38	138.91	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#918 - 	CGI_10014474	superfamily	241782	22	439	0	630.004	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#920 - 	CGI_10014476	superfamily	245201	30	281	9.55E-58	186.288	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#921 - 	CGI_10014477	superfamily	243310	24	210	3.22E-44	150.467	cl03120	ELO superfamily	C	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#922 - 	CGI_10014478	superfamily	241832	70	154	9.24E-19	78.169	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#923 - 	CGI_10014479	superfamily	241622	1084	1140	2.60E-13	67.5918	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#923 - 	CGI_10014479	superfamily	216736	690	793	8.09E-12	63.7432	cl03379	DIL superfamily	 - 	 - 	DIL domain; The DIL domain has no known function.
Q#923 - 	CGI_10014479	superfamily	241645	70	185	4.52E-09	55.0323	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#924 - 	CGI_10014480	superfamily	243078	6	145	5.04E-67	220.967	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#924 - 	CGI_10014480	superfamily	248318	162	218	3.97E-23	94.8101	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#924 - 	CGI_10014480	superfamily	152645	376	456	2.46E-33	124.937	cl13621	Hrs_helical superfamily	 - 	 - 	"Hepatocyte growth factor-regulated tyrosine kinase substrate; This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with pfam00790, pfam01363, pfam02809. This domain is the helical region of Hrs which forms the core complex of ESCRT with STAM."
Q#925 - 	CGI_10014481	superfamily	218885	5	141	3.21E-47	157.232	cl18483	DUF938 superfamily	C	 - 	Protein of unknown function (DUF938); This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown.
Q#925 - 	CGI_10014481	superfamily	247724	142	231	2.26E-16	72.9944	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#927 - 	CGI_10014483	superfamily	241584	345	439	1.67E-07	49.8023	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#927 - 	CGI_10014483	superfamily	241584	552	645	3.01E-06	45.9503	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#927 - 	CGI_10014483	superfamily	241584	654	744	1.54E-05	44.0243	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#927 - 	CGI_10014483	superfamily	241584	462	541	0.00111811	38.2463	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#927 - 	CGI_10014483	superfamily	245814	57	137	3.11E-15	72.6328	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#927 - 	CGI_10014483	superfamily	245814	254	334	7.69E-14	68.2896	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#927 - 	CGI_10014483	superfamily	245814	158	235	3.01E-09	54.7578	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#927 - 	CGI_10014483	superfamily	245814	14	50	0.00307239	36.9119	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#929 - 	CGI_10006264	superfamily	243066	20	121	5.78E-10	56.8569	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#932 - 	CGI_10006267	superfamily	245205	120	201	1.03E-15	69.9593	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#932 - 	CGI_10006267	superfamily	245205	12	80	0.000913363	36.4469	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#935 - 	CGI_10013762	superfamily	242902	17	98	2.44E-06	45.3155	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#936 - 	CGI_10013764	superfamily	216939	90	135	8.95E-05	37.2573	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#937 - 	CGI_10013765	superfamily	245882	25	406	0	544.578	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#938 - 	CGI_10013766	superfamily	201217	799	845	6.60E-12	62.5432	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#938 - 	CGI_10013766	superfamily	201217	716	770	4.36E-10	57.5356	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#938 - 	CGI_10013766	superfamily	201217	849	896	1.33E-06	47.1352	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#938 - 	CGI_10013766	superfamily	205718	951	980	1.59E-06	46.7146	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#938 - 	CGI_10013766	superfamily	205718	757	785	3.59E-06	45.559	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#938 - 	CGI_10013766	superfamily	201217	967	1014	9.27E-05	41.7424	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#938 - 	CGI_10013766	superfamily	201217	1019	1044	0.00537781	36.3496	cl08266	RCC1 superfamily	C	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#941 - 	CGI_10013769	superfamily	243061	1	102	1.99E-39	130.54	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#941 - 	CGI_10013769	superfamily	243061	108	153	1.95E-15	67.7522	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#942 - 	CGI_10013770	superfamily	241874	12	491	3.03E-170	500.47	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#943 - 	CGI_10013771	superfamily	207684	7	39	7.78E-07	43.5215	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#944 - 	CGI_10013772	superfamily	241547	69	347	2.94E-56	185.564	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#948 - 	CGI_10005274	superfamily	243035	7	84	6.81E-18	72.6525	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#949 - 	CGI_10005275	superfamily	241600	12	154	9.39E-25	95.385	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#950 - 	CGI_10005276	superfamily	111000	12	480	0	539.995	cl15499	Glyco_hydro_59 superfamily	C	 - 	Glycosyl hydrolase family 59; Glycosyl hydrolase family 59.  
Q#951 - 	CGI_10005277	superfamily	247916	12	59	8.98E-06	43.9107	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#951 - 	CGI_10005277	superfamily	245008	554	583	0.00108844	37.8575	cl09101	E_set superfamily	NC	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#953 - 	CGI_10008184	superfamily	248312	35	190	9.35E-08	48.5124	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#954 - 	CGI_10008185	superfamily	241574	681	801	1.40E-45	165.066	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#954 - 	CGI_10008185	superfamily	243051	127	281	2.75E-25	104.382	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#954 - 	CGI_10008185	superfamily	241609	547	621	3.90E-25	101.301	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#954 - 	CGI_10008185	superfamily	241609	379	440	6.30E-24	97.8339	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#954 - 	CGI_10008185	superfamily	241609	288	361	1.67E-19	85.1223	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#954 - 	CGI_10008185	superfamily	245213	498	539	1.03E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#954 - 	CGI_10008185	superfamily	241574	872	1052	1.56E-21	94.9601	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#954 - 	CGI_10008185	superfamily	241609	471	502	1.63E-07	50.3822	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#954 - 	CGI_10008185	superfamily	241609	635	665	0.000187189	40.8366	cl00100	KR superfamily	C	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#956 - 	CGI_10008187	superfamily	241609	170	238	1.06E-19	80.4999	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#956 - 	CGI_10008187	superfamily	241609	83	156	2.20E-17	73.9638	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#956 - 	CGI_10008187	superfamily	241609	6	37	4.82E-07	45.3746	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#956 - 	CGI_10008187	superfamily	245213	44	74	0.00403367	33.7642	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#957 - 	CGI_10008188	superfamily	241609	261	336	3.63E-32	116.323	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#957 - 	CGI_10008188	superfamily	243051	58	187	1.13E-20	86.2777	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#957 - 	CGI_10008188	superfamily	241609	193	262	1.98E-15	70.1118	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#958 - 	CGI_10008189	superfamily	241571	373	499	1.93E-12	63.9706	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#958 - 	CGI_10008189	superfamily	245213	335	365	0.00619364	34.9198	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#958 - 	CGI_10008189	superfamily	241583	149	292	4.95E-40	143.481	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#959 - 	CGI_10008190	superfamily	241609	816	891	5.46E-27	107.079	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#959 - 	CGI_10008190	superfamily	241609	1008	1081	1.44E-24	100.145	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#959 - 	CGI_10008190	superfamily	243051	578	732	2.75E-22	95.5225	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#959 - 	CGI_10008190	superfamily	241609	1095	1163	1.01E-21	91.6707	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#959 - 	CGI_10008190	superfamily	241609	744	812	3.29E-18	81.6555	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#959 - 	CGI_10008190	superfamily	241571	402	528	6.59E-10	58.1926	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#959 - 	CGI_10008190	superfamily	245213	959	1000	8.02E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#959 - 	CGI_10008190	superfamily	241583	176	352	6.00E-40	147.333	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#959 - 	CGI_10008190	superfamily	241609	895	965	2.41E-14	70.497	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#960 - 	CGI_10008191	superfamily	246975	42	65	0.00304541	35.3063	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#961 - 	CGI_10000472	superfamily	247866	70	213	1.50E-29	111.776	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#962 - 	CGI_10000165	superfamily	245201	1	118	1.15E-28	107.322	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#963 - 	CGI_10000166	superfamily	246680	9	106	1.02E-23	93.2461	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#963 - 	CGI_10000166	superfamily	245201	267	320	5.68E-09	54.85	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#964 - 	CGI_10001128	superfamily	247684	7	436	1.92E-91	289.562	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#967 - 	CGI_10006799	superfamily	246925	244	341	1.26E-05	46.1946	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#967 - 	CGI_10006799	superfamily	246925	276	513	1.33E-05	46.1946	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#967 - 	CGI_10006799	superfamily	214507	511	566	2.22E-05	42.4172	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#970 - 	CGI_10006802	superfamily	215827	58	229	2.49E-36	134.133	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#972 - 	CGI_10006804	superfamily	220533	52	706	0	727.982	cl12375	Dpy19 superfamily	 - 	 - 	"Q-cell neuroblast polarisation; Dyp-19, formerly known as DUF2211, is a transmembrane domain family that is required to orient the neuroblast cells, QR and QL accurately on the anterior-posterior axis: QL and QR are born in the same anterior-posterior position, but polarise and migrate left-right asymmetrically, QL migrating towards the posterior and QR migrating towards the anterior. It is also required, with unc-40, to express mab-5 correctly in the Q cell descendants. The Dpy-19 protein derives from the C. elegans DUMPY mutant."
Q#976 - 	CGI_10006808	superfamily	247856	114	161	0.0069236	32.9049	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#978 - 	CGI_10000646	superfamily	242849	33	106	6.14E-27	96.504	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#979 - 	CGI_10012480	superfamily	241645	9	85	5.45E-10	53.083	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#979 - 	CGI_10012480	superfamily	243076	115	188	1.33E-06	44.13	cl02539	BAG superfamily	 - 	 - 	BAG domain; Domain present in Hsp70 regulators.
Q#980 - 	CGI_10012481	superfamily	241645	9	81	4.79E-09	48.8458	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#981 - 	CGI_10012482	superfamily	241554	8	142	9.85E-34	128.917	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#981 - 	CGI_10012482	superfamily	241554	231	357	3.60E-28	112.739	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#981 - 	CGI_10012482	superfamily	241554	797	912	1.23E-26	108.117	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#981 - 	CGI_10012482	superfamily	241554	936	1063	1.55E-21	93.4791	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#981 - 	CGI_10012482	superfamily	241752	1428	1551	2.47E-15	75.0485	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#981 - 	CGI_10012482	superfamily	241554	1119	1222	1.42E-13	69.9819	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#981 - 	CGI_10012482	superfamily	241752	660	775	8.23E-08	53.1031	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#982 - 	CGI_10012483	superfamily	241554	232	357	2.16E-28	112.354	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#982 - 	CGI_10012483	superfamily	241554	411	551	8.72E-27	107.731	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#982 - 	CGI_10012483	superfamily	241752	771	897	7.20E-17	78.5153	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#982 - 	CGI_10012483	superfamily	241554	618	721	2.23E-13	68.8263	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#982 - 	CGI_10012483	superfamily	241752	907	1004	1.33E-09	56.9441	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#982 - 	CGI_10012483	superfamily	222429	14	91	1.72E-06	46.85	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#983 - 	CGI_10012484	superfamily	241554	60	149	2.39E-16	71.1375	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#984 - 	CGI_10012485	superfamily	241884	762	1006	5.32E-115	356.198	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#984 - 	CGI_10012485	superfamily	241554	206	351	1.09E-30	118.902	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#984 - 	CGI_10012485	superfamily	241554	55	195	8.69E-27	107.731	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#984 - 	CGI_10012485	superfamily	241752	543	668	1.87E-21	91.9973	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#985 - 	CGI_10012486	superfamily	241570	304	412	1.52E-17	80.0626	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#986 - 	CGI_10012487	superfamily	220692	137	260	0.000909103	39.8801	cl18570	7TM_GPCR_Srw superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#987 - 	CGI_10012488	superfamily	243092	179	473	4.69E-82	258.804	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#989 - 	CGI_10012490	superfamily	241874	207	806	0	657.599	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#990 - 	CGI_10012491	superfamily	247684	16	442	5.60E-94	296.496	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#991 - 	CGI_10012492	superfamily	247684	34	453	1.01E-99	311.904	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#992 - 	CGI_10012493	superfamily	204202	63	95	0.000252723	34.9237	cl07827	Vps4_C superfamily	N	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#1001 - 	CGI_10005913	superfamily	241593	29	148	1.85E-22	95.4316	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#1001 - 	CGI_10005913	superfamily	219431	506	549	1.67E-14	70.1524	cl06504	zf-CW superfamily	 - 	 - 	"CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found."
Q#1002 - 	CGI_10005914	superfamily	241636	76	261	1.54E-126	369.609	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#1003 - 	CGI_10005915	superfamily	247724	37	187	1.15E-40	142.215	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1003 - 	CGI_10005915	superfamily	247724	277	301	0.000564519	38.9817	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1006 - 	CGI_10005918	superfamily	247684	17	448	5.30E-107	331.164	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#1007 - 	CGI_10017521	superfamily	245201	695	1068	0	634.54	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1008 - 	CGI_10017522	superfamily	148406	25	138	1.25E-07	47.4752	cl06034	UPF0240 superfamily	N	 - 	Uncharacterized protein family (UPF0240); Uncharacterized protein family (UPF0240).  
Q#1013 - 	CGI_10017528	superfamily	243034	262	371	1.50E-16	75.1091	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#1013 - 	CGI_10017528	superfamily	215821	29	121	9.70E-38	133.52	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#1013 - 	CGI_10017528	superfamily	215821	146	236	3.73E-22	90.3774	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#1016 - 	CGI_10017531	superfamily	243058	102	209	1.00E-08	51.9315	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#1016 - 	CGI_10017531	superfamily	243058	224	311	2.02E-08	51.1611	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#1016 - 	CGI_10017531	superfamily	243058	45	137	0.000114371	39.9904	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#1017 - 	CGI_10017532	superfamily	242611	255	445	6.89E-88	268.412	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#1017 - 	CGI_10017532	superfamily	245606	73	189	6.46E-20	86.0463	cl11410	TPP_enzyme_PYR superfamily	C	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#1018 - 	CGI_10017533	superfamily	218118	66	133	4.63E-08	46.4533	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#1019 - 	CGI_10017534	superfamily	204301	7	1185	0	1415.27	cl14974	Nckap1 superfamily	 - 	 - 	Membrane-associated apoptosis protein; Expression of this protein was found to be markedly reduced in patients with Alzheimer's disease. It is involved in the regulation of actin polymerisation in the brain as part of a WAVE2 signalling complex.
Q#1020 - 	CGI_10017535	superfamily	243077	54	106	4.46E-16	71.4225	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#1021 - 	CGI_10017536	superfamily	216112	483	747	5.06E-60	207.149	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#1022 - 	CGI_10017537	superfamily	221913	406	615	5.12E-56	189.674	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#1022 - 	CGI_10017537	superfamily	222258	358	395	2.25E-05	44.4812	cl18656	AAA_30 superfamily	NC	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#1023 - 	CGI_10017538	superfamily	245213	226	260	5.38E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1023 - 	CGI_10017538	superfamily	245213	300	334	1.64E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1023 - 	CGI_10017538	superfamily	245213	1805	1846	5.67E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1023 - 	CGI_10017538	superfamily	245213	2296	2329	8.82E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1023 - 	CGI_10017538	superfamily	245213	1765	1796	0.00112031	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1023 - 	CGI_10017538	superfamily	243065	1851	2002	1.07E-28	115.962	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#1023 - 	CGI_10017538	superfamily	246918	2511	2560	3.53E-07	50.2779	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#1023 - 	CGI_10017538	superfamily	241600	1515	1551	7.42E-06	48.0055	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1023 - 	CGI_10017538	superfamily	205157	145	171	5.24E-05	43.2951	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#1023 - 	CGI_10017538	superfamily	245213	1715	1747	0.000259071	41.5656	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1023 - 	CGI_10017538	superfamily	241607	2384	2426	0.00265321	38.4294	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#1023 - 	CGI_10017538	superfamily	241600	343	385	0.00307478	40.3015	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1023 - 	CGI_10017538	superfamily	248288	2655	2713	0.0036237	38.1534	cl17734	DAN superfamily	 - 	 - 	"DAN domain; This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family after the first member to be reported. This family includes DAN, Cerberus and Gremlin. The gremlin protein is an antagonist of bone morphogenetic protein signaling. It is postulated that all members of this family antagonise different TGF beta pfam00019 ligands. Recent work shows that the DAN protein is not an efficient antagonist of BMP-2/4 class signals, we found that DAN was able to interact with GDF-5 in a frog embryo assay, suggesting that DAN may regulate signaling by the GDF-5/6/7 class of BMPs in vivo."
Q#1025 - 	CGI_10017540	superfamily	246751	52	298	3.11E-76	238.682	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#1028 - 	CGI_10017543	superfamily	245213	83	107	0.00689835	34.1494	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1032 - 	CGI_10017547	superfamily	246612	72	135	2.56E-07	49.4309	cl14057	BPL_LplA_LipB superfamily	NC	 - 	"Biotin/lipoate A/B protein ligase family; This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Lipoate-protein ligase A (LPLA) catalyzes the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor."
Q#1034 - 	CGI_10017549	superfamily	216686	80	256	5.22E-45	153.633	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#1036 - 	CGI_10017551	superfamily	241600	30	79	1.81E-05	40.7234	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1037 - 	CGI_10004351	superfamily	247805	18	217	4.41E-86	264.732	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#1037 - 	CGI_10004351	superfamily	247905	232	362	3.23E-33	122.346	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#1040 - 	CGI_10009521	superfamily	247789	161	252	0.00152795	37.6234	cl17235	ABC2_membrane superfamily	N	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#1041 - 	CGI_10013161	superfamily	217473	175	341	1.00E-26	110.532	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#1041 - 	CGI_10013161	superfamily	241750	408	426	0.00865753	37.4638	cl00281	metallo-dependent_hydrolases superfamily	NC	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#1049 - 	CGI_10013169	superfamily	141815	177	291	1.18E-21	91.6564	cl04275	Mtc superfamily	N	 - 	Tricarboxylate carrier; Tricarboxylate carrier.  
Q#1050 - 	CGI_10013170	superfamily	243084	73	179	9.28E-63	209.585	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#1050 - 	CGI_10013170	superfamily	243084	364	448	1.96E-48	168.996	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#1051 - 	CGI_10013171	superfamily	216363	297	375	0.000304174	38.9906	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#1052 - 	CGI_10013172	superfamily	241563	196	233	5.13E-05	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1053 - 	CGI_10013173	superfamily	243092	145	275	0.000765218	39.6256	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1055 - 	CGI_10013175	superfamily	217293	525	726	1.88E-37	141.231	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1055 - 	CGI_10013175	superfamily	241563	8	42	2.68E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1056 - 	CGI_10013176	superfamily	247044	39	151	2.92E-60	193.208	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1056 - 	CGI_10013176	superfamily	247044	166	249	6.54E-31	113.872	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1056 - 	CGI_10013176	superfamily	247044	315	390	5.11E-18	78.8304	cl15697	ADF_gelsolin superfamily	C	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1059 - 	CGI_10005505	superfamily	216363	47	97	0.000763328	34.3682	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#1064 - 	CGI_10005510	superfamily	243035	78	186	5.62E-21	84.2085	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1065 - 	CGI_10005511	superfamily	243035	5	100	1.88E-15	69.5709	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1065 - 	CGI_10005511	superfamily	243035	110	171	1.13E-09	53.0687	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1066 - 	CGI_10005979	superfamily	247743	163	275	0.000147255	41.8624	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1067 - 	CGI_10005980	superfamily	241758	825	1004	5.89E-56	192.847	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#1067 - 	CGI_10005980	superfamily	241782	111	446	5.91E-37	143.928	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#1067 - 	CGI_10005980	superfamily	246680	453	528	0.00498247	36.713	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#1068 - 	CGI_10005981	superfamily	247727	57	139	5.44E-13	66.2994	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#1068 - 	CGI_10005981	superfamily	247727	549	625	9.61E-05	41.2615	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#1069 - 	CGI_10005982	superfamily	243146	57	103	9.65E-11	53.4342	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1069 - 	CGI_10005982	superfamily	243146	33	68	3.20E-06	41.0047	cl02701	Kelch_3 superfamily	N	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1072 - 	CGI_10005985	superfamily	219080	460	581	2.01E-25	102.034	cl05851	DUF1115 superfamily	 - 	 - 	Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function.
Q#1072 - 	CGI_10005985	superfamily	243141	307	430	2.74E-12	63.8746	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#1074 - 	CGI_10017767	superfamily	241810	73	228	5.38E-84	249.387	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#1075 - 	CGI_10017768	superfamily	150884	9	45	1.16E-09	51.3665	cl10958	Med19 superfamily	NC	 - 	Mediator of RNA pol II transcription subunit 19; Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators.
Q#1077 - 	CGI_10017770	superfamily	247745	159	434	2.94E-33	130.13	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#1077 - 	CGI_10017770	superfamily	191851	895	1023	5.32E-32	124.279	cl06708	DUF1640 superfamily	 - 	 - 	Protein of unknown function (DUF1640); This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Q#1078 - 	CGI_10017771	superfamily	241644	14	134	7.51E-55	171.231	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#1079 - 	CGI_10017772	superfamily	247805	404	543	1.35E-23	99.7191	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#1079 - 	CGI_10017772	superfamily	241575	3	69	1.06E-11	62.6751	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#1079 - 	CGI_10017772	superfamily	247905	635	776	3.70E-10	59.5589	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#1079 - 	CGI_10017772	superfamily	241575	177	247	5.30E-07	48.8079	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#1079 - 	CGI_10017772	superfamily	243778	831	921	7.75E-29	113.088	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#1079 - 	CGI_10017772	superfamily	219532	960	1071	5.39E-22	93.9182	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#1080 - 	CGI_10017773	superfamily	247787	792	1035	3.25E-81	268.683	cl17233	RecA-like_NTPases superfamily	 - 	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#1080 - 	CGI_10017773	superfamily	247723	1371	1453	3.93E-41	148.336	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#1080 - 	CGI_10017773	superfamily	243066	558	652	6.00E-17	79.1985	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#1080 - 	CGI_10017773	superfamily	243066	343	469	3.62E-11	62.2497	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#1080 - 	CGI_10017773	superfamily	243146	30	68	5.03E-07	48.8118	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1080 - 	CGI_10017773	superfamily	243146	77	108	5.89E-06	45.6807	cl02701	Kelch_3 superfamily	C	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1080 - 	CGI_10017773	superfamily	243146	255	306	4.56E-05	43.0467	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1080 - 	CGI_10017773	superfamily	198867	676	724	0.000697862	39.8344	cl06652	BACK superfamily	C	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#1080 - 	CGI_10017773	superfamily	243146	91	146	0.00184221	38.4243	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1080 - 	CGI_10017773	superfamily	198867	472	530	0.00321034	37.7061	cl06652	BACK superfamily	C	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#1080 - 	CGI_10017773	superfamily	243146	200	254	0.004851	36.8835	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1082 - 	CGI_10017775	superfamily	191444	2460	2524	6.45E-05	43.8521	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#1085 - 	CGI_10017778	superfamily	241750	84	385	4.44E-109	329.98	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#1085 - 	CGI_10017778	superfamily	241750	451	518	1.86E-27	111.552	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#1085 - 	CGI_10017778	superfamily	246664	418	451	1.46E-07	52.6974	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#1086 - 	CGI_10017779	superfamily	243072	151	265	7.40E-17	77.4238	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1086 - 	CGI_10017779	superfamily	243072	34	200	2.16E-07	49.3042	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1086 - 	CGI_10017779	superfamily	243072	378	524	0.00381718	36.5927	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1088 - 	CGI_10017781	superfamily	241691	363	489	2.30E-05	43.6548	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#1089 - 	CGI_10017782	superfamily	248458	82	466	6.44E-35	133.593	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1092 - 	CGI_10017785	superfamily	241546	4	111	2.10E-21	90.0908	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#1092 - 	CGI_10017785	superfamily	215847	212	554	2.53E-70	240.426	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#1095 - 	CGI_10002601	superfamily	241750	503	699	4.54E-35	133.468	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#1096 - 	CGI_10023555	superfamily	247736	120	185	3.94E-08	48.0946	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#1102 - 	CGI_10023561	superfamily	247736	157	196	0.000584851	36.9238	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#1104 - 	CGI_10023563	superfamily	216566	978	1076	4.34E-08	53.3453	cl18370	Peptidase_M23 superfamily	 - 	 - 	"Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Escherichia coli murein hydrolase activator NlpD, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown."
Q#1105 - 	CGI_10023564	superfamily	207637	4395	4462	2.49E-07	51.7699	cl02541	CIDE_N superfamily	 - 	 - 	"CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein."
Q#1106 - 	CGI_10023565	superfamily	242406	137	240	1.86E-10	57.2161	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1108 - 	CGI_10023567	superfamily	241737	7	179	3.79E-46	150.772	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#1109 - 	CGI_10023568	superfamily	241737	53	207	1.06E-39	135.364	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#1111 - 	CGI_10023570	superfamily	220763	292	332	2.20E-10	57.3737	cl11101	NUFIP1 superfamily	N	 - 	"Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); Proteins in this family have been implicated in the assembly of the large subunit of the ribosome and in telomere maintenance. Some proteins in this family contain a CCCH zinc finger. This family contains a protein called human fragile X mental retardation-interacting protein 1, which is known to bind RNA and is phosphorylated upon DNA damage."
Q#1112 - 	CGI_10023571	superfamily	243072	73	192	6.15E-32	119.025	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1112 - 	CGI_10023571	superfamily	243072	133	298	3.00E-26	103.617	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1112 - 	CGI_10023571	superfamily	243072	7	118	5.33E-23	94.3726	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1112 - 	CGI_10023571	superfamily	245010	364	456	0.000226671	39.5235	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#1113 - 	CGI_10023572	superfamily	247724	13	222	1.56E-105	305.953	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1114 - 	CGI_10023573	superfamily	149515	563	584	5.72E-05	41.6724	cl07204	SRP72 superfamily	N	 - 	SRP72 RNA-binding domain; This region has been identified as the binding site of the SRP72 protein to SRP RNA.
Q#1115 - 	CGI_10023574	superfamily	247792	157	204	2.11E-06	45.8996	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1115 - 	CGI_10023574	superfamily	115400	730	753	0.00014775	40.2713	cl06002	SBBP superfamily	N	 - 	Beta-propeller repeat; This family is related to pfam00400 and is likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller.
Q#1115 - 	CGI_10023574	superfamily	241563	301	330	0.00403117	36.1611	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1116 - 	CGI_10023575	superfamily	243045	131	215	4.51E-11	60.3395	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#1118 - 	CGI_10023577	superfamily	245864	9	318	1.01E-47	167.455	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#1119 - 	CGI_10023578	superfamily	247986	16	123	1.65E-07	50.4494	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#1119 - 	CGI_10023578	superfamily	197504	235	371	5.64E-19	82.7225	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#1120 - 	CGI_10023579	superfamily	245864	74	167	7.99E-13	64.607	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#1121 - 	CGI_10023580	superfamily	246676	187	331	1.64E-38	138.247	cl14616	Cyt_b561 superfamily	C	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#1121 - 	CGI_10023580	superfamily	246710	37	187	7.45E-24	96.728	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#1122 - 	CGI_10023581	superfamily	247856	85	156	4.28E-09	49.4685	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1122 - 	CGI_10023581	superfamily	247856	49	105	1.38E-06	42.9201	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1122 - 	CGI_10023581	superfamily	244899	11	72	0.00037606	36.699	cl08302	S-100 superfamily	 - 	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#1123 - 	CGI_10023582	superfamily	247856	66	127	1.20E-13	62.5653	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1123 - 	CGI_10023582	superfamily	247856	101	174	1.58E-12	59.4837	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1124 - 	CGI_10023583	superfamily	241619	530	583	8.81E-08	50.5461	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#1124 - 	CGI_10023583	superfamily	241619	408	480	0.000131056	40.9161	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#1125 - 	CGI_10023584	superfamily	241619	795	866	9.48E-08	50.9313	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#1125 - 	CGI_10023584	superfamily	241619	650	728	0.000606571	39.4844	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#1125 - 	CGI_10023584	superfamily	241619	874	925	0.00075372	39.0992	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#1129 - 	CGI_10023589	superfamily	217062	40	285	8.26E-50	168.217	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#1130 - 	CGI_10023590	superfamily	217062	13	258	3.80E-51	169.372	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#1131 - 	CGI_10023591	superfamily	217062	13	222	3.10E-47	159.742	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#1133 - 	CGI_10023593	superfamily	245864	4	418	1.93E-102	314.602	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#1138 - 	CGI_10023598	superfamily	243110	103	308	1.10E-12	67.4545	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#1139 - 	CGI_10023599	superfamily	220692	14	303	2.66E-14	71.0813	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#1144 - 	CGI_10004423	superfamily	216566	778	844	0.000330674	40.6337	cl18370	Peptidase_M23 superfamily	N	 - 	"Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Escherichia coli murein hydrolase activator NlpD, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown."
Q#1145 - 	CGI_10004424	superfamily	207684	36	67	0.00140004	33.8916	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#1148 - 	CGI_10011233	superfamily	241584	368	461	0.000286703	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#1148 - 	CGI_10011233	superfamily	245814	185	263	0.000348544	39.344	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1149 - 	CGI_10011234	superfamily	215859	685	881	5.73E-58	197.824	cl18347	Peptidase_S9 superfamily	 - 	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#1149 - 	CGI_10011234	superfamily	215859	586	616	0.000164382	42.5887	cl18347	Peptidase_S9 superfamily	C	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#1151 - 	CGI_10011237	superfamily	247755	862	1082	3.12E-123	379.145	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#1151 - 	CGI_10011237	superfamily	247755	214	416	3.26E-109	340.986	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#1151 - 	CGI_10011237	superfamily	216049	584	773	1.42E-20	92.7341	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#1151 - 	CGI_10011237	superfamily	216049	1	170	7.30E-17	81.1782	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#1153 - 	CGI_10011239	superfamily	246925	141	216	5.05E-11	62.373	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#1157 - 	CGI_10011243	superfamily	243066	28	120	4.13E-16	73.0353	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#1157 - 	CGI_10011243	superfamily	198867	128	236	2.29E-07	48.1064	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#1160 - 	CGI_10011246	superfamily	247905	311	363	4.48E-09	53.7809	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#1160 - 	CGI_10011246	superfamily	247805	34	217	7.56E-05	41.1688	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#1163 - 	CGI_10014591	superfamily	220672	9	174	5.21E-18	78.0574	cl10957	Frag1 superfamily	N	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#1164 - 	CGI_10014592	superfamily	241974	504	579	1.65E-13	67.2666	cl00604	STAS superfamily	N	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#1164 - 	CGI_10014592	superfamily	216188	14	293	3.49E-52	181.647	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#1165 - 	CGI_10014593	superfamily	241974	706	780	1.91E-12	64.9554	cl00604	STAS superfamily	N	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#1165 - 	CGI_10014593	superfamily	241974	552	596	7.39E-05	41.8435	cl00604	STAS superfamily	C	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#1165 - 	CGI_10014593	superfamily	216188	218	497	6.06E-53	185.499	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#1165 - 	CGI_10014593	superfamily	205965	77	160	7.94E-26	102.876	cl18285	Sulfate_tra_GLY superfamily	 - 	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#1166 - 	CGI_10014594	superfamily	241594	34	317	2.83E-14	70.7971	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#1167 - 	CGI_10014595	superfamily	241614	134	239	5.39E-32	118.137	cl00105	LMWPc superfamily	N	 - 	Low molecular weight phosphatase family;
Q#1169 - 	CGI_10014597	superfamily	241571	989	1096	7.81E-18	81.3046	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1169 - 	CGI_10014597	superfamily	205157	216	251	1.92E-08	52.1547	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#1169 - 	CGI_10014597	superfamily	219525	947	984	2.59E-08	52.0361	cl06646	GCC2_GCC3 superfamily	N	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#1169 - 	CGI_10014597	superfamily	219525	826	874	1.57E-07	49.7249	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#1169 - 	CGI_10014597	superfamily	219525	881	928	1.16E-06	47.4137	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#1169 - 	CGI_10014597	superfamily	245213	509	538	1.98E-06	46.4712	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1169 - 	CGI_10014597	superfamily	241578	546	585	0.000123782	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1169 - 	CGI_10014597	superfamily	241578	463	506	0.000126336	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1169 - 	CGI_10014597	superfamily	205157	313	348	0.000423605	39.4431	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#1169 - 	CGI_10014597	superfamily	241578	248	289	0.000900149	40.8312	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1169 - 	CGI_10014597	superfamily	221695	450	471	0.00243792	37.4346	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#1169 - 	CGI_10014597	superfamily	241578	385	426	0.00902978	37.7496	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1170 - 	CGI_10014598	superfamily	247723	72	144	4.58E-44	145.268	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#1171 - 	CGI_10014599	superfamily	221616	161	221	1.21E-11	63.2209	cl13896	DUF3719 superfamily	C	 - 	"Protein of unknown function (DUF3719); This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved HLR sequence motif. There are two completely conserved residues (W and H) that may be functionally important."
Q#1173 - 	CGI_10014601	superfamily	247856	770	829	5.28E-07	48.3129	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1173 - 	CGI_10014601	superfamily	247856	886	944	0.000325597	39.8385	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1173 - 	CGI_10014601	superfamily	247856	282	323	0.00788725	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1174 - 	CGI_10014602	superfamily	243082	176	625	0	636.283	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#1175 - 	CGI_10014603	superfamily	119093	8	77	3.16E-09	50.3456	cl11200	UPF0561 superfamily	 - 	 - 	Uncharacterized protein family UPF0561; This family of proteins has no known function.
Q#1176 - 	CGI_10014604	superfamily	241992	571	1005	0	555.338	cl00628	Piwi-like superfamily	 - 	 - 	"Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism."
Q#1176 - 	CGI_10014604	superfamily	241765	444	563	1.15E-46	164.356	cl00301	PAZ superfamily	 - 	 - 	"PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain."
Q#1176 - 	CGI_10014604	superfamily	241765	343	413	1.19E-25	104.264	cl00301	PAZ superfamily	C	 - 	"PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain."
Q#1176 - 	CGI_10014604	superfamily	241992	1003	1126	1.64E-64	226.378	cl00628	Piwi-like superfamily	N	 - 	"Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism."
Q#1182 - 	CGI_10014610	superfamily	241554	22	94	2.13E-17	74.8785	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#1183 - 	CGI_10014611	superfamily	217311	41	525	1.80E-131	397.863	cl18402	DUF229 superfamily	 - 	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1184 - 	CGI_10014612	superfamily	243077	36	89	4.13E-18	77.9709	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#1184 - 	CGI_10014612	superfamily	247804	385	426	0.00194789	36.0142	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#1184 - 	CGI_10014612	superfamily	247804	244	295	2.15E-07	47.6894	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#1185 - 	CGI_10014613	superfamily	217293	14	223	4.47E-88	271.814	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1185 - 	CGI_10014613	superfamily	202474	230	496	4.15E-30	116.599	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#1186 - 	CGI_10014614	superfamily	248097	2	78	3.08E-06	40.3262	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#1188 - 	CGI_10011248	superfamily	246669	866	984	1.42E-45	160.921	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#1188 - 	CGI_10011248	superfamily	241623	340	689	2.83E-173	512.374	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#1188 - 	CGI_10011248	superfamily	241742	164	335	4.63E-44	158.575	cl00271	PI3Ka superfamily	 - 	 - 	"Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture."
Q#1188 - 	CGI_10011248	superfamily	243088	716	834	1.01E-34	129.46	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#1188 - 	CGI_10011248	superfamily	246669	3	146	3.70E-25	103.977	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#1193 - 	CGI_10011253	superfamily	243035	75	199	1.79E-15	74.1933	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1193 - 	CGI_10011253	superfamily	241571	397	502	2.62E-13	67.8226	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1193 - 	CGI_10011253	superfamily	241568	572	625	6.11E-11	59.3988	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#1193 - 	CGI_10011253	superfamily	241571	286	387	1.46E-10	59.7334	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1193 - 	CGI_10011253	superfamily	241568	630	689	0.00524521	35.9016	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#1193 - 	CGI_10011253	superfamily	111397	738	817	7.09E-07	48.1063	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#1193 - 	CGI_10011253	superfamily	241571	221	274	3.22E-05	43.1699	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1194 - 	CGI_10011254	superfamily	245213	8	42	2.50E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1194 - 	CGI_10011254	superfamily	219525	619	666	8.95E-09	52.8065	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#1194 - 	CGI_10011254	superfamily	219525	460	507	5.79E-06	44.7174	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#1194 - 	CGI_10011254	superfamily	219525	520	559	2.69E-05	42.7914	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#1194 - 	CGI_10011254	superfamily	219525	573	611	0.000579585	38.5542	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#1197 - 	CGI_10003094	superfamily	242889	319	416	1.02E-18	81.1101	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#1198 - 	CGI_10003095	superfamily	247740	17	167	3.34E-61	191.939	cl17186	TIM_phosphate_binding superfamily	C	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#1200 - 	CGI_10023970	superfamily	243035	18	129	1.45E-07	45.6886	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1207 - 	CGI_10023977	superfamily	219459	175	272	2.06E-26	104.251	cl06530	NOC3p superfamily	 - 	 - 	Nucleolar complex-associated protein; Nucleolar complex-associated protein (Noc3p) is conserved in eukaryotes and has essential roles in replication and rRNA processing in Saccharomyces cerevisiae.
Q#1207 - 	CGI_10023977	superfamily	245319	524	664	1.97E-24	100.368	cl10505	CBF superfamily	 - 	 - 	CBF/Mak21 family; CBF/Mak21 family.  
Q#1208 - 	CGI_10023978	superfamily	243035	308	432	4.00E-20	86.9049	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1208 - 	CGI_10023978	superfamily	243035	162	286	2.57E-18	81.9673	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1208 - 	CGI_10023978	superfamily	243035	49	147	2.50E-05	43.3574	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1209 - 	CGI_10023979	superfamily	241599	150	208	7.13E-22	86.9136	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#1210 - 	CGI_10023980	superfamily	241622	125	206	1.86E-22	93.7854	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#1210 - 	CGI_10023980	superfamily	241622	254	332	1.97E-16	76.4514	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#1210 - 	CGI_10023980	superfamily	241622	1070	1147	3.35E-08	52.5691	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#1210 - 	CGI_10023980	superfamily	143751	876	945	1.04E-09	56.7322	cl11968	harmonin_N_like superfamily	 - 	 - 	"N-terminal protein-binding module of harmonin and similar domains; This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected."
Q#1210 - 	CGI_10023980	superfamily	143751	7	85	5.42E-06	45.7966	cl11968	harmonin_N_like superfamily	 - 	 - 	"N-terminal protein-binding module of harmonin and similar domains; This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected."
Q#1211 - 	CGI_10023981	superfamily	199166	400	492	7.82E-14	70.0488	cl15308	AMN1 superfamily	NC	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#1211 - 	CGI_10023981	superfamily	199166	46	233	3.50E-05	43.8552	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#1213 - 	CGI_10023983	superfamily	247792	1761	1804	7.68E-12	62.8484	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1215 - 	CGI_10023985	superfamily	241626	463	584	5.48E-58	192.049	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#1217 - 	CGI_10023987	superfamily	243120	215	244	0.00139407	37.9808	cl02633	ARID superfamily	C	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#1218 - 	CGI_10023988	superfamily	247684	211	393	2.26E-06	47.1983	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#1220 - 	CGI_10023990	superfamily	212156	35	248	6.39E-161	459.591	cl17007	COE_DBD superfamily	 - 	 - 	"Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain; COE_DBD is the amino-terminal DNA binding domain of the COE protein family. The COE transcription factor is a regulator of development in several organs and tissues that contain the DBD domain as well as IPT/TIG (immunoglobulin-like, Plexins, transcription factors/transcription factor immunoglobulin) and basic helix-loop-helix (bHLH) domains. COE has four members in mammals (COE1-4) with high sequence similarity at the amino-terminal region. COE_DBD requires a zinc ion to bind DNA and contains a zinc finger motif (H-X(3)-C-X(2)-C-X(5)-C) termed the zinc knuckle. COE is homo- or heterodimerized through the bHLH domain to bind DNA. COE1-4 each has a variant due to alternative splicing. However, this alternative splicing does not occur at the DBD domain."
Q#1220 - 	CGI_10023990	superfamily	247038	280	364	6.39E-46	156.655	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#1222 - 	CGI_10023992	superfamily	241868	69	223	2.57E-48	161.465	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#1223 - 	CGI_10023993	superfamily	217575	94	219	7.13E-34	123.153	cl04090	eRF1_2 superfamily	 - 	 - 	"eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#1223 - 	CGI_10023993	superfamily	146221	222	359	4.52E-23	91.8451	cl04091	eRF1_3 superfamily	 - 	 - 	"eRF1 domain 3; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#1223 - 	CGI_10023993	superfamily	217574	17	90	4.01E-08	50.6846	cl04089	eRF1_1 superfamily	C	 - 	"eRF1 domain 1; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#1224 - 	CGI_10023994	superfamily	188340	2	68	9.65E-08	47.5723	cl18158	selen_PSTK_euk superfamily	N	 - 	"L-seryl-tRNA(Sec) kinase, eukaryotic; Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity."
Q#1225 - 	CGI_10023995	superfamily	146221	11	63	3.67E-05	37.1467	cl04091	eRF1_3 superfamily	N	 - 	"eRF1 domain 3; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#1226 - 	CGI_10023996	superfamily	245225	246	438	3.64E-36	137.379	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1226 - 	CGI_10023996	superfamily	245225	40	235	2.20E-25	105.471	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1228 - 	CGI_10023998	superfamily	245225	5	182	2.38E-33	129.289	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1228 - 	CGI_10023998	superfamily	245225	244	416	1.06E-25	106.948	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1229 - 	CGI_10023999	superfamily	245225	50	235	8.38E-40	142.386	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1230 - 	CGI_10024000	superfamily	245819	854	1030	1.11E-63	213.98	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#1230 - 	CGI_10024000	superfamily	245201	562	779	6.41E-34	130.82	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1230 - 	CGI_10024000	superfamily	245225	27	394	7.65E-132	407.789	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1230 - 	CGI_10024000	superfamily	219526	793	840	0.000193597	42.6063	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#1231 - 	CGI_10024001	superfamily	242232	19	68	6.26E-14	67.198	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#1231 - 	CGI_10024001	superfamily	242232	225	298	2.64E-13	66.1462	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#1231 - 	CGI_10024001	superfamily	242232	150	200	7.47E-06	43.7008	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#1231 - 	CGI_10024001	superfamily	242232	94	117	0.00330325	35.9968	cl00984	TM2 superfamily	C	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#1236 - 	CGI_10024006	superfamily	247723	37	117	2.71E-55	177.627	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#1236 - 	CGI_10024006	superfamily	247723	308	348	1.43E-17	76.6398	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#1239 - 	CGI_10024009	superfamily	241828	30	102	3.19E-13	61.375	cl00382	Ribosomal_L21p superfamily	C	 - 	Ribosomal prokaryotic L21 protein; Ribosomal prokaryotic L21 protein.  
Q#1240 - 	CGI_10024010	superfamily	243082	810	1116	8.14E-94	300.744	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#1240 - 	CGI_10024010	superfamily	241647	690	720	3.48E-08	51.3746	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#1240 - 	CGI_10024010	superfamily	241626	165	295	2.22E-07	50.3582	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#1240 - 	CGI_10024010	superfamily	117535	6	111	2.52E-27	108.781	cl07540	DUF1873 superfamily	 - 	 - 	Domain of unknown function (DUF1873); This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It has no known function.
Q#1242 - 	CGI_10024012	superfamily	243146	261	307	4.43E-10	55.3602	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1242 - 	CGI_10024012	superfamily	243146	227	272	5.49E-06	43.7011	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1246 - 	CGI_10024016	superfamily	243066	108	181	5.61E-12	60.7089	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#1247 - 	CGI_10024017	superfamily	246598	22	287	5.93E-153	432.447	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#1249 - 	CGI_10024019	superfamily	220830	40	92	2.52E-11	61.5728	cl11246	Ofd1_CTDD superfamily	N	 - 	"Oxoglutarate and iron-dependent oxygenase degradation C-term; Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen. The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts."
Q#1249 - 	CGI_10024019	superfamily	248293	202	283	0.00296015	35.4123	cl17739	MADF_DNA_bdg superfamily	 - 	 - 	Alcohol dehydrogenase transcription factor Myb/SANT-like; The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains.
Q#1250 - 	CGI_10024020	superfamily	244363	51	99	1.43E-15	68.6247	cl06336	Commd superfamily	C	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#1251 - 	CGI_10024021	superfamily	245847	31	175	4.39E-29	111.29	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#1251 - 	CGI_10024021	superfamily	245847	347	443	3.48E-15	72.1499	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#1254 - 	CGI_10002901	superfamily	245864	27	435	5.56E-38	143.573	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#1255 - 	CGI_10007895	superfamily	241733	6	81	3.19E-24	88.0866	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#1256 - 	CGI_10007896	superfamily	245213	38	74	1.62E-07	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1256 - 	CGI_10007896	superfamily	245213	76	112	4.30E-07	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1257 - 	CGI_10007897	superfamily	245213	265	302	0.000520922	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1259 - 	CGI_10007899	superfamily	247057	2	42	2.36E-06	40.0382	cl15755	SAM_superfamily superfamily	NC	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#1260 - 	CGI_10007900	superfamily	152053	16	32	0.00519167	31.3467	cl13123	Cu-binding_MopE superfamily	N	 - 	"Protein metal binding site; This family of proteins represents a unique protein copper binding site that involves a tryptophan metabolite, kynurenine in the protein MopE. The production of kyneurenin by modification of tryptophan and its involvement in copper binding is an innate property of MopE."
Q#1261 - 	CGI_10007901	superfamily	247792	16	66	6.57E-05	39.3512	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1263 - 	CGI_10006069	superfamily	199166	37	245	1.10E-11	62.3448	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#1263 - 	CGI_10006069	superfamily	199166	159	335	6.15E-10	57.3372	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#1263 - 	CGI_10006069	superfamily	243074	5	31	8.28E-06	42.4937	cl02535	F-box-like superfamily	N	 - 	F-box-like; This is an F-box-like family.
Q#1264 - 	CGI_10006070	superfamily	246908	493	579	3.65E-29	112.621	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#1264 - 	CGI_10006070	superfamily	245201	608	856	6.82E-148	438.435	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1264 - 	CGI_10006070	superfamily	245835	10	246	1.94E-54	188.747	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#1267 - 	CGI_10019202	superfamily	241832	22	96	4.07E-16	70.3496	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1267 - 	CGI_10019202	superfamily	243175	108	224	2.62E-13	63.3208	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#1268 - 	CGI_10019203	superfamily	241550	129	396	2.57E-49	173.904	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#1268 - 	CGI_10019203	superfamily	245839	480	574	1.06E-06	47.9587	cl12020	Anticodon_Ia_like superfamily	C	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#1269 - 	CGI_10019204	superfamily	220403	100	276	5.55E-51	171.949	cl18555	Tmemb_55A superfamily	N	 - 	"Transmembrane protein 55A; Members of this family catalyze the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate."
Q#1272 - 	CGI_10019207	superfamily	241563	190	223	3.35E-07	48.0523	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1272 - 	CGI_10019207	superfamily	247792	8	62	2.15E-05	42.818	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1272 - 	CGI_10019207	superfamily	216033	396	489	1.14E-21	90.856	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#1272 - 	CGI_10019207	superfamily	110440	634	661	4.24E-08	50.4841	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1272 - 	CGI_10019207	superfamily	110440	565	592	9.31E-07	46.6321	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1272 - 	CGI_10019207	superfamily	110440	518	545	9.40E-07	46.6321	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1272 - 	CGI_10019207	superfamily	110440	681	708	5.17E-06	44.3209	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1273 - 	CGI_10019208	superfamily	241782	62	482	2.45E-147	430.837	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#1274 - 	CGI_10019209	superfamily	222599	9	99	1.58E-20	79.6021	cl16717	DUF4326 superfamily	 - 	 - 	"Domain of unknown function (DUF4326); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 100 and 162 amino acids in length. There are two completely conserved residues (P and C) that may be functionally important."
Q#1275 - 	CGI_10019210	superfamily	222599	10	98	1.55E-10	54.9493	cl16717	DUF4326 superfamily	C	 - 	"Domain of unknown function (DUF4326); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 100 and 162 amino acids in length. There are two completely conserved residues (P and C) that may be functionally important."
Q#1277 - 	CGI_10019212	superfamily	243035	182	301	1.56E-29	109.632	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1278 - 	CGI_10019213	superfamily	215896	60	113	1.45E-08	48.8304	cl18351	Cu-oxidase superfamily	NC	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#1279 - 	CGI_10019214	superfamily	247725	156	283	1.99E-74	228.334	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1279 - 	CGI_10019214	superfamily	241631	10	129	1.59E-42	147.369	cl00136	Sec7 superfamily	N	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#1280 - 	CGI_10019215	superfamily	243035	77	193	2.28E-19	79.9713	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1283 - 	CGI_10019218	superfamily	192997	293	439	1.90E-28	112.675	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#1284 - 	CGI_10019220	superfamily	245210	5	68	4.61E-24	92.2358	cl09938	cond_enzymes superfamily	C	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#1286 - 	CGI_10019222	superfamily	247724	31	87	0.00303107	36.5358	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1288 - 	CGI_10019224	superfamily	243613	62	118	0.00514474	33.6967	cl04011	DPBB_1 superfamily	C	 - 	"Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen."
Q#1289 - 	CGI_10019225	superfamily	244910	134	205	0.000857301	36.0085	cl08320	Pollen_allerg_1 superfamily	 - 	 - 	"Pollen allergen; This family contains allergens lol PI, PII and PIII from Lolium perenne."
Q#1292 - 	CGI_10019228	superfamily	241578	35	197	3.01E-44	155.527	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1292 - 	CGI_10019228	superfamily	241578	286	446	1.66E-41	148.208	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1293 - 	CGI_10019230	superfamily	245364	632	756	3.25E-77	246.409	cl10717	CactinC_cactus superfamily	 - 	 - 	"Cactus-binding C-terminus of cactin protein; CactinC_cactus is the C-terminal 200 residues of the cactin protein which are necessary for the association of cactin with IkappaB-cactus as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo. Most members of the family also have a Cactin_mid domain pfam10312 further upstream."
Q#1293 - 	CGI_10019230	superfamily	220686	246	431	2.22E-57	194.449	cl10987	Cactin_mid superfamily	 - 	 - 	"Conserved mid region of cactin; This is the conserved middle region of a family of proteins referred to as cactins. The region contains two of three predicted coiled-coil domains. Most members of this family have a CactinC_cactus pfam09732 domain at the C-terminal end. Upstream of Mid_cactin in Drosophila members are a serine-rich region, some non-typical RD motifs and three predicted bipartite nuclear localisation signals, none of which are well-conserved. Cactin associates with IkappaB-cactus as one of the intracellular members of the Rel (NF-kappaB) pathway which is conserved in invertebrates and vertebrates. In mammals, this pathway controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo."
Q#1297 - 	CGI_10019234	superfamily	245226	9	181	2.61E-105	302.158	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#1298 - 	CGI_10019235	superfamily	243138	648	901	3.47E-111	344.744	cl02675	DZF superfamily	 - 	 - 	DZF domain; The function of this domain is unknown. It is often found associated with pfam00098 or pfam00035. This domain has been predicted to belong to the nucleotidyltransferase superfamily.
Q#1298 - 	CGI_10019235	superfamily	197732	215	244	2.41E-06	45.7063	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#1298 - 	CGI_10019235	superfamily	197732	439	467	2.64E-05	42.6247	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#1298 - 	CGI_10019235	superfamily	197732	265	294	0.000112181	41.0839	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#1300 - 	CGI_10019237	superfamily	247907	20	162	5.17E-24	101.726	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#1300 - 	CGI_10019237	superfamily	247907	197	359	4.84E-09	57.0429	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#1301 - 	CGI_10019238	superfamily	247743	131	296	1.96E-21	91.8239	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1301 - 	CGI_10019238	superfamily	247743	402	589	7.57E-16	75.6455	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1302 - 	CGI_10019239	superfamily	219904	23	95	4.37E-15	64.6767	cl07245	Ribosomal_L37 superfamily	 - 	 - 	Mitochondrial ribosomal protein L37; This family includes yeast MRPL37 a mitochondrial ribosomal protein.
Q#1304 - 	CGI_10019241	superfamily	190882	148	363	5.70E-64	205.146	cl04416	SCAMP superfamily	 - 	 - 	"SCAMP family; In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences."
Q#1305 - 	CGI_10019242	superfamily	241874	25	477	5.78E-136	405.75	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1306 - 	CGI_10019243	superfamily	242065	29	156	1.67E-49	167.284	cl00749	UPF0066 superfamily	 - 	 - 	"Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066.  This domain includes Escherichia coli YeaB, Archeoglobus fulgidus AF0241, and Agrobacterium tumefaciens VirR.  Proteins with this domain are probable S-adenosylmethionine-dependent methyltransferases but they have not been functionally characterized and the substrate is unknown."
Q#1306 - 	CGI_10019243	superfamily	242065	179	306	1.53E-44	153.802	cl00749	UPF0066 superfamily	 - 	 - 	"Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066.  This domain includes Escherichia coli YeaB, Archeoglobus fulgidus AF0241, and Agrobacterium tumefaciens VirR.  Proteins with this domain are probable S-adenosylmethionine-dependent methyltransferases but they have not been functionally characterized and the substrate is unknown."
Q#1308 - 	CGI_10019245	superfamily	241680	33	275	9.54E-72	223.67	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#1309 - 	CGI_10019246	superfamily	241752	1	63	1.32E-19	76.5893	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#1317 - 	CGI_10004325	superfamily	241574	268	332	9.06E-07	47.9657	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1317 - 	CGI_10004325	superfamily	241574	202	235	0.000500909	39.8766	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1319 - 	CGI_10004327	superfamily	241574	25	118	1.18E-22	93.8045	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1319 - 	CGI_10004327	superfamily	241574	275	331	0.00687248	36.0246	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1320 - 	CGI_10002266	superfamily	110440	462	488	0.000115003	40.0837	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1320 - 	CGI_10002266	superfamily	241563	37	73	0.000234776	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1322 - 	CGI_10003945	superfamily	247724	37	155	8.25E-47	164.988	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1322 - 	CGI_10003945	superfamily	247724	162	206	6.76E-20	88.382	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1322 - 	CGI_10003945	superfamily	241578	447	628	1.69E-10	60.7219	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1322 - 	CGI_10003945	superfamily	192987	413	470	0.00605975	36.3963	cl13724	TMF_TATA_bd superfamily	C	 - 	"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family."
Q#1327 - 	CGI_10001540	superfamily	245847	7	79	7.40E-12	58.7221	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#1328 - 	CGI_10003327	superfamily	243056	198	305	1.01E-08	53.1317	cl02495	RabGAP-TBC superfamily	N	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#1329 - 	CGI_10003328	superfamily	220691	119	191	0.00591057	36.827	cl18569	7TM_GPCR_Srv superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#1342 - 	CGI_10009551	superfamily	241578	512	646	9.26E-10	58.3462	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1342 - 	CGI_10009551	superfamily	241578	963	1120	5.88E-22	94.9744	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1342 - 	CGI_10009551	superfamily	241578	169	325	3.01E-16	77.8213	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1345 - 	CGI_10009554	superfamily	221683	66	144	7.27E-09	53.0415	cl15002	UPF0489 superfamily	 - 	 - 	UPF0489 domain; This family is probably an enzyme which is related to the Arginase family.
Q#1351 - 	CGI_10006012	superfamily	243074	9	55	0.000691335	41.3381	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#1352 - 	CGI_10012847	superfamily	243161	5	61	3.27E-11	55.0929	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#1357 - 	CGI_10012855	superfamily	248264	325	439	0.000532924	39.913	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#1360 - 	CGI_10012858	superfamily	110440	84	110	0.00195237	33.9205	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1365 - 	CGI_10009791	superfamily	245201	5	254	5.57E-138	392.086	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1366 - 	CGI_10009792	superfamily	242059	9	442	3.93E-40	149.819	cl00738	MBOAT superfamily	 - 	 - 	"MBOAT, membrane-bound O-acyltransferase family; The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue."
Q#1367 - 	CGI_10009793	superfamily	241571	242	361	2.40E-25	102.876	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1367 - 	CGI_10009793	superfamily	241571	95	213	3.33E-24	99.409	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1367 - 	CGI_10009793	superfamily	241571	529	638	9.22E-18	80.9194	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1367 - 	CGI_10009793	superfamily	241571	392	505	3.45E-17	79.3786	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1367 - 	CGI_10009793	superfamily	241571	648	775	2.51E-12	65.1262	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1367 - 	CGI_10009793	superfamily	241613	783	816	0.000707617	38.7685	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#1370 - 	CGI_10009796	superfamily	244881	10	311	1.24E-146	419.377	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#1371 - 	CGI_10009797	superfamily	241788	440	488	5.21E-19	82.5386	cl00327	Ribosomal_L22 superfamily	N	 - 	"Ribosomal protein L22/L17e.  L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit.  It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA.  L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes.  L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome."
Q#1371 - 	CGI_10009797	superfamily	245814	236	309	1.24E-05	43.2467	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1371 - 	CGI_10009797	superfamily	245814	143	201	2.10E-11	60.1131	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1371 - 	CGI_10009797	superfamily	245814	32	98	6.94E-05	41.259	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1372 - 	CGI_10009798	superfamily	245201	78	430	0	573.228	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1373 - 	CGI_10009799	superfamily	247948	99	146	2.12E-12	62.3114	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#1374 - 	CGI_10009800	superfamily	217293	32	136	2.70E-06	46.4719	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1375 - 	CGI_10009801	superfamily	115363	170	224	1.27E-09	54.6854	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#1375 - 	CGI_10009801	superfamily	241578	10	116	5.18E-05	42.4416	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1376 - 	CGI_10009802	superfamily	242406	49	107	3.41E-12	58.3717	cl01271	DUF1768 superfamily	C	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1377 - 	CGI_10014543	superfamily	246616	1	307	3.70E-34	128.194	cl14105	MetH superfamily	 - 	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#1378 - 	CGI_10014544	superfamily	246616	218	305	0.00161364	38.4871	cl14105	MetH superfamily	C	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#1381 - 	CGI_10014547	superfamily	245201	14	348	3.86E-139	406.743	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1381 - 	CGI_10014547	superfamily	221460	461	492	2.46E-05	42.0207	cl12053	OSR1_C superfamily	 - 	 - 	"Oxidative-stress-responsive kinase 1 C terminal; This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00069. There is a single completely conserved residue F that may be functionally important. OSR1 is involved in the signalling cascade which activates Na/K/2Cl cotransporter during osmotic stress. This domain is the C terminal domain of OSR1 which recognises a motif (Arg-Phe-Xaa-Val) on the OSR1-activating protein WNK1."
Q#1383 - 	CGI_10014549	superfamily	198827	19	63	0.000449235	34.3272	cl03803	BAF superfamily	NC	 - 	Barrier to autointegration factor; The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.
Q#1384 - 	CGI_10014550	superfamily	243119	108	152	9.56E-06	42.8061	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#1384 - 	CGI_10014550	superfamily	247907	282	384	0.000177293	40.0154	cl17353	LamG superfamily	C	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#1384 - 	CGI_10014550	superfamily	243119	66	101	0.000668119	37.4133	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#1385 - 	CGI_10014551	superfamily	241611	77	238	2.45E-08	52.0056	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#1388 - 	CGI_10014554	superfamily	241571	64	179	5.17E-13	67.4374	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1388 - 	CGI_10014554	superfamily	238012	838	882	2.17E-05	43.497	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#1388 - 	CGI_10014554	superfamily	238012	884	929	6.97E-05	41.9562	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#1388 - 	CGI_10014554	superfamily	243146	309	348	3.22E-06	46.1154	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1388 - 	CGI_10014554	superfamily	243146	422	473	0.00412865	36.8835	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1389 - 	CGI_10014555	superfamily	247948	12	67	1.22E-16	71.9414	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#1390 - 	CGI_10014556	superfamily	247948	12	67	1.12E-14	63.8522	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#1391 - 	CGI_10014557	superfamily	247723	377	497	9.52E-56	185.343	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#1391 - 	CGI_10014557	superfamily	247723	514	594	2.05E-54	181.529	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#1392 - 	CGI_10014558	superfamily	247684	9	461	1.63E-87	279.933	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#1393 - 	CGI_10014559	superfamily	206634	65	186	3.63E-54	170.635	cl16904	AKAP28 superfamily	 - 	 - 	"28 kDa A-kinase anchor; 28 kDa AKAP (AKAP28) is highly enriched in human airway axonemes. The mRNA for AKAP28 is up-regulated as primary airway cells differentiate and is specifically expressed in tissues containing cilia and/or flagella. Homologs of AKAP28 are present in all animals and in some, including mice the AKAP28-like domain are preceded by another uncharacterized domain"
Q#1394 - 	CGI_10014560	superfamily	206050	28	123	2.06E-21	85.7887	cl16449	KIAA1430 superfamily	 - 	 - 	KIAA1430 homologue; This is a family of KIAA1430 homologues. The function is not known.
Q#1395 - 	CGI_10014561	superfamily	243555	22	214	2.73E-13	67.031	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#1399 - 	CGI_10014565	superfamily	248100	72	132	0.000557878	36.3632	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#1401 - 	CGI_10014567	superfamily	246925	434	585	6.40E-05	44.6538	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#1401 - 	CGI_10014567	superfamily	243051	53	195	0.00427231	37.7426	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#1404 - 	CGI_10002873	superfamily	247780	310	588	5.25E-143	418.876	cl17226	NAD_bind_amino_acid_DH superfamily	 - 	 - 	"NAD(P) binding domain of amino acid dehydrogenase-like proteins; Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel  domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts."
Q#1404 - 	CGI_10002873	superfamily	215894	122	300	2.88E-103	313.044	cl02855	malic superfamily	 - 	 - 	"Malic enzyme, N-terminal domain; Malic enzyme, N-terminal domain.  "
Q#1407 - 	CGI_10008634	superfamily	217293	33	233	2.86E-34	127.364	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1407 - 	CGI_10008634	superfamily	202474	240	340	2.18E-13	68.0641	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#1413 - 	CGI_10008641	superfamily	241600	287	502	1.39E-94	288.755	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1415 - 	CGI_10011964	superfamily	247725	265	356	8.52E-59	196.024	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1415 - 	CGI_10011964	superfamily	149993	456	613	1.15E-48	170.386	cl07673	Talin_middle superfamily	 - 	 - 	"Talin, middle domain; Members of this family adopt a structure consisting of five alpha helices that fold into a bundle. They contain a Vinculin binding site (VBS) composed of a hydrophobic surface spanning five turns of helix four. Activation of the VBS causes subsequent recruitment of Vinculin, which enables maturation of small integrin/talin complexes into more stable adhesions. Formation of the complex between VBS and Vinculin requires prior unfolding of this middle domain: once released from the talin hydrophobic core, the VBS helix is then available to induce the 'bundle conversion' conformational change within the vinculin head domain thereby displacing the intramolecular interaction with the vinculin tail, allowing vinculin to bind actin."
Q#1415 - 	CGI_10011964	superfamily	215882	162	269	8.52E-28	109.678	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#1415 - 	CGI_10011964	superfamily	220215	46	154	3.45E-09	54.9238	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#1418 - 	CGI_10011967	superfamily	245226	145	341	4.19E-43	153.209	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#1420 - 	CGI_10011969	superfamily	218405	134	246	0.000169644	40.9429	cl18455	DUF676 superfamily	C	 - 	Putative serine esterase (DUF676); This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.
Q#1420 - 	CGI_10011969	superfamily	247101	241	311	0.000400199	40.2413	cl15849	Palm_thioest superfamily	N	 - 	Palmitoyl protein thioesterase; Palmitoyl protein thioesterase.  
Q#1421 - 	CGI_10011970	superfamily	247692	415	530	5.45E-18	83.8798	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#1421 - 	CGI_10011970	superfamily	247101	160	340	4.17E-05	44.2094	cl15849	Palm_thioest superfamily	 - 	 - 	Palmitoyl protein thioesterase; Palmitoyl protein thioesterase.  
Q#1424 - 	CGI_10011973	superfamily	248262	7	275	1.10E-131	381.962	cl17708	HMBS superfamily	 - 	 - 	"Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12.  HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB).  HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II.  HMBS is found in all organisms except viruses."
Q#1425 - 	CGI_10011974	superfamily	242432	248	309	3.57E-10	58.9123	cl01321	SURF1 superfamily	C	 - 	"SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring complex of the respiratory chain, is an assemblage of nuclear and mitochondrially-encoded subunits. Its assembly is mediated by nuclear encoded assembly factors, one of which is Surf1/Shy1. Mutations in human Surf1 are a major cause of Leigh syndrome, a severe neurodegenerative disorder."
Q#1425 - 	CGI_10011974	superfamily	242432	317	388	4.65E-10	57.7387	cl01321	SURF1 superfamily	N	 - 	"SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring complex of the respiratory chain, is an assemblage of nuclear and mitochondrially-encoded subunits. Its assembly is mediated by nuclear encoded assembly factors, one of which is Surf1/Shy1. Mutations in human Surf1 are a major cause of Leigh syndrome, a severe neurodegenerative disorder."
Q#1426 - 	CGI_10011975	superfamily	191068	20	75	1.08E-14	63.7971	cl04701	ETC_C1_NDUFA5 superfamily	 - 	 - 	ETC complex I subunit conserved region; Family of eukaryotic NADH-ubiquinone oxidoreductase subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N-terminus of the member proteins.
Q#1427 - 	CGI_10011976	superfamily	247725	307	417	1.85E-59	198.132	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1430 - 	CGI_10011979	superfamily	247755	717	937	2.54E-88	284.076	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#1430 - 	CGI_10011979	superfamily	248376	428	710	6.21E-26	109.42	cl17822	MutS_III superfamily	 - 	 - 	"MutS domain III; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in."
Q#1430 - 	CGI_10011979	superfamily	218486	285	405	1.72E-11	62.7637	cl04975	MutS_II superfamily	 - 	 - 	"MutS domain II; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam01624, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. This domain corresponds to domain II in Thermus aquaticus MutS as characterized in, and has similarity resembles RNAse-H-like domains (see pfam00075)."
Q#1431 - 	CGI_10011980	superfamily	247800	106	130	0.000113839	37.1776	cl17246	MarR_2 superfamily	NC	 - 	"MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif."
Q#1434 - 	CGI_10001708	superfamily	243035	23	146	4.52E-11	56.8593	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1436 - 	CGI_10004256	superfamily	215647	21	118	0.00084485	38.3585	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#1437 - 	CGI_10004257	superfamily	241596	77	120	8.08E-10	51.8311	cl00081	HLH superfamily	C	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#1439 - 	CGI_10004259	superfamily	247724	58	224	1.54E-11	59.4825	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1440 - 	CGI_10004260	superfamily	243092	1572	1687	6.45E-11	63.8932	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1440 - 	CGI_10004260	superfamily	205451	42	135	4.21E-06	46.8027	cl16203	DUF4062 superfamily	 - 	 - 	"Domain of unknown function (DUF4062); This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif."
Q#1440 - 	CGI_10004260	superfamily	243092	1176	1337	0.000274456	43.4776	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1440 - 	CGI_10004260	superfamily	247743	395	547	0.000904535	40.2608	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1443 - 	CGI_10005280	superfamily	203136	76	160	5.56E-05	40.0204	cl04867	LRAT superfamily	N	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#1448 - 	CGI_10005285	superfamily	246680	9	84	1.90E-16	74.1603	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#1448 - 	CGI_10005285	superfamily	241567	164	294	1.12E-08	54.5287	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#1449 - 	CGI_10005286	superfamily	243175	194	265	3.27E-16	71.8883	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#1449 - 	CGI_10005286	superfamily	241832	46	112	1.69E-17	74.9678	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1451 - 	CGI_10022918	superfamily	245225	3	86	3.36E-06	48.0765	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1451 - 	CGI_10022918	superfamily	243199	170	235	4.65E-05	43.4338	cl02808	RT_like superfamily	N	 - 	"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs."
Q#1452 - 	CGI_10022920	superfamily	247908	54	199	8.29E-56	177.871	cl17354	NIF superfamily	 - 	 - 	NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.
Q#1453 - 	CGI_10022921	superfamily	243072	52	157	4.96E-27	101.691	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1454 - 	CGI_10022922	superfamily	246669	2	62	5.78E-05	41.8747	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#1456 - 	CGI_10022924	superfamily	246683	59	155	9.89E-37	130.703	cl14648	Aldose_epim superfamily	C	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#1457 - 	CGI_10022925	superfamily	218118	94	151	7.18E-10	56.0833	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#1458 - 	CGI_10022926	superfamily	243238	77	552	0	582.283	cl02915	Voltage_gated_ClC superfamily	 - 	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#1458 - 	CGI_10022926	superfamily	246936	822	868	2.28E-19	85.3816	cl15354	CBS_pair superfamily	N	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#1460 - 	CGI_10022928	superfamily	209871	345	525	3.96E-85	269.909	cl14608	P53 superfamily	 - 	 - 	"P53 DNA-binding domain; P53 is a tumor suppressor gene product; mutations in p53 or lack of expression are found associated with a large fraction of all human cancers. P53 is activated by DNA damage and acts as a regulator of gene expression that ultimatively blocks progression through the cell cycle. P53 binds to DNA as a tetrameric transcription factor. In its inactive form, p53 is bound to the ring finger protein Mdm2, which promotes its ubiquitinylation and subsequent proteosomal degradation. Phosphorylation of p53 disrupts the Mdm2-p53 complex, while the stable and active p53 binds to regulatory regions of its target genes, such as the cyclin-kinase inhibitor p21, which complexes and inactivates cdk2 and other cyclin complexes."
Q#1460 - 	CGI_10022928	superfamily	247057	674	732	2.99E-30	114.722	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#1460 - 	CGI_10022928	superfamily	149007	554	595	1.63E-16	74.9011	cl06653	P53_tetramer superfamily	 - 	 - 	P53 tetramerisation motif; P53 tetramerisation motif.  
Q#1460 - 	CGI_10022928	superfamily	149567	210	234	7.11E-06	44.1366	cl07246	P53_TAD superfamily	 - 	 - 	P53 transactivation motif; The binding of the p53 transactivation domain by regulatory proteins regulates p53 transcription activation. This motif is comprised of a single amphipathic alpha helix and contains a highly conserved sequence.
Q#1461 - 	CGI_10022929	superfamily	243092	47	94	0.00199089	34.618	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1462 - 	CGI_10022930	superfamily	241645	320	393	6.34E-07	46.4955	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#1463 - 	CGI_10022931	superfamily	241597	14	84	2.05E-26	100.45	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#1464 - 	CGI_10022932	superfamily	220692	56	295	2.82E-15	74.5481	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#1465 - 	CGI_10022933	superfamily	243239	351	439	2.54E-31	116.651	cl02916	POLO_box superfamily	 - 	 - 	"Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides."
Q#1465 - 	CGI_10022933	superfamily	243239	454	537	9.12E-29	109.209	cl02916	POLO_box superfamily	 - 	 - 	"Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides."
Q#1465 - 	CGI_10022933	superfamily	245201	18	223	1.30E-60	202.365	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1468 - 	CGI_10022937	superfamily	241574	15	82	1.55E-10	54.5539	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1471 - 	CGI_10008552	superfamily	241743	97	187	7.40E-10	53.1397	cl00274	ML superfamily	N	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#1472 - 	CGI_10008553	superfamily	241743	155	193	0.00103381	36.5762	cl00274	ML superfamily	N	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#1473 - 	CGI_10008554	superfamily	241607	23	62	2.68E-07	42.257	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#1474 - 	CGI_10008555	superfamily	245206	6	244	5.52E-76	233.347	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#1475 - 	CGI_10008556	superfamily	220791	148	204	8.75E-06	42.8284	cl11149	Borealin superfamily	C	 - 	"Cell division cycle-associated protein 8; The chromosomal passenger complex of Aurora B kinase, INCENP, and Survivin has essential regulatory roles at centromeres and the central spindle in mitosis. Borealin is also a member of the complex. Approximately half of Aurora B in mitotic cells is complexed with INCENP, Borealin, and Survivin. Depletion of Borealin by RNA interference delays mitotic progression and results in kinetochore-spindle mis-attachments and an increase in bipolar spindles associated with ectopic asters."
Q#1476 - 	CGI_10008557	superfamily	246675	296	448	9.99E-92	295.875	cl14615	PI-PLCc_GDPD_SF superfamily	C	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#1476 - 	CGI_10008557	superfamily	247725	14	134	2.94E-59	200.558	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1476 - 	CGI_10008557	superfamily	246908	640	742	4.69E-51	176.687	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#1476 - 	CGI_10008557	superfamily	246908	528	626	4.96E-48	167.913	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#1476 - 	CGI_10008557	superfamily	246669	1077	1203	4.25E-45	160.4	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#1476 - 	CGI_10008557	superfamily	246708	940	1060	1.20E-49	173.086	cl14781	PI-PLC-Y superfamily	 - 	 - 	"Phosphatidylinositol-specific phospholipase C, Y domain; This associates with pfam00388 to form a single structural unit."
Q#1476 - 	CGI_10008557	superfamily	247683	795	842	2.94E-15	72.3647	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#1476 - 	CGI_10008557	superfamily	247725	854	920	9.62E-07	48.578	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1476 - 	CGI_10008557	superfamily	247725	468	505	1.34E-06	48.1928	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1477 - 	CGI_10008558	superfamily	248458	228	341	3.47E-06	48.4641	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1478 - 	CGI_10008559	superfamily	243072	173	292	5.16E-29	109.395	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1478 - 	CGI_10008559	superfamily	243072	63	193	3.51E-25	98.6098	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1478 - 	CGI_10008559	superfamily	243072	2	121	1.08E-14	69.3346	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1478 - 	CGI_10008559	superfamily	243072	266	347	3.26E-13	65.4826	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1479 - 	CGI_10008560	superfamily	241580	79	156	4.02E-39	135.759	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#1480 - 	CGI_10008561	superfamily	241832	7	106	8.93E-12	60.7268	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1480 - 	CGI_10008561	superfamily	241832	114	172	0.000201118	39.1271	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1481 - 	CGI_10008562	superfamily	243157	16	95	1.11E-37	127.44	cl02720	PB1 superfamily	 - 	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#1482 - 	CGI_10001583	superfamily	245814	236	293	1.93E-05	42.1828	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1483 - 	CGI_10007614	superfamily	241583	209	316	4.94E-24	97.8297	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#1483 - 	CGI_10007614	superfamily	216572	41	135	5.63E-05	40.7211	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#1485 - 	CGI_10007617	superfamily	243072	18	143	1.43E-18	79.3498	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1485 - 	CGI_10007617	superfamily	243072	91	272	8.32E-14	65.8678	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1489 - 	CGI_10007621	superfamily	245215	28	459	0	676.927	cl09945	XylA superfamily	 - 	 - 	Xylose isomerase [Carbohydrate transport and metabolism]
Q#1489 - 	CGI_10007621	superfamily	246976	460	851	3.66E-151	467.999	cl15483	Dymeclin superfamily	C	 - 	"Dyggve-Melchior-Clausen syndrome protein; Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 residues long and present in plants and animals. Mutations in the gene coding for this protein in humans give rise to the disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM 223800) which is an autosomal-recessive disorder characterized by the association of a spondylo-epi-metaphyseal dysplasia and mental retardation. DYM transcripts are widely expressed throughout human development and Dymeclin is not an integral membrane protein of the ER, but rather a peripheral membrane protein dynamically associated with the Golgi apparatus."
Q#1490 - 	CGI_10007622	superfamily	247999	503	550	1.36E-06	46.3296	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#1491 - 	CGI_10007623	superfamily	247805	1	77	0.000251028	38.4724	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#1492 - 	CGI_10007624	superfamily	247724	23	45	9.10E-05	35.7332	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1496 - 	CGI_10012255	superfamily	248264	65	125	1.60E-06	45.691	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#1498 - 	CGI_10012257	superfamily	241613	225	259	3.07E-12	61.0685	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#1498 - 	CGI_10012257	superfamily	241613	186	220	3.80E-12	60.6833	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#1498 - 	CGI_10012257	superfamily	245814	103	177	0.000251694	39.0257	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1500 - 	CGI_10012259	superfamily	241750	2	155	1.67E-42	143.098	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#1501 - 	CGI_10012260	superfamily	246680	9	91	1.11E-07	48.7372	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#1504 - 	CGI_10012263	superfamily	110440	181	208	0.0072863	32.7649	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1505 - 	CGI_10012264	superfamily	246918	99	153	4.66E-10	51.8187	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#1508 - 	CGI_10012267	superfamily	241563	68	109	1.58E-06	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1508 - 	CGI_10012267	superfamily	241563	28	59	0.000480661	38.2292	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1509 - 	CGI_10010396	superfamily	247792	510	551	2.51E-09	53.9888	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1509 - 	CGI_10010396	superfamily	222330	3	479	1.66E-124	379.805	cl16356	TRC8_N superfamily	 - 	 - 	TRC8 N-terminal domain; This region is found at the N-terminus of the TRC8 protein. TRC8 is an E3 ubiquitin-protein ligase also known as RNF139. This region contains 12 transmembrane domains. This region has been suggested to contain a sterol sensing domain. It has been found that TRC8 protein levels are sterol responsive and that it binds and stimulates ubiquitylation of the endoplasmic reticulum anchor protein INSIG.
Q#1510 - 	CGI_10010397	superfamily	247792	528	569	1.35E-07	48.9812	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1510 - 	CGI_10010397	superfamily	222330	31	497	7.14E-116	358.619	cl16356	TRC8_N superfamily	 - 	 - 	TRC8 N-terminal domain; This region is found at the N-terminus of the TRC8 protein. TRC8 is an E3 ubiquitin-protein ligase also known as RNF139. This region contains 12 transmembrane domains. This region has been suggested to contain a sterol sensing domain. It has been found that TRC8 protein levels are sterol responsive and that it binds and stimulates ubiquitylation of the endoplasmic reticulum anchor protein INSIG.
Q#1511 - 	CGI_10010398	superfamily	241599	155	211	4.49E-20	81.5208	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#1512 - 	CGI_10010399	superfamily	243362	84	150	3.48E-20	82.473	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#1512 - 	CGI_10010399	superfamily	199908	20	69	1.37E-11	56.4951	cl16908	DnaJ_zf superfamily	C	 - 	"Zinc finger domain of DnaJ and HSP40; Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. Hsp40 proteins are characterized by the presence of an N-terminal J domain, which mediates the interaction with Hsp70. This central domain contains four repeats of a CxxCxGxG motif and binds to two Zinc ions. It has been implicated in substrate binding."
Q#1515 - 	CGI_10010402	superfamily	241748	162	348	5.59E-39	140.401	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#1515 - 	CGI_10010402	superfamily	244955	24	80	4.15E-05	41.7981	cl08433	AMP_N superfamily	C	 - 	"Aminopeptidase P, N-terminal domain; This domain is structurally very similar to the creatinase N-terminal domain (pfam01321). However, little or no sequence similarity exists between the two families."
Q#1516 - 	CGI_10010403	superfamily	245201	180	368	2.08E-15	76.036	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1516 - 	CGI_10010403	superfamily	245201	633	695	1.84E-08	55.0488	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1517 - 	CGI_10010404	superfamily	245201	511	745	8.76E-17	81.0436	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1517 - 	CGI_10010404	superfamily	245201	944	1048	1.05E-12	68.332	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1518 - 	CGI_10010405	superfamily	245819	452	636	1.21E-59	199.728	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#1518 - 	CGI_10010405	superfamily	219812	126	362	1.90E-11	63.4792	cl07121	NIT superfamily	 - 	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#1518 - 	CGI_10010405	superfamily	219526	394	439	6.67E-08	52.2363	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#1519 - 	CGI_10010406	superfamily	247856	155	216	2.64E-16	70.2693	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1519 - 	CGI_10010406	superfamily	247856	81	142	1.66E-11	57.1725	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1520 - 	CGI_10010407	superfamily	216981	59	173	5.57E-16	73.7209	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#1520 - 	CGI_10010407	superfamily	243130	237	262	0.0089632	33.9779	cl02655	CUE superfamily	N	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#1521 - 	CGI_10010408	superfamily	218533	231	498	1.96E-98	308.993	cl10638	DUF726 superfamily	N	 - 	Protein of unknown function (DUF726); This family consists of several uncharacterized eukaryotic proteins.
Q#1523 - 	CGI_10010410	superfamily	221911	40	146	1.47E-43	145.794	cl18625	Fer2_3 superfamily	 - 	 - 	2Fe-2S iron-sulfur cluster binding domain; The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.
Q#1524 - 	CGI_10010411	superfamily	248312	63	167	2.54E-08	51.2088	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#1527 - 	CGI_10009921	superfamily	247916	137	198	0.000148824	41.2322	cl17362	Transglut_core superfamily	C	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#1528 - 	CGI_10009922	superfamily	241599	144	195	1.21E-16	72.276	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#1529 - 	CGI_10009923	superfamily	243072	515	626	5.62E-22	92.4466	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1529 - 	CGI_10009923	superfamily	245008	60	120	3.02E-06	45.2424	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#1530 - 	CGI_10009924	superfamily	248020	221	395	1.26E-23	100.617	cl17466	Sulfatase superfamily	N	 - 	Sulfatase; Sulfatase.  
Q#1530 - 	CGI_10009924	superfamily	248020	28	135	9.15E-16	77.1196	cl17466	Sulfatase superfamily	C	 - 	Sulfatase; Sulfatase.  
Q#1531 - 	CGI_10009925	superfamily	241645	75	153	5.00E-12	62.2756	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#1532 - 	CGI_10009926	superfamily	241626	31	109	2.57E-28	101.556	cl00125	RHOD superfamily	N	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#1533 - 	CGI_10009927	superfamily	241626	11	100	9.94E-33	115.409	cl00125	RHOD superfamily	N	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#1534 - 	CGI_10009928	superfamily	148050	5	136	1.12E-29	107.054	cl05627	GRIM-19 superfamily	 - 	 - 	"GRIM-19 protein; This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-# and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity."
Q#1537 - 	CGI_10009931	superfamily	243092	410	694	1.15E-16	80.0716	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1539 - 	CGI_10009933	superfamily	243093	85	160	4.90E-07	47.525	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#1544 - 	CGI_10007414	superfamily	241563	59	95	0.000151318	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1545 - 	CGI_10007415	superfamily	247727	160	257	1.18E-14	68.6106	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#1546 - 	CGI_10007416	superfamily	247727	165	257	1.40E-12	62.8326	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#1547 - 	CGI_10007417	superfamily	247727	159	256	8.98E-13	63.603	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#1548 - 	CGI_10007418	superfamily	247727	123	221	1.13E-11	60.1362	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#1549 - 	CGI_10007419	superfamily	245226	5	70	0.000414565	39.5907	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#1551 - 	CGI_10003628	superfamily	247044	36	148	1.35E-59	190.512	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1551 - 	CGI_10003628	superfamily	247044	163	258	8.88E-22	88.0632	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1551 - 	CGI_10003628	superfamily	247044	278	373	1.68E-24	95.7791	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1552 - 	CGI_10006576	superfamily	149284	208	354	3.04E-44	152.649	cl06952	CPL superfamily	 - 	 - 	CPL (NUC119) domain; This C terminal domain is fund in Penguin-like proteins associated with Pumilio like repeats.
Q#1552 - 	CGI_10006576	superfamily	243032	110	239	8.53E-05	42.9639	cl02427	Pumilio superfamily	NC	 - 	"Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats."
Q#1553 - 	CGI_10006577	superfamily	114591	430	528	1.03E-10	59.8642	cl05445	Mt_ATP-synt_D superfamily	N	 - 	"ATP synthase D chain, mitochondrial (ATP5H); This family consists of several ATP synthase D chain, mitochondrial (ATP5H) proteins. Subunit d has no extensive hydrophobic sequences, and is not apparently related to any subunit described in the simpler ATP synthases in bacteria and chloroplasts."
Q#1553 - 	CGI_10006577	superfamily	243092	232	344	0.0070652	37.3144	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1555 - 	CGI_10006579	superfamily	217814	1	146	1.16E-18	83.527	cl04345	Jun superfamily	N	 - 	Jun-like transcription factor; Jun-like transcription factor.  
Q#1555 - 	CGI_10006579	superfamily	243100	177	214	0.000363556	38.4592	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#1555 - 	CGI_10006579	superfamily	243100	356	393	0.000363556	38.4592	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#1556 - 	CGI_10006580	superfamily	247755	496	647	5.42E-59	199.45	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#1556 - 	CGI_10006580	superfamily	248376	282	502	1.62E-18	85.5378	cl17822	MutS_III superfamily	 - 	 - 	"MutS domain III; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in."
Q#1558 - 	CGI_10005836	superfamily	192535	39	248	0.00654023	36.4198	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#1559 - 	CGI_10005837	superfamily	192535	33	70	0.00531716	36.4198	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#1560 - 	CGI_10018322	superfamily	241640	70	194	2.61E-45	157.053	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#1561 - 	CGI_10018323	superfamily	241596	30	89	1.71E-15	69.1651	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#1561 - 	CGI_10018323	superfamily	243123	105	149	4.38E-10	54.1013	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#1563 - 	CGI_10018325	superfamily	216152	206	544	3.63E-64	215.641	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#1563 - 	CGI_10018325	superfamily	216152	5	170	2.41E-42	155.55	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#1564 - 	CGI_10018326	superfamily	247068	236	332	2.98E-12	63.8717	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#1564 - 	CGI_10018326	superfamily	247068	154	227	2.18E-07	49.2342	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#1564 - 	CGI_10018326	superfamily	247068	340	437	5.06E-06	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#1564 - 	CGI_10018326	superfamily	247068	457	536	0.000559224	38.8338	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#1565 - 	CGI_10018327	superfamily	248458	129	268	1.52E-10	61.5609	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1565 - 	CGI_10018327	superfamily	248458	367	505	6.19E-10	59.6349	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1566 - 	CGI_10018328	superfamily	241584	443	530	9.16E-05	41.3279	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#1566 - 	CGI_10018328	superfamily	245213	5	37	0.00124754	37.4562	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1566 - 	CGI_10018328	superfamily	245201	620	690	5.94E-05	44.2517	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1573 - 	CGI_10018335	superfamily	202823	94	152	1.04E-17	80.6608	cl08408	Ribosomal_L2_C superfamily	N	 - 	"Ribosomal Proteins L2, C-terminal domain; Ribosomal Proteins L2, C-terminal domain.  "
Q#1573 - 	CGI_10018335	superfamily	109247	11	90	7.79E-11	59.5129	cl02816	Ribosomal_L2 superfamily	 - 	 - 	"Ribosomal Proteins L2, RNA binding domain; Ribosomal Proteins L2, RNA binding domain.  "
Q#1574 - 	CGI_10018336	superfamily	247805	293	514	3.58E-98	305.178	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#1574 - 	CGI_10018336	superfamily	247905	524	655	8.50E-40	143.532	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#1576 - 	CGI_10018338	superfamily	241795	250	379	5.37E-72	223.665	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#1576 - 	CGI_10018338	superfamily	241795	105	235	1.89E-70	219.623	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#1576 - 	CGI_10018338	superfamily	207712	17	97	2.74E-23	92.7601	cl02728	DUF1126 superfamily	 - 	 - 	Repeat of unknown function (DUF1126); This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.
Q#1578 - 	CGI_10018340	superfamily	220131	687	969	1.67E-59	210.21	cl11721	DUF1943 superfamily	 - 	 - 	"Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined."
Q#1578 - 	CGI_10018340	superfamily	219034	982	1080	2.46E-10	61.1982	cl05778	DUF1081 superfamily	 - 	 - 	Domain of Unknown Function (DUF1081); This region is found in Apolipophorin proteins.
Q#1578 - 	CGI_10018340	superfamily	222032	2360	2405	0.00237836	39.9231	cl16218	CPSF100_C superfamily	N	 - 	"Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex."
Q#1581 - 	CGI_10013404	superfamily	241599	157	214	1.22E-21	85.758	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#1582 - 	CGI_10013405	superfamily	154937	171	243	1.14E-27	102.296	cl02489	SWIB superfamily	 - 	 - 	SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.
Q#1582 - 	CGI_10013405	superfamily	204056	5	56	2.55E-09	51.3297	cl07395	DEK_C superfamily	 - 	 - 	DEK C terminal domain; DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family. This domain is also found in chitin synthase proteins and in protein phosphatases.
Q#1586 - 	CGI_10013409	superfamily	220692	1	72	8.55E-06	41.8061	cl18570	7TM_GPCR_Srw superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#1588 - 	CGI_10013411	superfamily	220692	64	373	1.20E-22	95.7341	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#1593 - 	CGI_10013416	superfamily	216731	12	49	8.57E-05	37.6235	cl12258	A2M_N superfamily	N	 - 	MG2 domain; This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin.
Q#1594 - 	CGI_10013417	superfamily	244881	228	531	1.25E-118	363.436	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#1594 - 	CGI_10013417	superfamily	215788	8	98	1.45E-27	108.035	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#1594 - 	CGI_10013417	superfamily	203720	640	725	9.31E-26	103.012	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#1594 - 	CGI_10013417	superfamily	147487	60	157	5.84E-05	42.3898	cl05075	SVA superfamily	N	 - 	"Seminal vesicle autoantigen (SVA); This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19-kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP, has several known functions. In saliva, this protein plays a role in host defence by binding to microorganisms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4."
Q#1595 - 	CGI_10013418	superfamily	215827	2	131	2.47E-17	80.5903	cl02830	Tyrosinase superfamily	N	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#1596 - 	CGI_10013419	superfamily	247856	80	136	2.72E-08	46.7721	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1596 - 	CGI_10013419	superfamily	247856	13	72	1.91E-06	41.3793	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1598 - 	CGI_10013421	superfamily	247856	82	137	2.49E-12	58.3281	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1598 - 	CGI_10013421	superfamily	247856	13	75	1.56E-10	52.9353	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1600 - 	CGI_10013423	superfamily	154937	280	356	1.81E-26	102.39	cl02489	SWIB superfamily	 - 	 - 	SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.
Q#1602 - 	CGI_10013425	superfamily	243066	19	72	2.35E-09	50.3085	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#1604 - 	CGI_10013427	superfamily	245213	326	380	0.0029501	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1604 - 	CGI_10013427	superfamily	241571	74	160	0.00220995	37.0067	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1604 - 	CGI_10013427	superfamily	245213	383	414	0.0073	34.9152	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1605 - 	CGI_10013428	superfamily	245596	127	426	2.00E-159	460.133	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#1605 - 	CGI_10013428	superfamily	247085	439	553	7.70E-24	97.191	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#1607 - 	CGI_10004635	superfamily	241571	1057	1182	3.40E-10	58.963	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1607 - 	CGI_10004635	superfamily	245213	1014	1049	0.00233918	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1607 - 	CGI_10004635	superfamily	241583	799	980	2.97E-37	139.629	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#1612 - 	CGI_10004191	superfamily	247724	2	128	1.25E-40	138.822	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1613 - 	CGI_10022176	superfamily	217293	526	713	2.79E-22	96.5479	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1615 - 	CGI_10022178	superfamily	243078	20	137	1.64E-56	188.53	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#1621 - 	CGI_10022184	superfamily	243065	1028	1183	3.02E-35	134.452	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#1621 - 	CGI_10022184	superfamily	243065	579	726	7.16E-33	127.173	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#1621 - 	CGI_10022184	superfamily	243065	221	372	1.27E-32	126.788	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#1621 - 	CGI_10022184	superfamily	222049	1729	1821	2.38E-21	91.6314	cl16239	Mucin2_WxxW superfamily	 - 	 - 	"Mucin-2 protein WxxW repeating region; This family is repeating region found on mucins 2 and 5. The function is not known, but the repeat can be present in up to 32 copies, as in a member from Branchiostoma floridae. The region carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues."
Q#1621 - 	CGI_10022184	superfamily	244710	1223	1298	9.86E-20	86.6753	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#1621 - 	CGI_10022184	superfamily	244710	408	482	1.07E-14	72.0377	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#1621 - 	CGI_10022184	superfamily	244710	764	830	7.33E-14	69.7265	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#1621 - 	CGI_10022184	superfamily	222049	1465	1550	6.75E-13	66.9786	cl16239	Mucin2_WxxW superfamily	 - 	 - 	"Mucin-2 protein WxxW repeating region; This family is repeating region found on mucins 2 and 5. The function is not known, but the repeat can be present in up to 32 copies, as in a member from Branchiostoma floridae. The region carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues."
Q#1622 - 	CGI_10022185	superfamily	245213	660	684	0.00212571	36.8458	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1622 - 	CGI_10022185	superfamily	245864	387	584	9.16E-21	94.6526	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#1622 - 	CGI_10022185	superfamily	221981	174	222	0.00348597	36.5764	cl18630	Big_5 superfamily	N	 - 	Bacterial Ig-like domain; Bacterial Ig-like domain.  
Q#1623 - 	CGI_10022186	superfamily	243100	43	74	0.00074595	33.0664	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#1624 - 	CGI_10022187	superfamily	145367	67	104	8.88E-11	55.8148	cl03479	pKID superfamily	 - 	 - 	pKID domain; CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.
Q#1624 - 	CGI_10022187	superfamily	243100	251	282	5.61E-07	45.778	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#1625 - 	CGI_10022188	superfamily	245206	33	305	3.15E-89	270.688	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#1626 - 	CGI_10022189	superfamily	244824	29	417	0	527.131	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#1626 - 	CGI_10022189	superfamily	243149	423	511	6.71E-32	117.339	cl02706	Alpha-amylase_C superfamily	 - 	 - 	"Alpha amylase, C-terminal all-beta domain; Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain."
Q#1627 - 	CGI_10022190	superfamily	244824	1	364	7.13E-168	478.981	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#1627 - 	CGI_10022190	superfamily	243149	370	458	2.04E-32	118.109	cl02706	Alpha-amylase_C superfamily	 - 	 - 	"Alpha amylase, C-terminal all-beta domain; Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain."
Q#1628 - 	CGI_10022191	superfamily	243181	2	83	4.45E-47	160.093	cl02783	TopoII_MutL_Trans superfamily	N	 - 	"MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2.  MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families."
Q#1635 - 	CGI_10022199	superfamily	221377	100	143	0.00607213	34.3667	cl13449	DUF3504 superfamily	NC	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#1637 - 	CGI_10022202	superfamily	245226	195	238	1.93E-06	46.1397	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#1641 - 	CGI_10010184	superfamily	190709	5	104	2.54E-52	161.896	cl04204	UPF0139 superfamily	 - 	 - 	Uncharacterized protein family (UPF0139); Uncharacterised protein family (UPF0139).  
Q#1642 - 	CGI_10010185	superfamily	246748	21	329	4.24E-134	404.278	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#1643 - 	CGI_10010186	superfamily	207690	92	116	0.000777182	36.5269	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#1643 - 	CGI_10010186	superfamily	207690	15	39	0.00145163	35.7565	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#1645 - 	CGI_10010188	superfamily	245847	17	123	1.12E-09	51.7344	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#1646 - 	CGI_10010189	superfamily	238191	425	894	1.11E-114	365.116	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#1646 - 	CGI_10010189	superfamily	242406	208	358	1.46E-52	181.636	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1646 - 	CGI_10010189	superfamily	245201	32	99	1.40E-30	122.222	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1647 - 	CGI_10010190	superfamily	245201	7	261	1.86E-112	337.934	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1647 - 	CGI_10010190	superfamily	242406	436	549	1.43E-31	119.233	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1648 - 	CGI_10010191	superfamily	245201	492	746	6.21E-82	268.212	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1648 - 	CGI_10010191	superfamily	242406	894	1044	4.42E-53	183.176	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1648 - 	CGI_10010191	superfamily	242406	314	464	2.54E-51	178.169	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1649 - 	CGI_10010192	superfamily	242406	233	382	9.18E-51	169.096	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#1650 - 	CGI_10010193	superfamily	241754	202	533	0	545.701	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#1651 - 	CGI_10010194	superfamily	241832	567	661	7.12E-28	108.029	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1651 - 	CGI_10010194	superfamily	248022	203	516	9.25E-07	50.3539	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#1651 - 	CGI_10010194	superfamily	248022	59	101	0.000824379	40.7239	cl17468	Aa_trans superfamily	C	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#1653 - 	CGI_10010196	superfamily	241563	114	144	0.00590007	32.4512	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1655 - 	CGI_10010198	superfamily	247792	16	45	0.000111314	35.114	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1656 - 	CGI_10010199	superfamily	241563	75	110	4.72E-07	47.0888	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1658 - 	CGI_10010201	superfamily	241563	75	110	0.000174327	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1659 - 	CGI_10010202	superfamily	247792	16	59	1.21E-07	48.2108	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1659 - 	CGI_10010202	superfamily	241563	154	189	8.87E-06	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1661 - 	CGI_10013462	superfamily	243555	21	216	7.73E-14	69.3422	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#1662 - 	CGI_10013463	superfamily	246925	312	514	0.000342083	41.5722	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#1664 - 	CGI_10013465	superfamily	248458	75	413	1.81E-23	99.6956	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1666 - 	CGI_10013467	superfamily	248458	1	90	0.000315988	37.6785	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1667 - 	CGI_10013468	superfamily	241609	10	85	2.07E-24	95.1375	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1667 - 	CGI_10013468	superfamily	241609	284	360	1.68E-17	76.2627	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1667 - 	CGI_10013468	superfamily	245213	167	196	0.000285893	38.0014	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1667 - 	CGI_10013468	superfamily	241609	211	279	4.19E-16	72.4107	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1667 - 	CGI_10013468	superfamily	241609	89	161	4.64E-12	61.2522	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1668 - 	CGI_10013469	superfamily	241610	509	559	3.02E-14	68.0454	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#1668 - 	CGI_10013469	superfamily	241610	392	442	2.09E-13	65.7342	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#1670 - 	CGI_10013471	superfamily	243051	496	643	3.55E-25	103.997	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#1670 - 	CGI_10013471	superfamily	241609	732	807	6.01E-25	100.915	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1670 - 	CGI_10013471	superfamily	241609	1012	1080	7.07E-20	86.2779	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1670 - 	CGI_10013471	superfamily	241609	923	999	4.95E-19	83.9667	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1670 - 	CGI_10013471	superfamily	241571	359	485	1.06E-12	66.2818	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1670 - 	CGI_10013471	superfamily	245213	888	916	0.000342463	39.9274	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1670 - 	CGI_10013471	superfamily	241583	131	309	1.35E-38	143.481	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#1670 - 	CGI_10013471	superfamily	241609	657	728	1.96E-14	70.4847	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1670 - 	CGI_10013471	superfamily	241609	819	879	1.71E-13	67.7162	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1672 - 	CGI_10013473	superfamily	241574	27	72	1.73E-14	69.5369	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1672 - 	CGI_10013473	superfamily	241574	99	270	3.40E-14	68.7665	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1673 - 	CGI_10013474	superfamily	244824	70	86	0.00885295	34.9627	cl07893	AmyAc_family superfamily	C	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#1678 - 	CGI_10013479	superfamily	241574	512	667	2.65E-70	232.862	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1678 - 	CGI_10013479	superfamily	241574	768	829	0.00558042	37.9506	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1681 - 	CGI_10000828	superfamily	241583	53	149	2.80E-17	75.6854	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#1682 - 	CGI_10000898	superfamily	241698	20	85	7.12E-29	103.443	cl00220	cysteine_hydrolases superfamily	N	 - 	"Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function."
Q#1684 - 	CGI_10005103	superfamily	241563	59	99	1.56E-05	42.7095	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1684 - 	CGI_10005103	superfamily	128778	98	212	0.00379937	36.4739	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#1686 - 	CGI_10005105	superfamily	110440	112	139	0.00171035	33.5353	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1687 - 	CGI_10004514	superfamily	241832	71	139	2.11E-18	76.8938	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1688 - 	CGI_10004515	superfamily	148314	1	342	4.09E-26	108.048	cl05919	XRCC4 superfamily	 - 	 - 	"DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks."
Q#1688 - 	CGI_10004515	superfamily	148314	365	539	4.34E-08	53.735	cl05919	XRCC4 superfamily	C	 - 	"DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks."
Q#1689 - 	CGI_10004516	superfamily	241832	47	117	7.63E-26	97.6946	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1689 - 	CGI_10004516	superfamily	243175	137	242	2.54E-14	66.1104	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#1690 - 	CGI_10004517	superfamily	243175	63	194	3.38E-17	73.4291	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#1690 - 	CGI_10004517	superfamily	241832	1	46	1.38E-09	51.8558	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1691 - 	CGI_10004518	superfamily	243175	137	268	2.24E-15	69.1919	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#1691 - 	CGI_10004518	superfamily	241832	48	120	1.50E-19	80.3606	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1692 - 	CGI_10004519	superfamily	243175	143	211	6.96E-14	64.1844	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#1692 - 	CGI_10004519	superfamily	241832	26	91	2.48E-21	84.5978	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1693 - 	CGI_10004520	superfamily	194545	18	105	9.45E-29	100.71	cl03131	Dynein_light superfamily	 - 	 - 	Dynein light chain type 1; Dynein light chain type 1.  
Q#1694 - 	CGI_10004521	superfamily	243072	90	215	1.40E-41	140.211	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1694 - 	CGI_10004521	superfamily	243072	37	116	1.52E-11	58.9342	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1695 - 	CGI_10004522	superfamily	217895	21	134	1.52E-05	44.1711	cl04401	CD20 superfamily	 - 	 - 	"CD20-like family; This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton."
Q#1696 - 	CGI_10001186	superfamily	248020	28	132	2.52E-17	77.4015	cl17466	Sulfatase superfamily	C	 - 	Sulfatase; Sulfatase.  
Q#1697 - 	CGI_10001187	superfamily	241752	277	411	7.52E-17	77.7559	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#1698 - 	CGI_10005726	superfamily	238191	11	503	1.36E-108	335.071	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#1699 - 	CGI_10005727	superfamily	238191	28	518	3.33E-111	342.005	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#1700 - 	CGI_10005728	superfamily	238191	23	513	8.07E-110	338.153	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#1702 - 	CGI_10005730	superfamily	246676	186	346	2.35E-37	135.55	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#1702 - 	CGI_10005730	superfamily	246710	28	171	2.23E-16	75.9272	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#1703 - 	CGI_10005731	superfamily	246676	430	602	5.30E-40	147.491	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#1703 - 	CGI_10005731	superfamily	246710	119	277	3.07E-20	89.7944	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#1703 - 	CGI_10005731	superfamily	246710	294	399	3.43E-13	68.6084	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#1703 - 	CGI_10005731	superfamily	246676	863	934	1.14E-05	45.7986	cl14616	Cyt_b561 superfamily	N	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#1703 - 	CGI_10005731	superfamily	246710	760	825	0.000271468	41.2592	cl14783	DOMON_like superfamily	C	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#1709 - 	CGI_10004796	superfamily	248264	36	200	1.04E-49	160.866	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#1710 - 	CGI_10004797	superfamily	110440	158	185	0.00108511	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1711 - 	CGI_10001418	superfamily	243082	109	201	1.75E-33	121.126	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#1711 - 	CGI_10001418	superfamily	243082	25	157	0.00470137	35.8048	cl02553	Peptidase_C19 superfamily	NC	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#1712 - 	CGI_10001591	superfamily	245201	8	227	1.05E-83	252.457	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1715 - 	CGI_10006691	superfamily	241578	202	355	4.57E-42	146.663	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1715 - 	CGI_10006691	superfamily	241578	6	151	6.40E-23	93.5053	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1716 - 	CGI_10006692	superfamily	247980	5	182	2.48E-56	177.33	cl17426	DHFR superfamily	 - 	 - 	"Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy.  5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis."
Q#1717 - 	CGI_10006693	superfamily	243061	133	221	8.92E-09	51.5738	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#1717 - 	CGI_10006693	superfamily	243061	32	97	0.00122765	36.2907	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#1718 - 	CGI_10006694	superfamily	247980	25	56	4.39E-10	51.7343	cl17426	DHFR superfamily	N	 - 	"Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy.  5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis."
Q#1721 - 	CGI_10006697	superfamily	241578	1	159	4.24E-27	108.918	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1721 - 	CGI_10006697	superfamily	243119	417	470	0.0016003	37.4133	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#1722 - 	CGI_10006698	superfamily	241574	276	332	1.87E-09	57.5957	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1724 - 	CGI_10001942	superfamily	245818	20	106	3.47E-37	128.467	cl11966	Rel-Spo_like superfamily	N	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#1725 - 	CGI_10001943	superfamily	245818	10	193	5.49E-76	233.241	cl11966	Rel-Spo_like superfamily	C	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#1727 - 	CGI_10001074	superfamily	248458	21	137	6.83E-07	49.6197	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1727 - 	CGI_10001074	superfamily	248458	272	400	2.64E-05	44.6121	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1728 - 	CGI_10013178	superfamily	248012	137	227	1.18E-08	52.2757	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#1728 - 	CGI_10013178	superfamily	248012	2	100	0.000492997	38.4584	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#1729 - 	CGI_10013179	superfamily	248012	137	264	1.60E-11	60.7501	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#1729 - 	CGI_10013179	superfamily	248012	2	100	1.50E-05	43.0808	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#1730 - 	CGI_10013180	superfamily	243030	546	578	0.00664983	34.9155	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#1732 - 	CGI_10013182	superfamily	241563	819	851	0.000450752	40.0131	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1732 - 	CGI_10013182	superfamily	241563	1124	1156	0.000551992	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1734 - 	CGI_10013184	superfamily	217293	317	514	4.26E-48	168.965	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1734 - 	CGI_10013184	superfamily	202474	522	742	1.48E-43	157.045	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#1734 - 	CGI_10013184	superfamily	216290	83	203	2.67E-16	76.5581	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#1734 - 	CGI_10013184	superfamily	217685	219	298	1.21E-11	63.122	cl04225	Cu2_monoox_C superfamily	C	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#1735 - 	CGI_10013185	superfamily	245212	108	173	4.76E-06	44.5478	cl09940	S4 superfamily	 - 	 - 	"S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site;  Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes."
Q#1735 - 	CGI_10013185	superfamily	217293	217	373	6.05E-37	136.223	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1735 - 	CGI_10013185	superfamily	202474	382	558	4.09E-27	109.28	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#1736 - 	CGI_10013186	superfamily	243072	2041	2176	6.43E-28	112.477	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1736 - 	CGI_10013186	superfamily	243072	1946	2101	7.27E-20	88.9798	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1736 - 	CGI_10013186	superfamily	245213	528	567	8.91E-09	54.565	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	254	292	1.58E-07	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	877	911	1.67E-07	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	837	873	2.01E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1066	1101	2.73E-07	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	607	643	3.32E-07	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	645	681	3.52E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1225	1261	5.20E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1028	1064	1.88E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	683	719	2.76E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	569	605	3.51E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	990	1026	5.51E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1106	1140	2.16E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	412	447	3.19E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1459	1495	3.47E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	799	834	6.01E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1339	1376	0.000135618	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	371	409	0.000141435	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	761	796	0.000186932	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1263	1299	0.000347516	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	721	759	0.000736031	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	333	369	0.000740441	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1310	1337	0.000834379	39.9274	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	299	331	0.00141052	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1196	1223	0.00312278	38.0014	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	1147	1180	0.00809482	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	245213	217	251	0.00826439	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1736 - 	CGI_10013186	superfamily	191614	1635	1685	5.37E-05	43.7622	cl08449	NOD superfamily	 - 	 - 	"NOTCH protein; NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated."
Q#1736 - 	CGI_10013186	superfamily	243028	1515	1545	0.000827318	39.9698	cl02419	Notch superfamily	 - 	 - 	LNR domain; The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
Q#1736 - 	CGI_10013186	superfamily	243028	1599	1625	0.00126374	39.1994	cl02419	Notch superfamily	N	 - 	LNR domain; The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
Q#1736 - 	CGI_10013186	superfamily	243028	1550	1587	0.00139022	39.1994	cl02419	Notch superfamily	 - 	 - 	LNR domain; The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
Q#1737 - 	CGI_10013187	superfamily	244901	8	224	2.89E-121	350.387	cl08306	Peptidase_C12 superfamily	 - 	 - 	"Cysteine peptidase C12 contains ubiquitin carboxyl-terminal hydrolase (UCH) families L1, L3, L5 and BAP1; The ubiquitin C-terminal hydrolase (UCH; ubiquitinyl hydrolase; ubiquitin thiolesterase) family of deubiquitinating enzymes (DUBs) consists of four members to date: UCH-L1, UCH-L3, UCH-L5 (UCH37) and BRCA1-associated protein-1 (BAP1), all containing a conserved catalytic domain with cysteine peptidase activity.  UCH-L1 hydrolyzes carboxyl terminal esters and amides of ubiquitin (Ub). Dysfunction of this hydrolase activity can lead to an accumulation of alpha-synuclein, which is linked to Parkinson's disease (PD) and neurofibrillary tangles, linked to Alzheimer's disease (AD).  UCH-L1, in its dimeric form, has additional enzymatic activity as a ubiquitin ligase. UCH-L3 hydrolyzes isopeptide bonds at the C-terminal glycine of either Ub or Nedd8, a ubiquitin-like protein. UCH-L3 can also interact with Lys48-linked Ub dimers to protect it from degradation while inhibiting its hydrolase activity at the same time.  UCH-L1 and UCH-L3 are the most closely related of the UCH members. UCH-L5 (UCH37) is involved in the deubiquitinating activity in the 19S proteasome regulatory complex. It is also associated with the human Ino80 chromatin-remodeling complex (hINO80) in the nucleus. BAP1 binds to the wild-type BRCA1 RING finger domain, localized in the nucleus.  It consists of the N-terminal UCH domain and two predicted nuclear localization signals (NLSs), only one of which is functional. The full-length human BRCA1 is a ubiquitin ligase. However, BAP1 does not appear to function in the deubiquitination of autoubiquitinated  BRCA1. There is growing evidence that UCH enzymes and human malignancies are closely correlated. Studies show that UCH enzymes play a crucial role in some signaling pathways and in cell-cycle regulation."
Q#1738 - 	CGI_10013188	superfamily	243164	38	55	7.03E-07	42.1396	cl02748	zf-CDGSH superfamily	N	 - 	"Iron-binding zinc finger CDGSH type; The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, pfam10660. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm."
Q#1738 - 	CGI_10013188	superfamily	243164	57	91	0.00142506	33.2801	cl02748	zf-CDGSH superfamily	 - 	 - 	"Iron-binding zinc finger CDGSH type; The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, pfam10660. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm."
Q#1739 - 	CGI_10013189	superfamily	245456	166	418	1.90E-149	427.536	cl10970	AP_MHD_Cterm superfamily	 - 	 - 	"C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15."
Q#1739 - 	CGI_10013189	superfamily	242876	1	120	4.72E-06	44.6525	cl02092	Clat_adaptor_s superfamily	 - 	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#1741 - 	CGI_10013191	superfamily	247724	17	121	8.58E-38	137.899	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#1742 - 	CGI_10013192	superfamily	199156	191	206	0.000179906	38.2041	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#1744 - 	CGI_10012664	superfamily	241609	222	289	2.03E-23	95.5227	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1744 - 	CGI_10012664	superfamily	241571	49	168	4.72E-11	60.889	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1744 - 	CGI_10012664	superfamily	245213	178	207	0.000113277	40.6978	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1744 - 	CGI_10012664	superfamily	247042	332	616	3.92E-09	58.111	cl15693	Sema superfamily	C	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#1746 - 	CGI_10012666	superfamily	247044	603	696	6.00E-19	83.8201	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1746 - 	CGI_10012666	superfamily	247044	111	213	2.90E-21	90.7452	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1746 - 	CGI_10012666	superfamily	247044	711	807	2.28E-20	88.1233	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1746 - 	CGI_10012666	superfamily	247044	485	581	5.73E-17	78.0814	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1746 - 	CGI_10012666	superfamily	247044	227	317	6.71E-13	66.1068	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1746 - 	CGI_10012666	superfamily	247044	357	436	8.03E-08	51.096	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#1746 - 	CGI_10012666	superfamily	207613	872	905	1.45E-06	46.5434	cl02491	VHP superfamily	 - 	 - 	Villin headpiece domain; Villin headpiece domain.  
Q#1747 - 	CGI_10012667	superfamily	243034	561	659	5.54E-09	55.464	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#1747 - 	CGI_10012667	superfamily	243034	775	893	2.90E-06	47.3748	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#1747 - 	CGI_10012667	superfamily	243034	989	1085	3.04E-06	46.9896	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#1747 - 	CGI_10012667	superfamily	243034	9	102	0.000765354	39.6708	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#1748 - 	CGI_10012668	superfamily	241571	195	288	3.15E-15	69.7486	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1748 - 	CGI_10012668	superfamily	241571	50	168	1.81E-14	67.8226	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#1751 - 	CGI_10012671	superfamily	245815	33	513	0	953.717	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#1759 - 	CGI_10012680	superfamily	247725	205	317	7.45E-60	203.657	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1759 - 	CGI_10012680	superfamily	215882	125	229	2.90E-25	104.285	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#1759 - 	CGI_10012680	superfamily	220215	40	117	1.31E-21	92.2882	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#1759 - 	CGI_10012680	superfamily	192138	328	374	1.23E-07	51.0803	cl07378	FA superfamily	 - 	 - 	"FERM adjacent (FA); This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates."
Q#1761 - 	CGI_10002187	superfamily	245814	8	75	6.07E-07	43.2467	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1761 - 	CGI_10002187	superfamily	245814	91	131	0.00119136	34.4033	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1762 - 	CGI_10008685	superfamily	243092	430	708	2.89E-60	206.417	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1762 - 	CGI_10008685	superfamily	243074	347	391	4.77E-10	56.3609	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#1763 - 	CGI_10008686	superfamily	218753	4	355	4.37E-97	298.043	cl05390	Tcp11 superfamily	 - 	 - 	T-complex protein 11; This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the yeast Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants.
Q#1764 - 	CGI_10008687	superfamily	243095	237	460	3.33E-35	131.684	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#1764 - 	CGI_10008687	superfamily	243038	40	132	8.25E-26	101.67	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#1766 - 	CGI_10008689	superfamily	247907	91	224	1.73E-08	52.8057	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#1766 - 	CGI_10008689	superfamily	245213	412	449	0.000114028	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1766 - 	CGI_10008689	superfamily	245213	450	485	0.00138811	36.8458	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1766 - 	CGI_10008689	superfamily	248289	290	344	6.67E-13	63.9823	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#1766 - 	CGI_10008689	superfamily	248289	348	408	7.68E-09	52.4263	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#1770 - 	CGI_10008693	superfamily	243263	120	413	5.20E-55	201.097	cl02990	ASC superfamily	C	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#1772 - 	CGI_10002498	superfamily	248097	104	227	6.00E-26	98.4914	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#1772 - 	CGI_10002498	superfamily	248097	7	69	0.00294265	35.3186	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#1775 - 	CGI_10002646	superfamily	243119	167	213	0.00015376	38.1938	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#1778 - 	CGI_10002013	superfamily	242274	43	115	0.000116727	38.9326	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#1779 - 	CGI_10001004	superfamily	241677	73	113	0.00150725	36.6247	cl00197	cyclophilin superfamily	N	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#1779 - 	CGI_10001004	superfamily	241677	30	51	0.00839458	34.3135	cl00197	cyclophilin superfamily	C	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#1780 - 	CGI_10001005	superfamily	192529	32	87	7.77E-15	68.1229	cl10984	DUF2414 superfamily	 - 	 - 	Protein of unknown function (DUF2414); This is a family of proteins conserved from fungi to mammals. One mouse member is referred to as ELG protein but this is not a homologue of human ELG protein. The function is not known.
Q#1781 - 	CGI_10003222	superfamily	247856	441	495	4.25E-07	47.5425	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1781 - 	CGI_10003222	superfamily	246925	173	326	1.34E-18	85.4849	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#1782 - 	CGI_10003223	superfamily	246925	357	620	3.60E-17	82.0181	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#1782 - 	CGI_10003223	superfamily	247856	634	689	0.00199656	37.1421	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1783 - 	CGI_10003224	superfamily	241578	385	554	1.64E-19	87.2362	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#1783 - 	CGI_10003224	superfamily	247057	196	254	0.00272314	36.9309	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#1784 - 	CGI_10003225	superfamily	245596	236	421	2.94E-49	174.803	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#1786 - 	CGI_10003227	superfamily	242129	24	113	0.007049	34.7359	cl00832	DUF359 superfamily	N	 - 	Protein of unknown function (DUF359); This family of archaebacterial proteins are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Q#1787 - 	CGI_10021082	superfamily	243352	40	261	8.45E-82	249.433	cl03224	Porin3 superfamily	N	 - 	"Eukaryotic porin family that forms channels in the mitochondrial outer membrane; The porin family 3 contains two sub-families that play vital roles in the mitochondrial outer membrane, a translocase for unfolded pre-proteins (Tom40) and the voltage-dependent anion channel (VDAC) that regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane."
Q#1788 - 	CGI_10021084	superfamily	243035	140	260	2.60E-18	78.1153	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1789 - 	CGI_10021085	superfamily	243035	95	205	4.01E-26	98.4609	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#1789 - 	CGI_10021085	superfamily	245226	29	99	0.00848567	34.5034	cl10012	DnaQ_like_exo superfamily	NC	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#1790 - 	CGI_10021087	superfamily	247792	138	182	5.57E-07	47.8256	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#1790 - 	CGI_10021087	superfamily	243109	696	834	5.62E-08	51.9117	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#1790 - 	CGI_10021087	superfamily	216033	527	574	2.07E-05	43.4764	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#1790 - 	CGI_10021087	superfamily	241563	276	319	0.00336616	36.5463	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1791 - 	CGI_10021088	superfamily	243161	3	37	0.000383531	37.759	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#1795 - 	CGI_10021094	superfamily	243056	112	320	1.93E-61	205.286	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#1796 - 	CGI_10021095	superfamily	241563	60	95	0.000770051	35.3907	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1797 - 	CGI_10021096	superfamily	243092	27	130	0.000782312	38.8552	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1798 - 	CGI_10021097	superfamily	241563	37	73	0.000151298	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1798 - 	CGI_10021097	superfamily	110440	502	528	0.00285985	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1799 - 	CGI_10021098	superfamily	219295	20	133	4.05E-11	56.4332	cl06225	DUF1358 superfamily	 - 	 - 	Protein of unknown function (DUF1358); This family consists of several hypothetical eukaryotic proteins of around 125 residues in length. The function of this family is unknown.
Q#1800 - 	CGI_10021099	superfamily	216554	107	233	2.04E-37	134.914	cl15977	zf-DHHC superfamily	C	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#1801 - 	CGI_10021100	superfamily	241563	59	95	0.000105352	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1801 - 	CGI_10021100	superfamily	110440	484	510	0.00564133	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1803 - 	CGI_10021103	superfamily	241563	59	95	5.32E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1803 - 	CGI_10021103	superfamily	110440	486	512	0.00073894	37.7725	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1803 - 	CGI_10021103	superfamily	110440	527	554	0.00866407	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1808 - 	CGI_10021108	superfamily	217293	1	156	5.51E-32	119.66	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1808 - 	CGI_10021108	superfamily	202474	163	270	7.84E-15	71.1457	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#1809 - 	CGI_10021109	superfamily	217293	374	573	2.32E-38	142.387	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#1809 - 	CGI_10021109	superfamily	202474	581	689	6.81E-15	73.8421	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#1810 - 	CGI_10021110	superfamily	245312	153	256	0.00340049	37.2191	cl10482	KefB superfamily	C	 - 	"Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]"
Q#1811 - 	CGI_10021111	superfamily	243072	91	215	1.45E-36	134.819	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1811 - 	CGI_10021111	superfamily	243072	157	285	1.78E-27	109.01	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1811 - 	CGI_10021111	superfamily	243072	31	149	9.97E-26	104.003	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1814 - 	CGI_10021114	superfamily	246680	19	74	1.03E-05	43.3444	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#1815 - 	CGI_10021115	superfamily	246680	11	77	4.45E-08	50.278	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#1816 - 	CGI_10021116	superfamily	246680	43	100	0.000963233	37.1812	cl14633	DD_superfamily superfamily	N	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#1817 - 	CGI_10021117	superfamily	247743	376	512	3.99E-28	110.699	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1817 - 	CGI_10021117	superfamily	247743	10	86	1.07E-09	56.7707	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1820 - 	CGI_10021120	superfamily	247743	356	393	1.58E-09	55.6151	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1821 - 	CGI_10021121	superfamily	218536	29	99	0.0045042	33.4724	cl05038	AAR2 superfamily	C	 - 	AAR2 protein; This family consists of several eukaryotic AAR2-like proteins. The yeast protein AAR2 is involved in splicing pre-mRNA of the a1 cistron and other genes that are important for cell growth.
Q#1823 - 	CGI_10021123	superfamily	215859	440	643	9.54E-49	170.09	cl18347	Peptidase_S9 superfamily	 - 	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#1825 - 	CGI_10021125	superfamily	208690	705	1025	2.74E-157	471.471	cl07396	CRM1_C superfamily	 - 	 - 	"CRM1 C terminal; CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat."
Q#1825 - 	CGI_10021125	superfamily	219817	118	263	1.88E-45	161.632	cl07129	Xpo1 superfamily	 - 	 - 	"Exportin 1-like protein; The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus."
Q#1825 - 	CGI_10021125	superfamily	243689	43	107	2.39E-11	61.1053	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#1826 - 	CGI_10021126	superfamily	220818	299	661	1.71E-36	140.685	cl11215	UPF0564 superfamily	 - 	 - 	"Uncharacterized protein family UPF0564; This family of proteins has no known function. However, one of the members is annotated as an EF-hand family protein."
Q#1827 - 	CGI_10021127	superfamily	247868	2	414	9.92E-63	209.04	cl17314	PRK07608 superfamily	 - 	 - 	ubiquinone biosynthesis hydroxylase family protein; Provisional
Q#1828 - 	CGI_10021128	superfamily	202558	1	256	7.69E-136	409.427	cl03915	XRN_N superfamily	 - 	 - 	"XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalyzing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus."
Q#1829 - 	CGI_10021129	superfamily	241599	157	214	1.16E-22	89.61	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#1832 - 	CGI_10021132	superfamily	241563	61	99	0.000429596	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1833 - 	CGI_10021133	superfamily	215821	28	118	3.00E-09	50.7019	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#1835 - 	CGI_10003618	superfamily	241874	22	397	6.28E-40	153.12	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1835 - 	CGI_10003618	superfamily	241874	488	579	2.06E-08	56.0501	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1836 - 	CGI_10003619	superfamily	241874	138	405	6.57E-32	129.238	cl00456	SLC5-6-like_sbd superfamily	NC	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1836 - 	CGI_10003619	superfamily	241874	496	587	3.45E-09	58.3613	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1837 - 	CGI_10003620	superfamily	203591	93	223	4.29E-28	111.309	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#1838 - 	CGI_10003621	superfamily	203990	53	115	6.72E-06	41.1383	cl07882	Cmc1 superfamily	 - 	 - 	Cytochrome c oxidase biogenesis protein Cmc1 like; Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Q#1839 - 	CGI_10003622	superfamily	247786	15	278	1.04E-116	340.01	cl17232	F420_oxidored superfamily	 - 	 - 	NADP oxidoreductase coenzyme F420-dependent; NADP oxidoreductase coenzyme F420-dependent.  
Q#1840 - 	CGI_10002904	superfamily	248264	114	277	4.40E-48	159.325	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#1840 - 	CGI_10002904	superfamily	222263	39	126	3.29E-08	49.6237	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#1841 - 	CGI_10002905	superfamily	247725	29	156	1.35E-60	190.622	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1842 - 	CGI_10002906	superfamily	248097	9	119	2.06E-25	93.869	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#1843 - 	CGI_10002907	superfamily	248097	57	181	2.44E-28	103.499	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#1845 - 	CGI_10004107	superfamily	244906	87	152	6.78E-26	103.759	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#1846 - 	CGI_10004108	superfamily	241596	225	277	6.08E-13	65.6983	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#1847 - 	CGI_10004109	superfamily	243157	5	88	1.53E-20	85.0775	cl02720	PB1 superfamily	 - 	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#1847 - 	CGI_10004109	superfamily	241643	347	383	0.00758305	33.9631	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#1848 - 	CGI_10004110	superfamily	241760	110	151	4.05E-23	91.5525	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#1848 - 	CGI_10004110	superfamily	243157	3	89	6.85E-35	125.138	cl02720	PB1 superfamily	 - 	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#1850 - 	CGI_10004649	superfamily	241609	367	433	3.02E-25	98.219	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1850 - 	CGI_10004649	superfamily	241568	323	358	0.0032152	35.5164	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#1851 - 	CGI_10004650	superfamily	241609	134	197	2.33E-21	84.3519	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#1851 - 	CGI_10004650	superfamily	241568	85	120	0.00249783	34.0393	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#1852 - 	CGI_10004651	superfamily	248097	105	180	6.03E-09	53.0378	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#1853 - 	CGI_10004652	superfamily	247743	2759	2922	4.30E-10	61.3931	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1853 - 	CGI_10004652	superfamily	247743	3111	3201	2.84E-05	46.3703	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1853 - 	CGI_10004652	superfamily	193257	3828	4055	2.84E-44	164.388	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#1853 - 	CGI_10004652	superfamily	222302	1186	1303	4.79E-27	110.604	cl16342	DUF4151 superfamily	 - 	 - 	Domain of unknown function (DUF4151); This domain is found on dynein heavy chain proteins. The exact function is not known but it is conserved from plants to Sch. pombe to human.
Q#1853 - 	CGI_10004652	superfamily	193253	3570	3811	8.55E-21	96.6445	cl15084	MT superfamily	N	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#1853 - 	CGI_10004652	superfamily	193253	3389	3549	2.10E-14	76.9993	cl15084	MT superfamily	C	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#1853 - 	CGI_10004652	superfamily	247743	2411	2551	1.10E-12	68.8612	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#1854 - 	CGI_10004653	superfamily	248097	31	135	4.00E-13	61.5122	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#1856 - 	CGI_10017595	superfamily	241874	7	421	3.56E-51	183.14	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1857 - 	CGI_10017596	superfamily	241874	1	66	5.41E-17	76.7509	cl00456	SLC5-6-like_sbd superfamily	NC	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1857 - 	CGI_10017596	superfamily	241874	64	99	0.00817001	34.379	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#1859 - 	CGI_10017598	superfamily	247744	75	276	1.07E-27	107.057	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#1860 - 	CGI_10017599	superfamily	243072	110	235	6.22E-30	112.477	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1860 - 	CGI_10017599	superfamily	243072	176	302	3.06E-25	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1860 - 	CGI_10017599	superfamily	243072	15	136	1.33E-14	70.105	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1860 - 	CGI_10017599	superfamily	243073	382	417	2.95E-09	52.8577	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#1861 - 	CGI_10017600	superfamily	242889	193	293	2.77E-20	83.8065	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#1863 - 	CGI_10017602	superfamily	245213	102	132	0.00555043	32.6086	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#1865 - 	CGI_10017604	superfamily	245870	14	140	1.07E-13	69.2698	cl12097	DUF1772 superfamily	 - 	 - 	Domain of unknown function (DUF1772); This domain is of unknown function.
Q#1865 - 	CGI_10017604	superfamily	152105	156	277	3.41E-10	58.3131	cl13169	WBP-1 superfamily	 - 	 - 	"WW domain-binding protein 1; This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain."
Q#1866 - 	CGI_10017605	superfamily	245870	38	149	5.42E-09	50.3951	cl12097	DUF1772 superfamily	 - 	 - 	Domain of unknown function (DUF1772); This domain is of unknown function.
Q#1867 - 	CGI_10017606	superfamily	243948	15	213	1.16E-15	73.0928	cl04955	LanC_like superfamily	C	 - 	"LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans), in addition to  2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition. A related domain is also present in LanM and other pro- and eukaryotic proteins of unknown function."
Q#1869 - 	CGI_10017608	superfamily	149077	55	117	2.38E-06	43.7673	cl06719	TMC superfamily	 - 	 - 	"TMC domain; These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters."
Q#1871 - 	CGI_10017610	superfamily	245201	9	290	0	578.457	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1872 - 	CGI_10017611	superfamily	243072	515	637	4.79E-33	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1872 - 	CGI_10017611	superfamily	243072	183	301	2.31E-23	97.069	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1872 - 	CGI_10017611	superfamily	243072	46	171	9.77E-20	86.6686	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1872 - 	CGI_10017611	superfamily	247856	341	396	0.000237004	39.8385	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1873 - 	CGI_10017612	superfamily	241832	1	121	1.04E-34	119.542	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1875 - 	CGI_10017614	superfamily	247057	5	69	4.06E-36	127.414	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#1876 - 	CGI_10017615	superfamily	241622	18	96	2.46E-18	75.2958	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#1877 - 	CGI_10017616	superfamily	205477	310	368	2.02E-26	99.9101	cl16217	Telomere_Sde2_2 superfamily	 - 	 - 	"Telomere stability C-terminal; This short C-terminal domain is found in higher eukaryotes further downstream from the Sde2 family, pfam13019. It is found in all Sde2-related proteins except those from fission yeast, fly, and mosquito. Its exact function in telomere formation and maintenance has not yet been established."
Q#1878 - 	CGI_10017617	superfamily	241832	33	178	1.11E-62	193.548	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#1879 - 	CGI_10017618	superfamily	241672	355	775	9.57E-123	378.282	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#1879 - 	CGI_10017618	superfamily	243146	236	283	2.14E-07	48.8247	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1879 - 	CGI_10017618	superfamily	243146	183	233	1.92E-06	46.1283	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1879 - 	CGI_10017618	superfamily	243146	49	92	0.000227907	39.9522	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#1880 - 	CGI_10017619	superfamily	243092	231	349	8.01E-14	70.8268	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1882 - 	CGI_10017621	superfamily	241593	37	185	2.08E-09	55.7306	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#1884 - 	CGI_10017623	superfamily	241975	92	137	2.16E-12	60.245	cl00605	RNase_P_Rpp14 superfamily	N	 - 	"Rpp14/Pop5 family; tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. This protein is known as Pop5 in eukaryotes."
Q#1885 - 	CGI_10017624	superfamily	247868	295	348	2.27E-07	51.3634	cl17314	PRK07608 superfamily	N	 - 	ubiquinone biosynthesis hydroxylase family protein; Provisional
Q#1885 - 	CGI_10017624	superfamily	247868	106	333	0.000152572	42.4508	cl17314	PRK07608 superfamily	NC	 - 	ubiquinone biosynthesis hydroxylase family protein; Provisional
Q#1888 - 	CGI_10017627	superfamily	248458	320	439	2.15E-08	54.6273	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1888 - 	CGI_10017627	superfamily	248458	131	207	4.32E-08	53.4717	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1890 - 	CGI_10005309	superfamily	241563	71	104	1.82E-05	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1890 - 	CGI_10005309	superfamily	241563	21	59	0.000813494	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1892 - 	CGI_10005311	superfamily	243068	171	302	9.55E-09	54.7002	cl02523	Zona_pellucida superfamily	N	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#1894 - 	CGI_10005313	superfamily	241563	3	37	4.79E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1895 - 	CGI_10005314	superfamily	243400	114	495	0	640.173	cl03362	AICARFT_IMPCHas superfamily	 - 	 - 	"AICARFT/IMPCHase bienzyme; This is a family of bifunctional enzymes catalyzing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalyzed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase EC:2.1.2.3 (AICARFT), this enzyme catalyzes the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate. This is catalyzed by a pair of C-terminal deaminase fold domains in the protein, where the active site is formed by the dimeric interface of two monomeric units. The last step is catalyzed by the N-terminal IMP (Inosine monophosphate) cyclohydrolase domain EC:3.5.4.10 (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP."
Q#1895 - 	CGI_10005314	superfamily	241720	15	104	1.60E-41	147.746	cl00245	MGS-like superfamily	N	 - 	"MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site."
Q#1898 - 	CGI_10017289	superfamily	150884	34	132	7.30E-42	142.659	cl10958	Med19 superfamily	C	 - 	Mediator of RNA pol II transcription subunit 19; Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators.
Q#1899 - 	CGI_10017291	superfamily	247068	149	243	1.65E-20	84.6725	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#1899 - 	CGI_10017291	superfamily	247068	56	137	4.00E-14	67.3385	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#1899 - 	CGI_10017291	superfamily	247068	255	315	8.06E-06	43.4562	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#1900 - 	CGI_10017292	superfamily	242064	423	515	2.76E-57	188.122	cl00748	Ribosomal_L32_L32e superfamily	 - 	 - 	"Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea."
Q#1901 - 	CGI_10017293	superfamily	246680	259	330	5.92E-05	40.3966	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#1901 - 	CGI_10017293	superfamily	245874	35	129	4.85E-12	61.2882	cl12111	TNFR superfamily	 - 	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#1902 - 	CGI_10017294	superfamily	247637	25	40	0.00890379	31.6977	cl16912	MDR superfamily	NC	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#1904 - 	CGI_10017296	superfamily	245814	27	107	1.07E-16	69.7358	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1905 - 	CGI_10017297	superfamily	245814	237	300	1.59E-06	45.2163	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1905 - 	CGI_10017297	superfamily	247807	125	217	0.00135482	36.5042	cl17253	AAA_17 superfamily	 - 	 - 	AAA domain; AAA domain.  
Q#1907 - 	CGI_10017299	superfamily	245814	251	331	1.34E-15	70.5062	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1907 - 	CGI_10017299	superfamily	245814	51	118	2.46E-15	69.3579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1907 - 	CGI_10017299	superfamily	245814	148	214	1.77E-07	48.2979	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1909 - 	CGI_10017302	superfamily	243134	354	473	7.50E-36	131.232	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1909 - 	CGI_10017302	superfamily	243134	29	189	6.10E-31	117.75	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1909 - 	CGI_10017302	superfamily	243134	510	610	5.07E-26	103.883	cl02663	Fasciclin superfamily	N	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1909 - 	CGI_10017302	superfamily	243134	226	321	1.26E-23	96.9495	cl02663	Fasciclin superfamily	N	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1910 - 	CGI_10017303	superfamily	243134	29	148	2.55E-37	130.077	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1910 - 	CGI_10017303	superfamily	243134	185	283	2.77E-24	95.0235	cl02663	Fasciclin superfamily	N	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1911 - 	CGI_10017304	superfamily	243134	29	148	1.15E-37	131.232	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1911 - 	CGI_10017304	superfamily	243134	185	280	4.58E-25	97.3347	cl02663	Fasciclin superfamily	N	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#1912 - 	CGI_10017305	superfamily	246908	288	359	2.11E-10	56.6951	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#1914 - 	CGI_10017307	superfamily	202388	114	221	1.68E-48	156.688	cl03708	Sod_Fe_C superfamily	 - 	 - 	"Iron/manganese superoxide dismutases, C-terminal domain; superoxide dismutases (SODs) catalyze the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold."
Q#1914 - 	CGI_10017307	superfamily	200985	28	109	8.72E-34	117.773	cl02809	Sod_Fe_N superfamily	 - 	 - 	"Iron/manganese superoxide dismutases, alpha-hairpin domain; superoxide dismutases (SODs) catalyze the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?"
Q#1916 - 	CGI_10017309	superfamily	247725	217	313	1.09E-69	221.737	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#1916 - 	CGI_10017309	superfamily	215882	110	223	1.53E-32	121.234	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#1916 - 	CGI_10017309	superfamily	220215	26	103	2.96E-22	91.5178	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#1917 - 	CGI_10017310	superfamily	220668	37	434	4.41E-134	395.62	cl10953	Tmp39 superfamily	 - 	 - 	Putative transmembrane protein; This is a family of conserved proteins found from worms to humans. They are putative transmembrane proteins but the function is unknown.
Q#1918 - 	CGI_10017311	superfamily	219739	38	297	4.70E-69	221.882	cl06991	PIH1 superfamily	 - 	 - 	pre-RNA processing PIH1/Nop17; This domain is involved in pre-rRNA processing. It has has been shown to be required either for nucleolar retention or correct assembly of the box C/D snoRNP in Saccharomyces cerevisiae. The C-terminal region of this family has similarity to the CS domain pfam04969.
Q#1920 - 	CGI_10017313	superfamily	247684	15	35	7.98E-06	41.5084	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#1921 - 	CGI_10017314	superfamily	243040	156	274	2.86E-23	92.1846	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#1921 - 	CGI_10017314	superfamily	243040	24	130	3.37E-23	91.7994	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#1923 - 	CGI_10017316	superfamily	243109	8	72	9.67E-07	47.8824	cl02614	SPRY superfamily	C	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#1924 - 	CGI_10017317	superfamily	241583	211	361	4.35E-29	113.238	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#1924 - 	CGI_10017317	superfamily	216572	57	166	1.24E-09	55.3587	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#1925 - 	CGI_10017318	superfamily	243072	902	1023	8.73E-23	97.4542	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	2054	2160	4.09E-22	95.5282	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	2243	2358	8.07E-22	94.7578	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1764	1878	8.71E-22	94.3726	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1572	1687	1.30E-21	93.9874	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1859	1974	2.28E-21	93.217	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	2113	2230	3.28E-21	92.8318	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1413	1527	5.02E-21	92.4466	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1347	1463	2.18E-20	90.5206	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1920	2038	4.44E-20	89.7502	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1102	1217	1.50E-19	88.2094	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1636	1782	7.60E-16	77.0386	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	1200	1336	2.51E-13	69.7198	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	243072	973	1114	1.79E-12	67.0234	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#1925 - 	CGI_10017318	superfamily	248357	227	305	0.000521648	42.4065	cl17803	FMN_bind_2 superfamily	C	 - 	"Putative FMN-binding domain; In Bacillus subtilis, family member PAI 2/ORF-2 was found to be essential for growth. The SUPERFAMILY database finds that this domain is related to FMN-binding domains, suggesting this protein is also FMN-binding."
Q#1929 - 	CGI_10001890	superfamily	243091	2	49	3.51E-09	49.798	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#1930 - 	CGI_10001891	superfamily	243091	45	93	3.98E-09	49.0276	cl02566	SET superfamily	C	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#1932 - 	CGI_10002146	superfamily	241583	46	154	1.34E-22	89.6051	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#1935 - 	CGI_10004162	superfamily	216897	77	156	8.59E-16	71.5585	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#1935 - 	CGI_10004162	superfamily	216897	20	59	2.31E-09	53.4541	cl03463	Gal_Lectin superfamily	N	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#1936 - 	CGI_10004163	superfamily	220965	173	302	9.45E-26	98.6824	cl12631	DUF2870 superfamily	 - 	 - 	Protein of unknown function (DUF2870); This is a eukaryotic family of proteins with unknown function.
Q#1937 - 	CGI_10004164	superfamily	241659	156	233	1.13E-14	66.3895	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#1937 - 	CGI_10004164	superfamily	241659	51	125	4.29E-12	59.4559	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#1938 - 	CGI_10004165	superfamily	241659	57	122	2.69E-16	71.0119	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#1938 - 	CGI_10004165	superfamily	241659	153	231	1.55E-14	66.0043	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#1939 - 	CGI_10004166	superfamily	241659	44	121	2.31E-14	63.6931	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#1940 - 	CGI_10004167	superfamily	241643	377	411	0.000454299	39.3647	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#1940 - 	CGI_10004167	superfamily	219122	901	1172	3.01E-56	197.517	cl05933	DUF1162 superfamily	 - 	 - 	Protein of unknown function (DUF1162); This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins.
Q#1941 - 	CGI_10004168	superfamily	219797	155	738	2.83E-171	513.016	cl09596	ACC_central superfamily	 - 	 - 	"Acetyl-CoA carboxylase, central region; The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyzes the rate-limiting step in this process."
Q#1941 - 	CGI_10004168	superfamily	219797	19	85	1.22E-09	60.407	cl09596	ACC_central superfamily	N	 - 	"Acetyl-CoA carboxylase, central region; The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyzes the rate-limiting step in this process."
Q#1942 - 	CGI_10000340	superfamily	248458	1	130	4.23E-06	43.8417	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#1943 - 	CGI_10004523	superfamily	241574	496	651	2.92E-52	181.245	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#1943 - 	CGI_10004523	superfamily	241584	139	263	0.00066345	38.6315	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#1943 - 	CGI_10004523	superfamily	241584	38	126	0.00281452	36.7055	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#1944 - 	CGI_10004524	superfamily	192535	46	250	0.00342204	37.9606	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#1945 - 	CGI_10004525	superfamily	238191	1	419	7.01E-95	297.707	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#1946 - 	CGI_10004526	superfamily	238191	1	392	8.16E-93	290.388	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#1947 - 	CGI_10004527	superfamily	241743	66	208	1.90E-23	92.6362	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#1948 - 	CGI_10003169	superfamily	202587	288	325	7.67E-14	64.9166	cl03974	EB1 superfamily	 - 	 - 	"EB1-like C-terminal motif; This motif is found at the C-terminus of proteins that are related to the EB1 protein. The EB1 proteins contain an N-terminal CH domain pfam00307. The human EB1 protein was originally discovered as a protein interacting with the C-terminus of the APC protein. This interaction is often disrupted in colon cancer, due to deletions affecting the APC C-terminus. Several EB1 orthologues are also included in this family. The interaction between EB1 and APC has been shown to have a potent synergistic effect on microtubule polymerisation. Neither of EB1 or APC alone has this effect. It is thought that EB1 targets APC to the + ends of microtubules, where APC promotes microtubule polymerisation. This process is regulated by APC phosphorylation by Cdc2, which disrupts APC-EB1 binding. Human EB1 protein can functionally substitute for the yeast EB1 homologue Mal3. In addition, Mal3 can substitute for human EB1 in promoting microtubule polymerisation with APC."
Q#1948 - 	CGI_10003169	superfamily	241559	77	191	6.20E-11	58.4448	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#1949 - 	CGI_10003170	superfamily	241884	1	192	8.78E-115	328.005	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#1950 - 	CGI_10003171	superfamily	241755	3	337	3.29E-165	468.715	cl00288	EPT_RTPC-like superfamily	 - 	 - 	"This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while  RTPC has 3 similar repeats with a 4th slightly different domain inserted between the 2nd and 3rd repeat. They evidently share the same active site location, although the catalytic residues differ."
Q#1951 - 	CGI_10003172	superfamily	243092	44	363	2.30E-39	143.244	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#1952 - 	CGI_10003173	superfamily	248305	127	459	4.62E-95	307.346	cl17751	Glyco_transf_22 superfamily	C	 - 	Alg9-like mannosyltransferase family; Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Q#1952 - 	CGI_10003173	superfamily	248305	562	697	6.32E-28	117.442	cl17751	Glyco_transf_22 superfamily	N	 - 	Alg9-like mannosyltransferase family; Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Q#1953 - 	CGI_10003174	superfamily	247740	555	857	1.11E-178	521.074	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#1953 - 	CGI_10003174	superfamily	248054	216	261	2.93E-06	45.926	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#1954 - 	CGI_10004989	superfamily	241583	209	448	2.29E-79	256.532	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#1954 - 	CGI_10004989	superfamily	216572	40	137	2.11E-07	49.9659	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#1955 - 	CGI_10004990	superfamily	245226	52	173	3.39E-13	63.0884	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#1956 - 	CGI_10004991	superfamily	247736	59	120	1.36E-06	42.1688	cl17182	NAT_SF superfamily	N	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#1957 - 	CGI_10004992	superfamily	241547	42	277	7.67E-97	288.014	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#1960 - 	CGI_10002604	superfamily	241563	66	100	1.99E-05	42.2744	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1960 - 	CGI_10002604	superfamily	110440	478	502	0.00960455	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#1962 - 	CGI_10004667	superfamily	245882	3	345	2.28E-154	444.041	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#1965 - 	CGI_10004670	superfamily	241568	427	485	4.74E-06	44.376	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#1967 - 	CGI_10022335	superfamily	241600	7	175	1.51E-72	220.19	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1968 - 	CGI_10022336	superfamily	241600	12	128	2.49E-48	164.336	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1968 - 	CGI_10022336	superfamily	241600	150	191	1.98E-17	78.8215	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1969 - 	CGI_10022338	superfamily	241600	4	189	1.18E-79	238.679	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1971 - 	CGI_10022340	superfamily	241600	5	217	8.99E-89	263.332	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#1973 - 	CGI_10022342	superfamily	247856	66	85	0.00444169	31.7493	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#1974 - 	CGI_10022343	superfamily	241567	105	283	4.26E-32	125.02	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#1975 - 	CGI_10022344	superfamily	241567	741	993	3.60E-33	129.643	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#1976 - 	CGI_10022345	superfamily	241563	14	46	0.00491065	34.9556	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#1977 - 	CGI_10022346	superfamily	243050	493	544	6.13E-31	114.358	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#1977 - 	CGI_10022346	superfamily	243050	375	426	1.06E-30	113.638	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#1977 - 	CGI_10022346	superfamily	243050	434	486	5.71E-30	111.658	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#1977 - 	CGI_10022346	superfamily	243050	316	368	4.94E-25	98.168	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#1977 - 	CGI_10022346	superfamily	217602	108	187	2.92E-06	46.8385	cl04141	Paxillin superfamily	N	 - 	Paxillin family; Paxillin family.  
Q#1978 - 	CGI_10022347	superfamily	245843	11	108	4.41E-56	171.653	cl12033	Spt4 superfamily	 - 	 - 	"Transcription elongation factor Spt4; Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles.   Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus.   Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 complex. Spt4 homolog is not found in bacteria."
Q#1979 - 	CGI_10022348	superfamily	247755	1362	1582	2.86E-111	352.181	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#1979 - 	CGI_10022348	superfamily	247755	755	960	2.80E-103	329.045	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#1979 - 	CGI_10022348	superfamily	216049	322	585	5.12E-21	95.0453	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#1979 - 	CGI_10022348	superfamily	216049	1144	1268	1.60E-13	71.5482	cl18356	ABC_membrane superfamily	C	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#1986 - 	CGI_10022355	superfamily	245814	906	971	1.05E-05	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1986 - 	CGI_10022355	superfamily	245814	811	878	0.00615667	37.0835	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1986 - 	CGI_10022355	superfamily	245814	1090	1172	4.79E-12	64.4488	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1986 - 	CGI_10022355	superfamily	245814	1001	1063	5.29E-11	60.8835	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#1986 - 	CGI_10022355	superfamily	204945	1557	1592	5.96E-06	45.8412	cl13890	Smoothelin superfamily	N	 - 	"Smoothelin cytoskeleton protein; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00307. Smoothelin is a cytoskeletal protein specifically expressed in differentiated smooth muscle cells and has been shown to co-localize with smooth muscle alpha actin."
Q#1987 - 	CGI_10022356	superfamily	241559	2	102	2.01E-24	90.4479	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#1993 - 	CGI_10022362	superfamily	243039	233	368	1.50E-64	205.042	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#1993 - 	CGI_10022362	superfamily	190233	135	194	1.22E-14	68.2498	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#1993 - 	CGI_10022362	superfamily	190233	26	79	1.43E-07	48.2194	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#1995 - 	CGI_10022364	superfamily	245819	716	859	5.96E-48	168.527	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#1995 - 	CGI_10022364	superfamily	245201	417	643	4.92E-25	104.626	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#1995 - 	CGI_10022364	superfamily	245225	26	316	5.57E-33	131.601	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#1995 - 	CGI_10022364	superfamily	219526	655	702	3.79E-06	47.2287	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#2001 - 	CGI_10022372	superfamily	247743	1438	1583	7.59E-07	50.9927	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#2001 - 	CGI_10022372	superfamily	247792	3072	3111	0.00507477	38.2589	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2002 - 	CGI_10022373	superfamily	247916	265	320	2.46E-08	52.3851	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#2003 - 	CGI_10022374	superfamily	242251	27	122	0.000760474	34.9527	cl01015	FUN14 superfamily	 - 	 - 	FUN14 family; This family of short proteins are found in eukaryotes and some archaea. Although the function of these proteins is not known they may contain transmembrane helices.
Q#2005 - 	CGI_10024709	superfamily	245201	414	618	8.32E-18	83.4401	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2005 - 	CGI_10024709	superfamily	247684	639	1047	3.55E-58	208.3	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2007 - 	CGI_10024711	superfamily	243058	878	972	1.83E-06	47.3091	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#2007 - 	CGI_10024711	superfamily	218493	13	160	3.98E-42	151.741	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#2013 - 	CGI_10024717	superfamily	241578	17	115	2.09E-05	44.3676	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2015 - 	CGI_10024719	superfamily	243035	315	351	0.000544474	39.5054	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2015 - 	CGI_10024719	superfamily	245309	52	157	0.00608558	35.9734	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#2019 - 	CGI_10024723	superfamily	243035	371	438	4.03E-05	42.607	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2021 - 	CGI_10024725	superfamily	241564	36	102	1.02E-25	98.1067	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#2021 - 	CGI_10024725	superfamily	241564	132	199	2.38E-24	94.2547	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#2022 - 	CGI_10024726	superfamily	243092	216	371	6.46E-21	91.2424	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2023 - 	CGI_10024727	superfamily	243120	13	140	2.58E-19	85.7084	cl02633	ARID superfamily	 - 	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#2023 - 	CGI_10024727	superfamily	190261	566	620	0.000105865	42.5358	cl03504	RFX_DNA_binding superfamily	 - 	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#2024 - 	CGI_10024728	superfamily	218913	135	293	5.47E-05	43.1201	cl18486	Trehalose_recp superfamily	N	 - 	"Trehalose receptor; In Drosophila, taste is perceived by gustatory neurons located in sensilla distributed on several different appendages throughout the body of the animal. This family represents the taste receptor sensitive to trehalose."
Q#2025 - 	CGI_10024729	superfamily	241607	80	104	0.00016849	35.3234	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#2025 - 	CGI_10024729	superfamily	241607	40	64	0.000255066	34.553	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#2026 - 	CGI_10024730	superfamily	218766	23	184	3.14E-27	102.53	cl05413	NDUF_B8 superfamily	 - 	 - 	"NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits."
Q#2028 - 	CGI_10024732	superfamily	241563	66	99	8.42E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2029 - 	CGI_10024733	superfamily	246680	10	82	4.95E-09	55.313	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#2029 - 	CGI_10024733	superfamily	241554	1173	1348	5.75E-49	174.381	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#2029 - 	CGI_10024733	superfamily	241752	1663	1783	1.99E-24	101.627	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#2029 - 	CGI_10024733	superfamily	247723	422	495	1.12E-09	57.2772	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2029 - 	CGI_10024733	superfamily	247723	510	579	7.47E-05	43.0308	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2029 - 	CGI_10024733	superfamily	247723	326	396	0.00126384	39.2077	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2029 - 	CGI_10024733	superfamily	247723	586	653	0.00175094	38.8225	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2030 - 	CGI_10024734	superfamily	247736	65	118	1.28E-08	49.5817	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#2030 - 	CGI_10024734	superfamily	247736	92	147	0.000142775	38.4646	cl17182	NAT_SF superfamily	N	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#2031 - 	CGI_10024735	superfamily	241572	13	85	7.65E-11	58.404	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#2033 - 	CGI_10024737	superfamily	247755	459	606	1.27E-75	243.566	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2034 - 	CGI_10024738	superfamily	150796	15	104	9.12E-32	109.134	cl10865	C6_DPF superfamily	 - 	 - 	Cysteine-rich domain; This is the N-terminal approximately 100 amino acids of a family of proteins found from nematodes to humans. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Q#2036 - 	CGI_10024740	superfamily	245864	285	457	3.10E-25	106.594	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#2036 - 	CGI_10024740	superfamily	245864	32	81	0.00171431	39.1838	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#2037 - 	CGI_10024741	superfamily	244859	98	325	5.36E-07	49.1069	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#2038 - 	CGI_10024742	superfamily	248347	1	225	1.15E-20	92.5316	cl17793	Peptidase_C69 superfamily	C	 - 	Peptidase family C69; Peptidase family C69.  
Q#2039 - 	CGI_10024743	superfamily	241810	36	118	6.98E-36	121.522	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#2039 - 	CGI_10024743	superfamily	201966	100	166	2.75E-34	117.332	cl03349	Ribosomal_L27e superfamily	N	 - 	Ribosomal L27e protein family; The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif. C-terminal region is represented by this family.
Q#2040 - 	CGI_10024744	superfamily	202711	47	213	2.33E-68	209.901	cl04190	Mob1_phocein superfamily	 - 	 - 	"Mob1/phocein family; Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin."
Q#2042 - 	CGI_10024746	superfamily	247941	54	230	1.60E-06	45.9665	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#2043 - 	CGI_10024747	superfamily	245864	34	348	4.58E-46	164.374	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#2044 - 	CGI_10024748	superfamily	243555	17	206	2.99E-19	86.291	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#2046 - 	CGI_10002738	superfamily	189857	68	155	3.40E-09	51.4818	cl07832	Caveolin superfamily	N	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#2047 - 	CGI_10002739	superfamily	189857	1	117	2.99E-33	115.04	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#2049 - 	CGI_10002741	superfamily	189857	3	123	5.17E-36	122.359	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#2050 - 	CGI_10002742	superfamily	247746	99	213	0.00105611	38.0082	cl17192	ATP-synt_B superfamily	 - 	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#2050 - 	CGI_10002742	superfamily	241563	62	103	0.00452125	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2053 - 	CGI_10008123	superfamily	241578	205	385	6.92E-46	162.77	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2053 - 	CGI_10008123	superfamily	207701	15	77	1.35E-17	80.4162	cl02699	VIT superfamily	N	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#2053 - 	CGI_10008123	superfamily	148333	670	779	2.72E-11	62.6838	cl05947	ITI_HC_C superfamily	C	 - 	"Inter-alpha-trypsin inhibitor heavy chain C-terminus; This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix. All family members contain the pfam00092 domain."
Q#2057 - 	CGI_10006631	superfamily	241596	83	138	2.10E-14	64.5427	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#2058 - 	CGI_10006632	superfamily	220691	118	232	0.00180177	38.3678	cl18569	7TM_GPCR_Srv superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#2059 - 	CGI_10006633	superfamily	217816	73	269	1.50E-59	190.958	cl18428	FSH1 superfamily	 - 	 - 	Serine hydrolase (FSH1); This is a family of serine hydrolases.
Q#2060 - 	CGI_10006634	superfamily	245601	32	334	8.68E-26	103.993	cl11399	HP superfamily	 - 	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#2061 - 	CGI_10006635	superfamily	243072	544	665	5.73E-31	119.796	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2061 - 	CGI_10006635	superfamily	243072	707	822	3.74E-23	97.4542	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2061 - 	CGI_10006635	superfamily	115363	88	153	1.77E-16	76.2565	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#2061 - 	CGI_10006635	superfamily	241760	162	205	1.59E-12	64.4019	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#2061 - 	CGI_10006635	superfamily	115363	233	297	1.05E-09	56.6114	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#2065 - 	CGI_10010082	superfamily	243092	299	610	6.87E-50	178.297	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2065 - 	CGI_10010082	superfamily	243092	70	378	3.21E-25	106.65	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2065 - 	CGI_10010082	superfamily	217837	747	854	1.48E-20	88.8037	cl04367	Utp12 superfamily	 - 	 - 	Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.
Q#2068 - 	CGI_10010085	superfamily	241597	76	147	8.48E-36	125.488	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#2068 - 	CGI_10010085	superfamily	152771	146	175	2.62E-05	41.4358	cl13733	SOXp superfamily	C	 - 	"SOX transcription factor; This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with pfam00505. There are two conserved sequence motifs: KKDK and LPG. This family is made up of SOX transcription factors. These are involved in upregulation of nestin, a neural promoter."
Q#2069 - 	CGI_10010086	superfamily	241666	95	336	1.31E-57	189.531	cl00184	CAS_like superfamily	 - 	 - 	"Clavaminic acid synthetase (CAS) -like;  CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to succinate and CO2"
Q#2071 - 	CGI_10010088	superfamily	241550	29	254	9.41E-103	301.144	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#2072 - 	CGI_10010089	superfamily	243116	519	702	1.72E-39	150.649	cl02626	DNA_pol_A superfamily	C	 - 	"Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase  beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains."
Q#2072 - 	CGI_10010089	superfamily	243116	682	829	2.84E-22	98.4523	cl02626	DNA_pol_A superfamily	N	 - 	"Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase  beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains."
Q#2073 - 	CGI_10010090	superfamily	246908	1044	1142	7.26E-42	150.197	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#2073 - 	CGI_10010090	superfamily	243073	1166	1213	2.55E-17	78.2153	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#2074 - 	CGI_10010091	superfamily	243072	12	100	7.66E-11	61.2454	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2074 - 	CGI_10010091	superfamily	247792	222	268	0.00448852	36.6548	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2075 - 	CGI_10010092	superfamily	243119	119	169	6.48E-05	38.1938	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#2075 - 	CGI_10010092	superfamily	243119	20	66	9.50E-05	37.7985	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#2077 - 	CGI_10016490	superfamily	248345	287	413	3.44E-12	64.197	cl17791	SAC3_GANP superfamily	N	 - 	"SAC3/GANP/Nin1/mts3/eIF-3 p25 family; This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits."
Q#2078 - 	CGI_10016491	superfamily	241733	24	109	2.39E-58	177.008	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#2079 - 	CGI_10016492	superfamily	241574	405	599	2.32E-82	264.063	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#2079 - 	CGI_10016492	superfamily	241574	689	751	0.000393842	41.4174	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#2083 - 	CGI_10016496	superfamily	242063	103	278	0.00315222	35.7366	cl00746	RDD superfamily	 - 	 - 	"RDD family; This family of proteins contain three highly conserved amino acids: one arginine and two aspartates, hence the name of RDD family. This region contains two predicted transmembrane regions. The arginine occurs at the N terminus of the first helix and the first aspartate occurs in the middle of this helix. The molecular function of this region is unknown. However this region may be involved in transport of an as yet unknown set of ligands (Bateman A pers. obs.)."
Q#2084 - 	CGI_10016497	superfamily	247736	76	127	0.000360472	36.0926	cl17182	NAT_SF superfamily	N	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#2087 - 	CGI_10016500	superfamily	247743	4	120	0.000206043	39.8756	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#2088 - 	CGI_10016501	superfamily	243034	153	262	1.08E-07	50.4564	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2090 - 	CGI_10016503	superfamily	243034	484	593	0.000139435	41.5968	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2090 - 	CGI_10016503	superfamily	243034	806	912	0.000579871	39.6708	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2091 - 	CGI_10016504	superfamily	245213	220	258	0.00963833	33.7642	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2093 - 	CGI_10016506	superfamily	245864	39	469	4.50E-36	138.18	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#2094 - 	CGI_10016507	superfamily	118716	17	190	1.96E-79	243.732	cl10882	Oscp1 superfamily	 - 	 - 	"Organic solute transport protein 1; Oscp1 is a family of proteins conserved from plants to humans. It is called organic solute transport protein or oxido-red- nitro domain-containing protein 1, however no reference could be find to confirm the function of the protein."
Q#2095 - 	CGI_10016508	superfamily	247637	1	330	5.78E-139	400.442	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#2096 - 	CGI_10016509	superfamily	247637	1	330	5.78E-139	400.442	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#2099 - 	CGI_10016512	superfamily	248012	58	168	6.17E-20	81.8552	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2100 - 	CGI_10016513	superfamily	248012	84	194	5.08E-17	75.692	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2102 - 	CGI_10016515	superfamily	243040	29	153	2.74E-58	192.709	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#2103 - 	CGI_10016516	superfamily	246936	247	369	7.28E-16	73.2936	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#2103 - 	CGI_10016516	superfamily	216595	131	200	2.40E-10	58.3458	cl03275	DUF21 superfamily	N	 - 	"Domain of unknown function DUF21; This transmembrane region has no known function. Many of the sequences in this family are annotated as hemolysins, however this is due to a similarity to Treponema hyodysenteriae hemolysin C that does not contain this domain. This domain is found in the N-terminus of the proteins adjacent to two intracellular CBS domains pfam00571."
Q#2104 - 	CGI_10003713	superfamily	241874	26	109	4.50E-10	55.1798	cl00456	SLC5-6-like_sbd superfamily	NC	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2105 - 	CGI_10003714	superfamily	241874	7	315	1.13E-120	367.962	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2105 - 	CGI_10003714	superfamily	241874	352	471	1.03E-10	62.5725	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2106 - 	CGI_10003715	superfamily	245608	84	292	8.50E-78	237.982	cl11421	FAA_hydrolase superfamily	 - 	 - 	"Fumarylacetoacetate (FAA) hydrolase family; This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase, encoded by mhpD in E. coli, is involved in the phenylpropionic acid pathway of E. coli and catalyzes the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli is involved in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida is a 4-Oxalocrotonate decarboxylase."
Q#2109 - 	CGI_10000725	superfamily	241802	5	34	0.00793326	34.3447	cl00342	Trp-synth-beta_II superfamily	NC	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#2113 - 	CGI_10001655	superfamily	247684	1	185	1.07E-35	130.475	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2115 - 	CGI_10001657	superfamily	247692	4	94	4.47E-12	60.7678	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#2117 - 	CGI_10007116	superfamily	245213	208	230	0.000296002	40.3126	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2120 - 	CGI_10007119	superfamily	245213	184	206	0.00418182	37.231	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2121 - 	CGI_10002984	superfamily	245874	115	178	1.09E-09	55.125	cl12111	TNFR superfamily	C	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#2121 - 	CGI_10002984	superfamily	245874	19	115	4.85E-07	47.421	cl12111	TNFR superfamily	 - 	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#2121 - 	CGI_10002984	superfamily	246680	300	365	0.000979893	36.9838	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#2122 - 	CGI_10002985	superfamily	246680	52	109	0.000951773	33.8482	cl14633	DD_superfamily superfamily	N	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#2123 - 	CGI_10002986	superfamily	243146	103	153	8.40E-09	52.2915	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2123 - 	CGI_10002986	superfamily	243074	23	58	1.73E-06	45.5753	cl02535	F-box-like superfamily	C	 - 	F-box-like; This is an F-box-like family.
Q#2123 - 	CGI_10002986	superfamily	243146	214	260	0.000413614	38.8095	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2123 - 	CGI_10002986	superfamily	243146	267	318	0.00108566	37.2687	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2124 - 	CGI_10002987	superfamily	219566	776	982	3.06E-59	202.478	cl06691	DUF1620 superfamily	 - 	 - 	Protein of unknown function (DUF1620); These sequences are mainly derived from predicted eukaryotic proteins. The region in question lies towards the C-terminus of these large proteins and is approximately 300 amino acid residues long.
Q#2128 - 	CGI_10001279	superfamily	241874	1	77	2.36E-25	103.139	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2128 - 	CGI_10001279	superfamily	241874	168	227	1.47E-06	47.1918	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2129 - 	CGI_10001280	superfamily	241874	8	47	3.71E-17	74.2494	cl00456	SLC5-6-like_sbd superfamily	NC	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2130 - 	CGI_10012753	superfamily	243948	51	410	1.46E-130	382.408	cl04955	LanC_like superfamily	 - 	 - 	"LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans), in addition to  2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition. A related domain is also present in LanM and other pro- and eukaryotic proteins of unknown function."
Q#2132 - 	CGI_10012755	superfamily	201708	1	33	0.000216982	37.0735	cl03146	Ribosomal_L9_N superfamily	N	 - 	"Ribosomal protein L9, N-terminal domain; Ribosomal protein L9, N-terminal domain.  "
Q#2133 - 	CGI_10012756	superfamily	243035	174	263	5.22E-15	68.8005	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2133 - 	CGI_10012756	superfamily	245309	58	149	0.00103063	36.318	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#2135 - 	CGI_10012759	superfamily	218541	105	450	2.37E-85	269.227	cl09364	MCD superfamily	 - 	 - 	"Malonyl-CoA decarboxylase (MCD); This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidized. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK)."
Q#2136 - 	CGI_10012760	superfamily	241688	2	327	2.17E-40	145.277	cl00210	Isoprenoid_Biosyn_C1 superfamily	 - 	 - 	"Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD."
Q#2140 - 	CGI_10012764	superfamily	248458	99	483	9.72E-17	80.4357	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#2143 - 	CGI_10012767	superfamily	247684	24	227	4.46E-26	104.281	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2144 - 	CGI_10012768	superfamily	247684	34	152	1.05E-29	111.985	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2145 - 	CGI_10012769	superfamily	247684	13	432	4.08E-73	241.413	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2148 - 	CGI_10012772	superfamily	243072	48	153	5.38E-26	104.388	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2151 - 	CGI_10012776	superfamily	241622	932	1002	3.85E-11	61.8138	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#2151 - 	CGI_10012776	superfamily	216901	603	791	4.72E-84	274.848	cl03466	Rap_GAP superfamily	 - 	 - 	Rap/ran-GAP; Rap/ran-GAP.  
Q#2151 - 	CGI_10012776	superfamily	221287	1455	1702	1.90E-13	71.001	cl13342	DUF3401 superfamily	 - 	 - 	"Domain of unknown function (DUF3401); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 231 to 250 amino acids in length. This domain is found associated with pfam02145, pfam00595."
Q#2151 - 	CGI_10012776	superfamily	248213	1686	1725	9.42E-05	42.5621	cl17659	DivIC superfamily	C	 - 	Septum formation initiator; DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil.
Q#2153 - 	CGI_10012778	superfamily	243035	35	159	1.32E-28	108.091	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2153 - 	CGI_10012778	superfamily	243035	293	374	1.57E-15	71.8821	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2153 - 	CGI_10012778	superfamily	243035	171	296	3.58E-22	90.3517	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2154 - 	CGI_10020123	superfamily	241609	294	372	6.51E-31	118.635	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#2154 - 	CGI_10020123	superfamily	241609	383	458	1.22E-27	109.39	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#2154 - 	CGI_10020123	superfamily	241609	543	626	1.00E-21	92.4411	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#2154 - 	CGI_10020123	superfamily	241609	464	539	1.76E-15	74.3367	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#2154 - 	CGI_10020123	superfamily	241613	791	825	6.10E-07	48.357	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#2154 - 	CGI_10020123	superfamily	241613	661	691	8.58E-06	44.8902	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#2154 - 	CGI_10020123	superfamily	246925	935	1139	6.60E-09	58.1358	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#2154 - 	CGI_10020123	superfamily	220695	1227	1451	6.16E-07	51.4255	cl18571	7TM_GPCR_Srx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#2154 - 	CGI_10020123	superfamily	220695	6	229	8.38E-05	44.8771	cl18571	7TM_GPCR_Srx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#2155 - 	CGI_10020124	superfamily	241609	117	192	4.58E-20	80.8851	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#2155 - 	CGI_10020124	superfamily	241609	74	105	4.42E-10	53.0786	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#2156 - 	CGI_10020125	superfamily	202715	118	218	2.65E-30	109.205	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#2157 - 	CGI_10020126	superfamily	245818	627	743	1.77E-34	129.599	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#2157 - 	CGI_10020126	superfamily	245818	121	219	1.77E-15	74.5159	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#2157 - 	CGI_10020126	superfamily	217750	838	891	1.05E-11	62.2114	cl04280	PAP_assoc superfamily	 - 	 - 	Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.
Q#2157 - 	CGI_10020126	superfamily	217750	275	328	2.17E-10	58.3594	cl04280	PAP_assoc superfamily	 - 	 - 	Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.
Q#2158 - 	CGI_10020127	superfamily	245226	967	1116	5.72E-84	269.74	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#2159 - 	CGI_10020128	superfamily	243077	25	79	8.45E-15	70.2669	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#2159 - 	CGI_10020128	superfamily	203591	249	385	1.02E-33	126.332	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#2159 - 	CGI_10020128	superfamily	203591	156	249	6.29E-05	42.3584	cl06275	DUF1399 superfamily	N	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#2160 - 	CGI_10020129	superfamily	203591	86	219	4.94E-36	130.569	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#2160 - 	CGI_10020129	superfamily	226728	184	258	1.07E-05	45.6909	cl18775	COG4278 superfamily	NC	 - 	Uncharacterized conserved protein [Function unknown]
Q#2162 - 	CGI_10020131	superfamily	241638	134	258	9.29E-12	59.6893	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#2163 - 	CGI_10020132	superfamily	201778	26	108	5.72E-13	64.1522	cl18219	GFO_IDH_MocA superfamily	N	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#2163 - 	CGI_10020132	superfamily	217272	123	230	1.62E-11	59.8556	cl18400	GFO_IDH_MocA_C superfamily	 - 	 - 	"Oxidoreductase family, C-terminal alpha/beta domain; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#2164 - 	CGI_10020133	superfamily	247725	1754	1892	1.13E-70	235.222	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2164 - 	CGI_10020133	superfamily	243096	1567	1748	4.25E-50	177.875	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#2164 - 	CGI_10020133	superfamily	247683	1479	1531	2.63E-33	125.186	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#2166 - 	CGI_10020135	superfamily	241600	435	646	3.16E-98	302.237	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2166 - 	CGI_10020135	superfamily	241600	259	383	2.30E-62	207.863	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2166 - 	CGI_10020135	superfamily	241600	17	151	9.63E-57	192.455	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2166 - 	CGI_10020135	superfamily	241600	184	218	0.000137942	42.4177	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2166 - 	CGI_10020135	superfamily	241600	161	190	0.00465548	37.6418	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2170 - 	CGI_10020139	superfamily	241647	113	143	0.000142067	38.2778	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#2172 - 	CGI_10020141	superfamily	216347	206	623	4.75E-129	389.973	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#2174 - 	CGI_10020143	superfamily	241547	77	305	1.61E-50	168.615	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#2176 - 	CGI_10020145	superfamily	241636	78	248	1.61E-56	181.247	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#2177 - 	CGI_10020146	superfamily	247723	26	96	6.45E-22	87.0423	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2177 - 	CGI_10020146	superfamily	247723	100	167	4.84E-15	68.1347	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2177 - 	CGI_10020146	superfamily	247723	205	272	5.25E-14	65.0531	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2178 - 	CGI_10020147	superfamily	247799	89	154	3.84E-15	69.8127	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#2178 - 	CGI_10020147	superfamily	247799	12	72	3.15E-13	64.5035	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#2178 - 	CGI_10020147	superfamily	247799	321	385	2.13E-10	56.3307	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#2178 - 	CGI_10020147	superfamily	247799	223	299	4.14E-08	49.8659	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#2179 - 	CGI_10020148	superfamily	241600	217	420	1.08E-55	185.137	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2179 - 	CGI_10020148	superfamily	192987	64	150	0.000233815	39.4779	cl13724	TMF_TATA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family."
Q#2180 - 	CGI_10020149	superfamily	246681	191	332	3.44E-55	179.205	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#2183 - 	CGI_10020152	superfamily	242274	10	158	5.13E-06	43.6541	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#2186 - 	CGI_10017321	superfamily	220601	1	305	1.22E-87	267.771	cl10846	TM231 superfamily	 - 	 - 	"Transmembrane protein 231; This is a family of transmembrane proteins, given the number 231, of unknown function. It is conserved in eukaryotes."
Q#2188 - 	CGI_10017323	superfamily	243146	295	341	5.61E-09	51.8934	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2188 - 	CGI_10017323	superfamily	243146	257	306	2.03E-06	44.8567	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2189 - 	CGI_10017324	superfamily	241874	1	129	9.51E-21	87.9468	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2190 - 	CGI_10017325	superfamily	241874	209	369	2.09E-57	194.648	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2190 - 	CGI_10017325	superfamily	241874	31	162	6.20E-51	179.682	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2192 - 	CGI_10017327	superfamily	243066	22	120	1.99E-11	58.8564	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#2195 - 	CGI_10017330	superfamily	216962	1	77	6.40E-34	113.94	cl03517	SRP14 superfamily	 - 	 - 	Signal recognition particle 14kD protein; The signal recognition particle (SRP) is a multimeric protein involved in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP14 and SRP9 form a complex essential for SRP RNA binding.
Q#2197 - 	CGI_10017332	superfamily	246669	4	129	8.88E-62	189.406	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#2198 - 	CGI_10017333	superfamily	247741	50	278	1.08E-75	233.192	cl17187	Aldolase_Class_I superfamily	 - 	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#2200 - 	CGI_10017335	superfamily	241842	55	150	7.12E-39	129.238	cl00400	Fe-S_biosyn superfamily	 - 	 - 	Iron-sulphur cluster biosynthesis; This family is involved in iron-sulphur cluster biosynthesis. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins.
Q#2201 - 	CGI_10017336	superfamily	247725	181	252	3.12E-27	107.772	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2201 - 	CGI_10017336	superfamily	220215	21	109	1.74E-12	64.5538	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#2204 - 	CGI_10017339	superfamily	150852	29	109	7.52E-24	95.4689	cl10926	KxDL superfamily	 - 	 - 	Uncharacterized conserved protein; This is a family of short proteins which are conserved over a region of 80 residues. There is a characteristic KxDL motif towards the C-terminus. The function is unknown.
Q#2208 - 	CGI_10017343	superfamily	245670	504	686	3.18E-66	223.973	cl11519	DENN superfamily	 - 	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#2208 - 	CGI_10017343	superfamily	243635	386	470	6.62E-20	87.39	cl04085	uDENN superfamily	 - 	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#2208 - 	CGI_10017343	superfamily	208095	763	833	5.13E-18	81.4859	cl04084	dDENN superfamily	 - 	 - 	dDENN domain; This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
Q#2208 - 	CGI_10017343	superfamily	245029	139	198	5.45E-05	43.7904	cl09190	MAPEG superfamily	N	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#2209 - 	CGI_10017344	superfamily	241555	4	162	5.24E-66	206.017	cl00020	GAT_1 superfamily	N	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#2210 - 	CGI_10017345	superfamily	247912	2	188	8.37E-10	57.8965	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#2212 - 	CGI_10017347	superfamily	247912	36	294	4.93E-20	89.0976	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#2212 - 	CGI_10017347	superfamily	221337	330	413	0.00925312	34.2147	cl13401	DUF3471 superfamily	 - 	 - 	"Domain of unknown function (DUF3471); This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144."
Q#2214 - 	CGI_10017349	superfamily	242232	338	392	6.85E-13	64.2202	cl00984	TM2 superfamily	C	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#2214 - 	CGI_10017349	superfamily	242232	203	255	1.55E-11	60.3682	cl00984	TM2 superfamily	C	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#2214 - 	CGI_10017349	superfamily	242232	125	174	2.86E-10	56.0272	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#2214 - 	CGI_10017349	superfamily	242232	263	311	4.06E-05	41.3896	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#2214 - 	CGI_10017349	superfamily	220708	413	474	0.00783375	35.0715	cl11017	WWbp superfamily	N	 - 	"WW-domain ligand protein; The WWbp domain is characterized by several short PY and PT-like motifs of the PPPPY form. These appear to bind directly to the WW domains of WWP1 and WWP2 and other such diverse proteins as dystrophin and YAP (Yes-associated protein). This is the WW-domain binding protein WWbp via PY and PY_like motifs. The presence of a phosphotyrosine residue in the pWBP-1 peptide abolishes WW domain binding which suggests a potential regulatory role for tyrosine phosphorylation in modulating WW domain-ligand interactions. Given the likelihood that WWP1 and WWP2 function as E3 ubiquitin-protein ligases, it is possible that initial substrate-specific recognition occurs via WW domain-substrate protein interaction followed by ubiquitin transfer and subsequent proteolysis. This domain lies just downstream of the GRAM (pfam02893) in many members."
Q#2215 - 	CGI_10017350	superfamily	242232	101	174	5.08E-14	64.6054	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#2216 - 	CGI_10017351	superfamily	216686	142	333	4.01E-53	176.36	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#2221 - 	CGI_10008344	superfamily	248264	113	169	1.50E-08	50.3134	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#2231 - 	CGI_10005609	superfamily	213107	12	50	1.43E-16	74.1941	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#2231 - 	CGI_10005609	superfamily	210118	252	274	0.00155406	36.5347	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#2231 - 	CGI_10005609	superfamily	210118	540	562	0.00561185	34.9939	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#2231 - 	CGI_10005609	superfamily	210118	492	513	0.00838641	34.6087	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#2232 - 	CGI_10005610	superfamily	199575	1	115	2.83E-51	168.942	cl15439	BTG superfamily	 - 	 - 	BTG family; BTG family.  
Q#2233 - 	CGI_10005611	superfamily	243082	338	517	7.44E-30	119.895	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#2233 - 	CGI_10005611	superfamily	197845	578	597	0.0035825	36.3502	cl11736	UIM superfamily	 - 	 - 	Ubiquitin-interacting motif; Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Q#2236 - 	CGI_10005614	superfamily	247684	37	458	1.39E-81	264.525	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2237 - 	CGI_10005615	superfamily	245226	49	133	5.18E-14	67.3586	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#2238 - 	CGI_10005616	superfamily	245226	187	223	0.00244689	36.1245	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#2240 - 	CGI_10005618	superfamily	247684	1	204	6.54E-46	162.832	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2242 - 	CGI_10013734	superfamily	247740	14	292	3.24E-178	497.154	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#2243 - 	CGI_10013735	superfamily	241555	15	222	6.15E-81	242.816	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#2244 - 	CGI_10013736	superfamily	247856	53	78	0.000185946	34.8309	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2245 - 	CGI_10013737	superfamily	241754	32	364	0	624.026	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#2249 - 	CGI_10013742	superfamily	242428	34	324	8.19E-50	176.42	cl01315	NRDE superfamily	 - 	 - 	"NRDE protein; In eukaryotes this family is predicted to play a role in protein secretion and Golgi organisation. In plants this family includes Solanum habrochaites Cwp, which is involved in water permeability in the cuticles of fruit. Mouse T10 has been found to be expressed during early embryogenesis in mice. This protein contains a conserved NRDE motif."
Q#2250 - 	CGI_10013743	superfamily	243035	226	337	2.22E-06	44.9182	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2250 - 	CGI_10013743	superfamily	243035	19	115	0.000828086	37.2142	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2251 - 	CGI_10013744	superfamily	241563	162	200	9.37E-05	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2252 - 	CGI_10013745	superfamily	241563	159	197	0.000121898	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2254 - 	CGI_10008723	superfamily	243157	3	82	2.14E-10	57.6729	cl02720	PB1 superfamily	 - 	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#2255 - 	CGI_10008724	superfamily	216878	16	116	7.60E-54	166.317	cl03452	DAD superfamily	 - 	 - 	"DAD family; Members of this family are thought to be integral membrane proteins. Some members of this family have been shown to cause apoptosis if mutated, these proteins are known as DAD for defender against death. The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation."
Q#2256 - 	CGI_10008725	superfamily	244906	624	700	3.67E-09	54.0684	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#2258 - 	CGI_10008727	superfamily	150815	7	54	3.96E-09	47.7817	cl10887	Phospho_p8 superfamily	 - 	 - 	"DNA-binding nuclear phosphoprotein p8; P8 is a short 80-82 amino acid protein that is conserved from nematodes to humans. It carries at least one protein kinase C domain suggesting a possible role in signal transduction and it is thought to be a phosphoprotein, but the sites of phosphorylation and the kinases involved remain to be determined."
Q#2259 - 	CGI_10008728	superfamily	243090	739	929	6.11E-25	104.152	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#2259 - 	CGI_10008728	superfamily	243090	964	1066	1.03E-13	69.7284	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#2259 - 	CGI_10008728	superfamily	243090	97	225	0.00302343	37.5901	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#2260 - 	CGI_10008729	superfamily	203990	501	556	4.19E-06	44.9903	cl07882	Cmc1 superfamily	C	 - 	Cytochrome c oxidase biogenesis protein Cmc1 like; Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Q#2261 - 	CGI_10008730	superfamily	218518	19	282	1.16E-19	86.6802	cl08436	CENP-N superfamily	N	 - 	"Kinetochore protein CHL4 like; CHL4 is a protein involved in chromosome segregation. It is a component of the central kinetochore which mediates the attachment of the centromere to the mitotic spindle. CENP-N is one of the components that assembles onto the CENP-A-nucleosome-associated (NAC) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC."
Q#2262 - 	CGI_10008731	superfamily	242010	21	193	4.29E-06	46.4047	cl00660	PRK01198 superfamily	C	 - 	V-type ATP synthase subunit C; Provisional
Q#2263 - 	CGI_10008732	superfamily	241571	24	91	0.000256377	35.4659	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#2268 - 	CGI_10008737	superfamily	215827	198	381	8.44E-38	140.681	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#2269 - 	CGI_10008739	superfamily	241547	54	170	3.46E-38	136.139	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#2271 - 	CGI_10008741	superfamily	246597	1	165	2.45E-126	360.91	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#2272 - 	CGI_10008742	superfamily	241600	68	280	8.33E-88	263.332	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2273 - 	CGI_10008743	superfamily	246597	1	68	1.54E-44	147.509	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#2274 - 	CGI_10008744	superfamily	241600	67	194	2.69E-46	154.742	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2275 - 	CGI_10008745	superfamily	246597	7	108	1.11E-61	191.807	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#2276 - 	CGI_10008746	superfamily	246597	1	118	4.54E-91	269.232	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#2277 - 	CGI_10008747	superfamily	241600	67	280	5.61E-86	258.71	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2278 - 	CGI_10008748	superfamily	218118	81	149	1.98E-15	67.6392	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#2279 - 	CGI_10006547	superfamily	241599	331	387	9.68E-16	71.8908	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2279 - 	CGI_10006547	superfamily	198730	227	301	2.03E-42	146.43	cl02582	Pou superfamily	 - 	 - 	Pou domain - N-terminal to homeobox domain; Pou domain - N-terminal to homeobox domain.  
Q#2280 - 	CGI_10006548	superfamily	248097	159	285	2.13E-19	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2280 - 	CGI_10006548	superfamily	192445	32	139	0.00271122	36.6211	cl10818	Med4 superfamily	C	 - 	"Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter."
Q#2281 - 	CGI_10006549	superfamily	246680	7	66	2.14E-21	86.4651	cl14633	DD_superfamily superfamily	N	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#2282 - 	CGI_10006550	superfamily	222150	513	538	0.00486315	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2283 - 	CGI_10006551	superfamily	247723	78	160	1.82E-21	89.9806	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2283 - 	CGI_10006551	superfamily	247727	433	522	2.34E-07	49.3507	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#2283 - 	CGI_10006551	superfamily	247875	235	358	2.04E-17	81.17	cl17321	2OG-FeII_Oxy_2 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; 2OG-Fe(II) oxygenase superfamily.  
Q#2283 - 	CGI_10006551	superfamily	216897	38	85	3.35E-08	51.5281	cl03463	Gal_Lectin superfamily	C	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#2284 - 	CGI_10006552	superfamily	247856	236	292	0.000120538	39.0681	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2284 - 	CGI_10006552	superfamily	247856	199	259	0.000274522	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2284 - 	CGI_10006552	superfamily	247856	83	133	0.00394151	34.8309	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2287 - 	CGI_10006555	superfamily	247725	42	135	3.52E-51	173.991	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2287 - 	CGI_10006555	superfamily	248318	714	766	1.83E-14	69.3869	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#2287 - 	CGI_10006555	superfamily	219103	186	304	2.17E-50	172.556	cl05893	Myotub-related superfamily	 - 	 - 	"Myotubularin-related; This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease."
Q#2287 - 	CGI_10006555	superfamily	206020	364	418	5.08E-34	124.928	cl18286	Y_phosphatase_m superfamily	 - 	 - 	"Myotubularin Y_phosphatase-like; This short region is highly conserved and seems to be common to many myotubularin proteins with protein tyrosine pyrophosphate activity. As the family has a number of highly conserved residues such as histidine, cysteine, glutamine and aspartate, it is possible that this represents a catalytic core of the active enzymatic part of the proteins."
Q#2288 - 	CGI_10006556	superfamily	247725	5	137	1.28E-35	130.255	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2289 - 	CGI_10006557	superfamily	241573	502	805	5.45E-100	320.433	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#2290 - 	CGI_10012497	superfamily	245213	40	79	2.33E-05	37.7136	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2290 - 	CGI_10012497	superfamily	221695	20	43	5.77E-05	36.279	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#2290 - 	CGI_10012497	superfamily	245213	1	29	0.00148554	32.604	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2291 - 	CGI_10012498	superfamily	241578	84	124	2.80E-06	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2291 - 	CGI_10012498	superfamily	221695	28	51	7.32E-06	39.7458	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#2291 - 	CGI_10012498	superfamily	241578	43	83	0.000410168	37.3644	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2291 - 	CGI_10012498	superfamily	245213	4	41	0.00355346	32.6086	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2292 - 	CGI_10012499	superfamily	245213	133	169	0.00352194	34.9198	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2292 - 	CGI_10012499	superfamily	221695	29	50	0.00725673	33.9678	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#2294 - 	CGI_10012502	superfamily	247907	248	402	8.43E-30	115.978	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2294 - 	CGI_10012502	superfamily	247907	34	180	4.42E-28	110.971	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2294 - 	CGI_10012502	superfamily	247907	441	598	1.43E-24	100.956	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2294 - 	CGI_10012502	superfamily	245213	628	661	0.000723843	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2294 - 	CGI_10012502	superfamily	247907	666	713	0.000236155	40.8645	cl17353	LamG superfamily	C	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2295 - 	CGI_10012503	superfamily	245213	334	370	3.90E-09	52.639	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2296 - 	CGI_10012504	superfamily	241574	915	1156	3.92E-90	290.641	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#2296 - 	CGI_10012504	superfamily	247725	199	307	3.71E-29	113.934	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2296 - 	CGI_10012504	superfamily	215882	112	224	2.94E-23	97.3514	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#2296 - 	CGI_10012504	superfamily	220215	25	106	3.09E-22	93.0586	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#2297 - 	CGI_10012505	superfamily	241941	63	127	9.36E-14	62.6117	cl00551	Acylphosphatase superfamily	N	 - 	Acylphosphatase; Acylphosphatase.  
Q#2300 - 	CGI_10012508	superfamily	243063	2	176	4.72E-78	234.443	cl02511	GH64-TLP-SF superfamily	N	 - 	"glycoside hydrolase family 64 (beta-1,3-glucanases which produce specific pentasaccharide oligomers) and thaumatin-like proteins; This superfamily includes glycoside hydrolases of family 64 (GH64), these are mostly bacterial beta-1,3-glucanases which cleave long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers  and are implicated in fungal cell wall degradation. Also included in this superfamily are thaumatin, the sweet-tasting protein from the African berry Thaumatococcus daniellii, and thaumatin-like proteins (TLPs) which are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Like GH64s, some TLPs also hydrolyze the beta-1,3-glucans of the type commonly found in fungal walls. Plant TLPs are classified as pathogenesis-related (PR) protein family 5 (PR5), their expression is induced by environmental stresses such as pathogen/pest attack, drought and cold. Several members of the plant TLP family have been reported as food allergens from fruits, and pollen allergens from conifers. Streptomyces matensis laminaripentaose-producing, beta-1,3-glucanase (GH64-LPHase), and TLPs have in common, a core N-terminal barrel domain (domain I) composed of 10 beta-strands, two coming from the C-terminal region of the protein. In TLPs, this core domain is flanked by two shorter domains (domains II and III). Small TLPs, such as Triticum aestivum thaumatin-like xylanase inhibitor, have a deletion in the third domain (domain II). GH64-LPHase has a second C-terminal domain which corresponds positional to, but is much larger than, domain III of TLP. GH64-LPHase and TLPs are described as crescent-fold structures. Critical functional residues, common to GH64-LPHase and TLPs are a Glu and an Asp residue. LPHase has an electronegative, substrate-binding cleft and the afore mentioned conserved Glu and Asp residues are the catalytic residues essential for beta-1,3-glucan cleavage. In TLPs, these residues are two of the four conserved residues which contribute to the strong electronegative character of the cleft which is associated with the antifungal activity of TLPs."
Q#2305 - 	CGI_10012513	superfamily	247724	11	97	3.08E-20	84.5205	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2306 - 	CGI_10012514	superfamily	248012	4	129	4.37E-15	67.3484	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2307 - 	CGI_10012515	superfamily	243035	6	66	1.85E-15	65.3951	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2308 - 	CGI_10012516	superfamily	243035	139	240	8.70E-20	81.8973	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2309 - 	CGI_10012517	superfamily	248012	1	88	4.57E-05	37.6381	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2310 - 	CGI_10020568	superfamily	217293	22	225	7.46E-34	126.208	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#2310 - 	CGI_10020568	superfamily	202474	232	282	1.09E-07	51.1153	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#2311 - 	CGI_10020569	superfamily	217293	22	225	6.35E-33	123.512	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#2311 - 	CGI_10020569	superfamily	202474	232	282	8.40E-08	51.5005	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#2312 - 	CGI_10020570	superfamily	217293	23	225	2.72E-35	129.675	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#2312 - 	CGI_10020570	superfamily	202474	233	283	0.00113733	38.7889	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#2314 - 	CGI_10020572	superfamily	246710	42	180	1.82E-33	125.693	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#2314 - 	CGI_10020572	superfamily	246710	599	715	1.88E-32	122.996	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#2314 - 	CGI_10020572	superfamily	216290	203	331	8.76E-37	134.723	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#2314 - 	CGI_10020572	superfamily	217685	346	485	4.46E-34	128.221	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#2316 - 	CGI_10020574	superfamily	245201	14	264	2.03E-156	454.094	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2317 - 	CGI_10020575	superfamily	241645	1	112	3.33E-44	142.123	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#2321 - 	CGI_10020579	superfamily	238191	1135	1659	3.31E-121	395.162	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#2321 - 	CGI_10020579	superfamily	238191	568	1079	5.99E-119	388.614	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#2321 - 	CGI_10020579	superfamily	238191	43	536	7.68E-108	356.642	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#2321 - 	CGI_10020579	superfamily	243061	2130	2230	1.33E-46	165.208	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2321 - 	CGI_10020579	superfamily	243061	2022	2121	1.70E-42	153.652	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2321 - 	CGI_10020579	superfamily	243061	1912	2012	6.16E-40	146.333	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2321 - 	CGI_10020579	superfamily	243061	1807	1904	2.62E-35	132.851	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2321 - 	CGI_10020579	superfamily	243061	1700	1799	3.78E-32	123.606	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2321 - 	CGI_10020579	superfamily	243061	2238	2317	1.38E-19	87.3974	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2322 - 	CGI_10020580	superfamily	247724	11	208	1.01E-120	344.584	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2323 - 	CGI_10020581	superfamily	202668	504	608	7.10E-22	93.1126	cl04110	BK_channel_a superfamily	 - 	 - 	Calcium-activated BK potassium channel alpha subunit; Calcium-activated BK potassium channel alpha subunit.  
Q#2323 - 	CGI_10020581	superfamily	219619	284	351	3.11E-11	61.4547	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#2324 - 	CGI_10020582	superfamily	243074	22	67	1.71E-11	61.3685	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#2325 - 	CGI_10020584	superfamily	248312	28	205	3.14E-08	50.8149	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#2326 - 	CGI_10020585	superfamily	241672	264	586	2.88E-66	220.263	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#2326 - 	CGI_10020585	superfamily	242231	1	234	8.70E-113	342.144	cl00983	Indigoidine_A superfamily	 - 	 - 	"Indigoidine synthase A like protein; Indigoidine is a blue pigment synthesised by Erwinia chrysanthemi implicated in pathogenicity and protection from oxidative stress. IdgA is involved in indigoidine biosynthesis, but its specific function is unknown. The recommended name for this protein is now pseudouridine-5'-phosphate glycosidase."
Q#2327 - 	CGI_10020586	superfamily	243072	74	177	9.76E-18	75.883	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2328 - 	CGI_10020587	superfamily	202224	175	289	1.66E-22	91.5883	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#2330 - 	CGI_10020589	superfamily	247858	27	166	9.71E-14	64.3314	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#2331 - 	CGI_10020590	superfamily	241613	114	149	1.18E-09	54.5202	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#2331 - 	CGI_10020590	superfamily	241613	155	186	1.49E-05	42.579	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#2331 - 	CGI_10020590	superfamily	245814	21	104	1.75E-08	52.1225	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2332 - 	CGI_10020591	superfamily	241583	52	261	6.84E-13	66.4931	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#2333 - 	CGI_10020592	superfamily	218118	65	130	4.00E-18	74.1876	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#2334 - 	CGI_10020593	superfamily	218118	48	125	6.72E-24	89.5956	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#2335 - 	CGI_10020594	superfamily	218118	30	105	2.63E-17	71.4912	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#2336 - 	CGI_10020595	superfamily	243126	253	292	3.96E-14	66.8456	cl02650	FYRN superfamily	C	 - 	F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.
Q#2336 - 	CGI_10020595	superfamily	243127	299	331	1.32E-08	51.9234	cl02651	FYRC superfamily	N	 - 	F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.
Q#2337 - 	CGI_10020596	superfamily	241599	155	212	2.40E-15	68.0388	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2339 - 	CGI_10020599	superfamily	241599	149	203	6.53E-19	78.054	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2343 - 	CGI_10020603	superfamily	216686	92	259	3.97E-27	105.483	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#2344 - 	CGI_10020604	superfamily	221377	202	348	8.07E-06	44.3819	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#2354 - 	CGI_10020614	superfamily	248469	20	127	2.59E-14	68.9359	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#2354 - 	CGI_10020614	superfamily	248469	161	258	2.10E-09	54.6835	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#2356 - 	CGI_10015095	superfamily	217473	54	325	1.86E-25	106.68	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#2358 - 	CGI_10015097	superfamily	219797	108	748	0	573.108	cl09596	ACC_central superfamily	 - 	 - 	"Acetyl-CoA carboxylase, central region; The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyzes the rate-limiting step in this process."
Q#2359 - 	CGI_10015098	superfamily	217473	164	324	4.96E-21	93.1985	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#2362 - 	CGI_10015101	superfamily	217473	204	351	7.02E-24	102.058	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#2365 - 	CGI_10015104	superfamily	192054	15	168	9.95E-72	219.002	cl07222	RFC1 superfamily	 - 	 - 	"Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo."
Q#2372 - 	CGI_10004381	superfamily	241600	62	234	9.91E-55	176.662	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2373 - 	CGI_10004382	superfamily	241600	2	154	4.07E-38	130.86	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2374 - 	CGI_10004383	superfamily	247725	5	117	1.77E-77	227.573	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2375 - 	CGI_10004384	superfamily	247725	403	526	9.46E-71	224.494	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2375 - 	CGI_10004384	superfamily	243096	209	392	1.46E-26	106.228	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#2376 - 	CGI_10004385	superfamily	247725	175	301	5.34E-73	239.526	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2376 - 	CGI_10004385	superfamily	215882	83	187	3.24E-22	94.2698	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#2376 - 	CGI_10004385	superfamily	220215	12	75	4.69E-16	75.3394	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#2376 - 	CGI_10004385	superfamily	192138	292	326	1.01E-07	50.6952	cl07378	FA superfamily	C	 - 	"FERM adjacent (FA); This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates."
Q#2381 - 	CGI_10009185	superfamily	247892	81	429	0	669.17	cl17338	PRK06075 superfamily	 - 	 - 	NADH dehydrogenase subunit D; Validated
Q#2382 - 	CGI_10009186	superfamily	222090	346	541	6.69E-14	71.9202	cl18636	Methyltransf_22 superfamily	 - 	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#2382 - 	CGI_10009186	superfamily	243109	888	961	0.00101218	39.7932	cl02614	SPRY superfamily	C	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#2387 - 	CGI_10009192	superfamily	241913	45	114	5.21E-06	42.9785	cl00509	hot_dog superfamily	C	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#2388 - 	CGI_10009193	superfamily	112546	373	419	9.54E-05	40.1128	cl04240	EPTP superfamily	 - 	 - 	"EPTP domain; Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold."
Q#2388 - 	CGI_10009193	superfamily	112546	311	367	0.000186754	39.3424	cl04240	EPTP superfamily	 - 	 - 	"EPTP domain; Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold."
Q#2388 - 	CGI_10009193	superfamily	112546	209	257	0.000442615	38.1868	cl04240	EPTP superfamily	 - 	 - 	"EPTP domain; Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold."
Q#2388 - 	CGI_10009193	superfamily	112546	157	204	0.000993782	37.0312	cl04240	EPTP superfamily	 - 	 - 	"EPTP domain; Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold."
Q#2388 - 	CGI_10009193	superfamily	112546	262	300	0.00136163	36.646	cl04240	EPTP superfamily	 - 	 - 	"EPTP domain; Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold."
Q#2389 - 	CGI_10009194	superfamily	241578	22	178	1.46E-35	135.882	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2389 - 	CGI_10009194	superfamily	241578	234	386	4.05E-32	125.867	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2389 - 	CGI_10009194	superfamily	241578	444	600	1.01E-31	124.711	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2389 - 	CGI_10009194	superfamily	241578	677	823	7.49E-18	84.1546	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2389 - 	CGI_10009194	superfamily	243119	858	912	2.40E-05	44.732	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#2390 - 	CGI_10009195	superfamily	243119	281	339	0.000993312	37.0281	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#2390 - 	CGI_10009195	superfamily	243119	97	153	0.0051708	34.7169	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#2391 - 	CGI_10000572	superfamily	247727	57	139	4.04E-12	59.751	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#2392 - 	CGI_10009450	superfamily	247948	14	70	1.35E-12	60.7706	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#2394 - 	CGI_10009452	superfamily	241572	38	134	4.21E-08	49.5445	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#2394 - 	CGI_10009452	superfamily	241572	179	250	1.23E-06	45.6966	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#2395 - 	CGI_10009453	superfamily	243083	499	583	9.52E-31	115.544	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#2396 - 	CGI_10009454	superfamily	243034	83	184	5.59E-17	73.5683	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2397 - 	CGI_10009455	superfamily	241563	416	447	3.41E-05	42.6595	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2397 - 	CGI_10009455	superfamily	247792	273	314	0.00278408	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2397 - 	CGI_10009455	superfamily	212612	24	219	5.53E-27	111.226	cl08346	Rib_hydrolase superfamily	 - 	 - 	"ADP-ribosyl cyclase, also known as cyclic ADP-ribose hydrolase or CD38; ADP-ribosyl cyclase (EC:3.2.2.5) synthesizes the second messenger cyclic-ADP ribose (cADPR), which in turn releases calcium from internal stores. Mammals possess two membrane proteins, CD38 and BST-1/CD157, which exhibit ADP-ribosyl cyclase activity, as well as intracellular soluble ADP-ribose cyclases. CD38 is involved in differentiation, adhesion, and cell proliferation, and has been implicated in diseases such as AIDS, diabetes, and B-cell chronic lymphocytic leukemia. The extramembrane domain of CD38 acts as a multifunctional enzyme, and can synthesize cADPR from NAD+, hydrolyze NAD+ and cADPR to ADPR, as well as catalyze the exchange of the nicotinamide group of NADP+ with nicotinic acid under acidic conditions, to yield NAADP+ (nicotinic acid-adenine dinucleotide phosphate), a metabolite involved in Ca2+ mobilization from acidic stores."
Q#2397 - 	CGI_10009455	superfamily	110440	855	881	0.00124326	37.7725	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2398 - 	CGI_10009456	superfamily	222150	236	260	0.00800398	33.9045	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2400 - 	CGI_10009458	superfamily	247046	240	464	1.58E-17	80.5569	cl15705	DUF563 superfamily	 - 	 - 	Protein of unknown function (DUF563); Family of uncharacterized proteins.
Q#2401 - 	CGI_10000648	superfamily	248097	11	72	0.00878168	31.0814	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2405 - 	CGI_10021462	superfamily	242169	6	83	7.76E-05	37.2135	cl00886	Robl_LC7 superfamily	 - 	 - 	"Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role."
Q#2406 - 	CGI_10021463	superfamily	241571	3	114	1.07E-09	56.2666	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#2407 - 	CGI_10021464	superfamily	243092	406	642	1.77E-48	171.749	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2407 - 	CGI_10021464	superfamily	243074	324	367	2.62E-12	62.5241	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#2408 - 	CGI_10021465	superfamily	219448	239	338	7.71E-11	60.0213	cl06523	DRMBL superfamily	 - 	 - 	DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.
Q#2408 - 	CGI_10021465	superfamily	241867	30	144	1.97E-07	50.9736	cl00446	Lactamase_B superfamily	C	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#2409 - 	CGI_10021466	superfamily	220606	60	241	1.86E-37	135.718	cl10857	Tmemb_40 superfamily	 - 	 - 	Predicted membrane protein; This is a region of 280 amino acids from a group of proteins conserved from plants to humans. It is predicted to be a membrane protein but its function is otherwise unknown.
Q#2411 - 	CGI_10021468	superfamily	247755	319	381	1.85E-28	110.231	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2411 - 	CGI_10021468	superfamily	247755	423	495	6.53E-27	105.994	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2411 - 	CGI_10021468	superfamily	247755	171	220	1.33E-13	68.244	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2411 - 	CGI_10021468	superfamily	247755	282	346	3.39E-07	49.74	cl17201	ABC_ATPase superfamily	NC	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2411 - 	CGI_10021468	superfamily	247755	388	455	0.00317082	38.299	cl17201	ABC_ATPase superfamily	NC	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2415 - 	CGI_10021472	superfamily	245835	32	313	2.29E-98	313.883	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#2415 - 	CGI_10021472	superfamily	243095	523	708	1.84E-87	281.232	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#2415 - 	CGI_10021472	superfamily	247683	762	814	2.57E-19	83.9901	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#2416 - 	CGI_10021473	superfamily	151051	18	111	1.38E-13	69.9627	cl11131	Nrf1_DNA-bind superfamily	N	 - 	"NLS-binding and DNA-binding and dimerisation domains of Nrf1; In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity."
Q#2417 - 	CGI_10021474	superfamily	151051	21	113	2.44E-16	78.4371	cl11131	Nrf1_DNA-bind superfamily	N	 - 	"NLS-binding and DNA-binding and dimerisation domains of Nrf1; In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity."
Q#2419 - 	CGI_10021476	superfamily	243066	18	123	2.37E-24	98.0733	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#2419 - 	CGI_10021476	superfamily	198867	132	231	2.51E-20	86.4435	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#2419 - 	CGI_10021476	superfamily	243146	424	469	5.17E-13	64.5019	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2419 - 	CGI_10021476	superfamily	243146	365	409	7.68E-13	63.8346	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2419 - 	CGI_10021476	superfamily	243146	472	517	2.28E-09	54.1015	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2419 - 	CGI_10021476	superfamily	243146	507	545	6.29E-08	49.5822	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2419 - 	CGI_10021476	superfamily	243146	340	376	1.60E-05	42.9307	cl02701	Kelch_3 superfamily	N	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2419 - 	CGI_10021476	superfamily	243146	283	327	3.58E-05	41.7751	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2420 - 	CGI_10021477	superfamily	241599	240	289	4.75E-06	43.3861	cl00084	homeodomain superfamily	C	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2421 - 	CGI_10021478	superfamily	241599	528	577	2.11E-05	42.6157	cl00084	homeodomain superfamily	C	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2421 - 	CGI_10021478	superfamily	245201	142	285	2.44E-12	65.3357	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2421 - 	CGI_10021478	superfamily	245201	212	387	0.00869943	37.0299	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2422 - 	CGI_10021479	superfamily	247744	388	506	2.51E-38	139.59	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#2422 - 	CGI_10021479	superfamily	246925	116	306	0.00399139	38.8758	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#2423 - 	CGI_10021480	superfamily	243205	1	348	0	615.863	cl02823	phosphagen_kinases superfamily	 - 	 - 	"Phosphagen (guanidino) kinases; Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) and hypotaurocyamine kinase (HTK). The majority of bacterial phosphagen kinases appear to lack the N-terminal domain and have not been functionally characterized."
Q#2424 - 	CGI_10021481	superfamily	243205	6	349	0	581.966	cl02823	phosphagen_kinases superfamily	 - 	 - 	"Phosphagen (guanidino) kinases; Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) and hypotaurocyamine kinase (HTK). The majority of bacterial phosphagen kinases appear to lack the N-terminal domain and have not been functionally characterized."
Q#2425 - 	CGI_10021482	superfamily	243205	31	98	6.74E-07	44.9976	cl02823	phosphagen_kinases superfamily	C	 - 	"Phosphagen (guanidino) kinases; Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) and hypotaurocyamine kinase (HTK). The majority of bacterial phosphagen kinases appear to lack the N-terminal domain and have not been functionally characterized."
Q#2426 - 	CGI_10021483	superfamily	202405	16	50	5.86E-18	70.9999	cl03723	ATP-gua_PtransN superfamily	C	 - 	"ATP:guanido phosphotransferase, N-terminal domain; The N-terminal domain has an all-alpha fold."
Q#2429 - 	CGI_10021486	superfamily	149426	64	212	2.67E-23	94.3853	cl18038	SEFIR superfamily	 - 	 - 	"SEFIR domain; This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways."
Q#2431 - 	CGI_10021488	superfamily	248097	16	151	2.76E-15	68.0977	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2432 - 	CGI_10021489	superfamily	248097	7	111	1.64E-13	67.2902	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2432 - 	CGI_10021489	superfamily	248097	249	370	8.01E-08	50.3414	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2432 - 	CGI_10021489	superfamily	248097	118	239	9.26E-08	50.3414	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2432 - 	CGI_10021489	superfamily	248097	394	496	2.76E-05	42.6745	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2433 - 	CGI_10021490	superfamily	203591	2	135	1.93E-30	117.087	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#2434 - 	CGI_10021491	superfamily	243096	732	924	5.09E-23	98.524	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#2434 - 	CGI_10021491	superfamily	247725	914	1089	7.34E-17	80.3001	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2435 - 	CGI_10021492	superfamily	248028	9	265	1.79E-56	183.859	cl17474	Steroid_dh superfamily	 - 	 - 	"3-oxo-5-alpha-steroid 4-dehydrogenase; This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development."
Q#2436 - 	CGI_10021493	superfamily	248097	104	228	5.90E-16	71.1422	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2437 - 	CGI_10021494	superfamily	245367	59	156	0.00899675	38.2648	cl10727	DUF2042 superfamily	NC	 - 	Uncharacterized conserved protein (DUF2042); This entry is the conserved N-terminal 300 residues of a group of proteins found from protozoa to Humans. The function is unknown.
Q#2439 - 	CGI_10021496	superfamily	207657	47	96	0.00345015	34.4075	cl02577	HALZ superfamily	 - 	 - 	Homeobox associated leucine zipper; Homeobox associated leucine zipper.  
Q#2443 - 	CGI_10021500	superfamily	241563	61	100	0.00059485	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2444 - 	CGI_10021501	superfamily	222429	17	95	4.23E-09	51.8576	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#2446 - 	CGI_10001322	superfamily	247637	306	448	5.79E-63	208.65	cl16912	MDR superfamily	C	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#2446 - 	CGI_10001322	superfamily	247746	112	187	0.000912021	38.693	cl17192	ATP-synt_B superfamily	NC	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#2447 - 	CGI_10001390	superfamily	245847	28	75	7.46E-05	37.0968	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#2449 - 	CGI_10000765	superfamily	241746	978	1041	0.00493518	37.1357	cl00277	Restriction_endonuclease_like superfamily	N	 - 	"Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI"
Q#2451 - 	CGI_10001595	superfamily	243362	249	290	0.00329417	36.6343	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#2451 - 	CGI_10001595	superfamily	110440	371	397	0.00509269	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2452 - 	CGI_10001596	superfamily	243092	16	87	1.43E-14	67.7452	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2452 - 	CGI_10001596	superfamily	222150	118	141	3.63E-05	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2455 - 	CGI_10001836	superfamily	241832	10	123	6.22E-60	183.494	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#2456 - 	CGI_10001611	superfamily	243124	880	992	3.42E-12	65.5261	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#2456 - 	CGI_10001611	superfamily	238012	172	211	0.00288964	36.9486	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#2457 - 	CGI_10007864	superfamily	216254	64	184	3.71E-23	91.5406	cl08303	Recep_L_domain superfamily	 - 	 - 	Receptor L domain; The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
Q#2458 - 	CGI_10007865	superfamily	247743	380	488	5.11E-05	42.5183	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#2458 - 	CGI_10007865	superfamily	248284	140	178	0.00210238	39.3214	cl17730	GlpB superfamily	C	 - 	Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]
Q#2459 - 	CGI_10007866	superfamily	247792	36	79	1.03E-08	53.2184	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2459 - 	CGI_10007866	superfamily	241563	173	212	3.19E-07	48.8227	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2459 - 	CGI_10007866	superfamily	150427	788	1015	9.42E-88	288.524	cl18043	DUF2048 superfamily	C	 - 	Uncharacterized conserved protein (DUF2048); The proteins in this family are conserved from plants to vertebrates. The function is unknown.
Q#2459 - 	CGI_10007866	superfamily	150427	1079	1190	5.23E-16	79.3607	cl18043	DUF2048 superfamily	N	 - 	Uncharacterized conserved protein (DUF2048); The proteins in this family are conserved from plants to vertebrates. The function is unknown.
Q#2459 - 	CGI_10007866	superfamily	128778	219	342	6.38E-11	61.5118	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#2459 - 	CGI_10007866	superfamily	110440	511	538	1.22E-07	49.7137	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2460 - 	CGI_10007867	superfamily	241745	31	172	2.33E-48	158.024	cl00276	Maf_Ham1 superfamily	 - 	 - 	"Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides, such as hypoxanthine/xanthine NTP, but not standard nucleotides."
Q#2461 - 	CGI_10007868	superfamily	247068	56	83	0.00473076	33.0558	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2464 - 	CGI_10007871	superfamily	241659	272	340	0.000185785	39.1095	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#2465 - 	CGI_10007872	superfamily	241563	7	43	0.000291243	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2467 - 	CGI_10007875	superfamily	217900	2	34	2.15E-13	68.3775	cl04403	APG9 superfamily	N	 - 	"Autophagy protein Apg9; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways."
Q#2470 - 	CGI_10020841	superfamily	243038	126	180	0.00135583	38.8609	cl02442	DEP superfamily	N	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#2473 - 	CGI_10020844	superfamily	245596	80	324	8.19E-37	134.531	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#2474 - 	CGI_10020845	superfamily	241578	96	212	1.46E-08	53.3386	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2474 - 	CGI_10020845	superfamily	247724	401	452	0.00273701	37.9114	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2476 - 	CGI_10020847	superfamily	247744	871	1016	1.90E-31	122.819	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#2476 - 	CGI_10020847	superfamily	241578	188	309	1.08E-11	64.1242	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2476 - 	CGI_10020847	superfamily	115363	503	567	1.20E-07	50.4482	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#2476 - 	CGI_10020847	superfamily	207713	760	797	1.66E-05	44.253	cl02729	WWE superfamily	C	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#2477 - 	CGI_10020848	superfamily	245814	199	285	1.92E-05	42.8615	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2477 - 	CGI_10020848	superfamily	245814	82	175	2.07E-07	48.9227	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2477 - 	CGI_10020848	superfamily	245814	319	388	8.90E-06	44.0564	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2479 - 	CGI_10020850	superfamily	241607	51	87	8.11E-05	35.7086	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#2480 - 	CGI_10020851	superfamily	242184	1	54	2.90E-27	98.0282	cl00909	Ribosomal_L24e_L24 superfamily	 - 	 - 	"Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site.  L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination.  L24 may be an important protein in eukaryotic reproduction:  in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identified in bacteria, but a functionally equivalent protein may exist.  Bacterial L19 forms an interprotein beta sheet with L14 that is similar to the L24e/L14 interprotein beta sheet observed in the archaeal L24e structures. Some eukaryotic L24 proteins were initially identified as L30, and this alignment model contains several sequences called L30."
Q#2481 - 	CGI_10020852	superfamily	245342	378	483	1.94E-22	92.797	cl10594	ERCC4 superfamily	 - 	 - 	ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Q#2483 - 	CGI_10020854	superfamily	219619	118	172	5.41E-19	80.7147	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#2483 - 	CGI_10020854	superfamily	219619	306	383	6.37E-11	57.9879	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#2484 - 	CGI_10020855	superfamily	245847	635	740	1.34E-08	53.5101	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#2485 - 	CGI_10020856	superfamily	243049	12	70	0.000255959	37.4451	cl02472	IGFBP superfamily	C	 - 	Insulin-like growth factor binding protein; Insulin-like growth factor binding protein.  
Q#2486 - 	CGI_10020857	superfamily	217685	75	160	2.54E-27	109.346	cl04225	Cu2_monoox_C superfamily	N	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#2486 - 	CGI_10020857	superfamily	110440	487	514	5.33E-05	41.6245	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2486 - 	CGI_10020857	superfamily	216290	10	33	0.000196643	40.7346	cl03089	Cu2_monooxygen superfamily	N	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#2486 - 	CGI_10020857	superfamily	110440	600	628	0.00209911	37.0021	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2487 - 	CGI_10020858	superfamily	241995	4	270	1.71E-80	246.359	cl00635	Ntn_Asparaginase_2_like superfamily	 - 	 - 	"Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and  L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue."
Q#2488 - 	CGI_10020859	superfamily	241623	81	353	4.27E-153	438.601	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#2489 - 	CGI_10020861	superfamily	243034	786	886	0.000739026	39.2856	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2491 - 	CGI_10020863	superfamily	242536	272	353	5.98E-28	104.871	cl01497	ATase superfamily	 - 	 - 	"The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of the C-terminal domain, suggesting an important structural role for the N-terminal domain in orienting the C-terminal domain for proper catalysis. Some ATase C-terminal domain homologs are either single-domain proteins that lack an N-terminal domain, or have a tryptophan substituted in place of the acceptor cysteine (i.e. the motif PCHR is replaced by PWHR). ATase null mutant mice are viable, fertile, and have a normal lifespan."
Q#2491 - 	CGI_10020863	superfamily	247724	1	130	3.66E-25	99.188	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2492 - 	CGI_10020864	superfamily	243082	592	751	2.28E-58	202.132	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#2492 - 	CGI_10020864	superfamily	243082	151	354	3.84E-14	73.4639	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#2493 - 	CGI_10020865	superfamily	246597	51	149	2.43E-56	179.866	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#2493 - 	CGI_10020865	superfamily	246597	1	46	8.68E-23	90.8849	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#2494 - 	CGI_10020866	superfamily	243181	171	299	2.11E-30	117.753	cl02783	TopoII_MutL_Trans superfamily	 - 	 - 	"MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2.  MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families."
Q#2494 - 	CGI_10020866	superfamily	244692	611	754	5.78E-38	139.027	cl07336	MutL_C superfamily	 - 	 - 	"MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation."
Q#2495 - 	CGI_10020867	superfamily	243187	668	845	1.91E-115	354.288	cl02789	EFG_like_IV superfamily	 - 	 - 	"Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm."
Q#2495 - 	CGI_10020867	superfamily	247724	140	339	9.81E-105	327.303	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2495 - 	CGI_10020867	superfamily	243183	840	919	6.33E-48	165.882	cl02785	Elongation_Factor_C superfamily	 - 	 - 	"Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p.  This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain.  EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown."
Q#2495 - 	CGI_10020867	superfamily	243185	485	578	6.36E-48	166.215	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#2496 - 	CGI_10020868	superfamily	220393	35	201	4.49E-36	131.729	cl10751	Tmem26 superfamily	N	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#2497 - 	CGI_10020869	superfamily	220393	1	246	1.30E-43	153.3	cl10751	Tmem26 superfamily	 - 	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#2498 - 	CGI_10020870	superfamily	247907	1482	1662	1.42E-13	70.91	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2498 - 	CGI_10020870	superfamily	247907	1250	1414	1.93E-11	64.7469	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2498 - 	CGI_10020870	superfamily	247907	1762	1913	9.07E-11	62.4357	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2498 - 	CGI_10020870	superfamily	245213	2427	2463	7.58E-09	54.565	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	1116	1153	2.20E-08	53.4094	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	2227	2264	1.22E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	434	470	1.92E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	472	507	6.59E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	588	624	1.38E-06	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	626	661	2.19E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	354	390	3.23E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	1990	2027	3.96E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	552	586	2.95E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	891	927	2.97E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	1078	1114	4.07E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	510	548	9.95E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	743	797	0.000139244	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	2388	2419	0.000232505	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	2149	2185	0.00025437	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	312	348	0.000333049	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	983	1019	0.000568903	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	1695	1730	0.000753366	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	1156	1199	0.00130842	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	2187	2224	0.00237384	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	862	889	0.00272194	38.3866	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	2111	2146	0.00685316	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2498 - 	CGI_10020870	superfamily	245213	799	843	0.00566995	37.2264	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2499 - 	CGI_10020871	superfamily	243050	106	160	1.39E-30	110.205	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#2499 - 	CGI_10020871	superfamily	243050	45	98	4.36E-22	87.0465	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#2499 - 	CGI_10020871	superfamily	241599	181	239	2.93E-18	76.128	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2500 - 	CGI_10020872	superfamily	244539	210	593	4.11E-131	392.022	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#2500 - 	CGI_10020872	superfamily	241863	8	138	4.44E-32	120.96	cl00438	Flavodoxin_2 superfamily	 - 	 - 	Flavodoxin-like fold; This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
Q#2501 - 	CGI_10020873	superfamily	241599	231	289	1.04E-22	89.61	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2501 - 	CGI_10020873	superfamily	238076	79	128	2.43E-23	93.2526	cl18938	PAX superfamily	N	 - 	Paired Box domain
Q#2502 - 	CGI_10020874	superfamily	214531	177	216	4.93E-05	40.6629	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#2502 - 	CGI_10020874	superfamily	214531	1	30	0.00173166	36.4257	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#2502 - 	CGI_10020874	superfamily	205157	377	413	0.00270953	35.5911	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#2504 - 	CGI_10020876	superfamily	218655	126	174	0.00216833	35.2901	cl05269	DUF778 superfamily	N	 - 	Protein of unknown function (DUF778); This family consists of several eukaryotic proteins of unknown function.
Q#2505 - 	CGI_10020877	superfamily	241613	114	147	9.35E-06	42.579	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#2505 - 	CGI_10020877	superfamily	241578	237	282	1.80E-08	53.1575	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2505 - 	CGI_10020877	superfamily	214531	320	357	4.65E-06	43.3593	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#2505 - 	CGI_10020877	superfamily	241613	170	199	0.0057444	34.4898	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#2506 - 	CGI_10002065	superfamily	241596	69	122	7.22E-09	52.6015	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#2507 - 	CGI_10000980	superfamily	241832	6	201	1.64E-81	244.867	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#2508 - 	CGI_10002553	superfamily	247750	355	578	3.27E-122	367.469	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#2510 - 	CGI_10003119	superfamily	243035	101	225	3.38E-24	93.8385	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2511 - 	CGI_10015594	superfamily	243109	249	427	1.06E-86	273.304	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#2511 - 	CGI_10015594	superfamily	207684	7	40	3.23E-10	56.6183	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#2511 - 	CGI_10015594	superfamily	247807	462	582	0.00376167	36.5042	cl17253	AAA_17 superfamily	 - 	 - 	AAA domain; AAA domain.  
Q#2512 - 	CGI_10015595	superfamily	241619	21	94	0.000806592	36.4028	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#2513 - 	CGI_10015596	superfamily	248032	12	194	1.49E-61	191.277	cl17478	NTPase_1 superfamily	 - 	 - 	"NTPase; This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue."
Q#2514 - 	CGI_10015597	superfamily	246925	85	192	0.000260673	40.0314	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#2515 - 	CGI_10015598	superfamily	241642	154	213	2.05E-12	59.4314	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#2515 - 	CGI_10015598	superfamily	241642	33	90	4.94E-07	44.7938	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#2515 - 	CGI_10015598	superfamily	216143	100	152	2.47E-11	56.4016	cl02979	SNAP-25 superfamily	 - 	 - 	SNAP-25 family; SNAP-25 (synaptosome-associated protein 25 kDa) proteins are components of SNARE complexes. Members of this family contain a cluster of cysteine residues that can be palmitoylated for membrane attachment.
Q#2516 - 	CGI_10015600	superfamily	241642	115	156	3.30E-06	45.5642	cl00152	t_SNARE superfamily	C	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#2516 - 	CGI_10015600	superfamily	241642	10	51	1.14E-05	44.0234	cl00152	t_SNARE superfamily	N	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#2516 - 	CGI_10015600	superfamily	216143	61	113	1.47E-07	49.468	cl02979	SNAP-25 superfamily	 - 	 - 	SNAP-25 family; SNAP-25 (synaptosome-associated protein 25 kDa) proteins are components of SNARE complexes. Members of this family contain a cluster of cysteine residues that can be palmitoylated for membrane attachment.
Q#2516 - 	CGI_10015600	superfamily	246968	450	519	0.00211833	37.7248	cl15456	ADAM_CR superfamily	 - 	 - 	ADAM cysteine-rich; ADAMs are membrane-anchored proteases that proteolytically modify cell surface and extracellular matrix (ECM) in order to alter cell behaviour. It has been shown that the cysteine-rich domain of ADAM13 regulates the protein's metalloprotease activity.
Q#2516 - 	CGI_10015600	superfamily	221119	573	603	0.00819525	35.396	cl12993	Sugarporin_N superfamily	N	 - 	"Maltoporin periplasmic N-terminal extension; This domain would appear to be the periplasmic, N-terminal extension of the outer membrane maltoporins, pfam02264, LamB."
Q#2517 - 	CGI_10015601	superfamily	147609	13	178	2.07E-24	93.9603	cl05205	p25-alpha superfamily	 - 	 - 	"p25-alpha; This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila."
Q#2519 - 	CGI_10015603	superfamily	216939	110	152	3.12E-07	44.9613	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#2519 - 	CGI_10015603	superfamily	216939	2	80	4.99E-06	41.8797	cl03492	PC4 superfamily	 - 	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#2523 - 	CGI_10015607	superfamily	147119	186	379	2.65E-90	285.233	cl04762	SMK-1 superfamily	 - 	 - 	"Component of IIS longevity pathway SMK-1; SMK-1 is a component of the IIs longevity pathway which regulates aging in C.elegans. Specifically, SMK-1 influences DAF-16-dependant regulation of the aging process by regulating the transcriptional specificity of DAF-16 activity. SMK-1 plays a role in longevity by modulating the transcriptional specificity of DAF-16."
Q#2523 - 	CGI_10015607	superfamily	247725	25	107	0.000125274	41.2848	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2524 - 	CGI_10015608	superfamily	217584	35	157	8.24E-32	115.917	cl04100	MOSC_N superfamily	 - 	 - 	"MOSC N-terminal beta barrel domain; This domain is found to the N-terminus of pfam03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold."
Q#2524 - 	CGI_10015608	superfamily	217583	190	315	1.35E-07	48.5131	cl04097	MOSC superfamily	 - 	 - 	"MOSC domain; The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters."
Q#2525 - 	CGI_10015609	superfamily	243065	313	468	3.94E-25	105.562	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#2525 - 	CGI_10015609	superfamily	243065	1667	1820	1.01E-24	104.446	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#2525 - 	CGI_10015609	superfamily	243065	756	911	1.02E-24	104.406	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#2525 - 	CGI_10015609	superfamily	243065	2114	2270	1.10E-24	104.406	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#2525 - 	CGI_10015609	superfamily	243065	1212	1367	1.57E-24	104.021	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#2525 - 	CGI_10015609	superfamily	216897	114	191	2.10E-23	97.752	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#2525 - 	CGI_10015609	superfamily	243093	205	283	5.69E-10	59.081	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#2525 - 	CGI_10015609	superfamily	244710	1420	1494	7.44E-06	46.5647	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#2525 - 	CGI_10015609	superfamily	244710	2319	2397	1.53E-05	45.4091	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#2525 - 	CGI_10015609	superfamily	244710	963	1037	3.28E-05	44.6387	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#2525 - 	CGI_10015609	superfamily	244710	507	581	4.24E-05	44.2535	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#2525 - 	CGI_10015609	superfamily	205157	2497	2523	0.000138186	42.1395	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#2526 - 	CGI_10015610	superfamily	248097	234	335	1.59E-12	63.053	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2529 - 	CGI_10015613	superfamily	241581	416	509	5.70E-05	44.6846	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#2529 - 	CGI_10015613	superfamily	241754	14	322	2.35E-132	423.261	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#2530 - 	CGI_10015614	superfamily	247743	49	82	0.00670405	32.942	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#2535 - 	CGI_10003444	superfamily	241563	63	100	0.0078761	34.6203	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2537 - 	CGI_10003446	superfamily	243689	34	107	7.80E-06	45.6973	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#2537 - 	CGI_10003446	superfamily	241563	915	956	0.00227919	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2540 - 	CGI_10003467	superfamily	247805	1238	1387	1.75E-15	76.222	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#2540 - 	CGI_10003467	superfamily	247905	1599	1708	1.89E-14	72.6556	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#2540 - 	CGI_10003467	superfamily	221397	575	1013	5.81E-81	276.124	cl14983	DUF3535 superfamily	 - 	 - 	"Domain of unknown function (DUF3535); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with pfam00271, pfam02985, pfam00176. This domain has two completely conserved residues (P and K) that may be functionally important."
Q#2541 - 	CGI_10003468	superfamily	247044	489	600	6.13E-52	177.415	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#2541 - 	CGI_10003468	superfamily	247044	728	825	1.11E-32	122.743	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#2541 - 	CGI_10003468	superfamily	247044	616	710	2.19E-10	58.5334	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#2541 - 	CGI_10003468	superfamily	246925	71	283	0.000114552	43.8834	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#2542 - 	CGI_10003469	superfamily	247044	172	272	1.46E-26	101.539	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#2542 - 	CGI_10003469	superfamily	247044	65	150	7.02E-14	66.6225	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#2542 - 	CGI_10003469	superfamily	247044	283	381	8.87E-25	96.9828	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#2544 - 	CGI_10011466	superfamily	241622	458	538	2.59E-12	63.3546	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#2544 - 	CGI_10011466	superfamily	241622	79	156	3.45E-12	62.9694	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#2544 - 	CGI_10011466	superfamily	241622	171	252	1.98E-11	60.6582	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#2547 - 	CGI_10011469	superfamily	248097	45	159	2.46E-15	68.4458	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2549 - 	CGI_10011471	superfamily	246681	95	164	4.22E-46	157.987	cl14643	SRPBCC superfamily	N	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#2550 - 	CGI_10011472	superfamily	243110	7	197	1.09E-18	84.4033	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#2551 - 	CGI_10011473	superfamily	241750	93	362	9.02E-41	145.118	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#2552 - 	CGI_10011474	superfamily	247921	2	54	0.00798565	31.4733	cl17367	Herpes_VP19C superfamily	NC	 - 	Herpesvirus capsid shell protein VP19C; Herpesvirus capsid shell protein VP19C.  
Q#2554 - 	CGI_10011476	superfamily	241563	60	95	0.000129205	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2556 - 	CGI_10011478	superfamily	241563	60	95	0.000119096	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2556 - 	CGI_10011478	superfamily	149105	104	227	0.0028165	38.5701	cl12353	TMPIT superfamily	C	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#2556 - 	CGI_10011478	superfamily	110440	484	510	0.00662842	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2557 - 	CGI_10011479	superfamily	241563	38	73	7.56E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2559 - 	CGI_10011481	superfamily	243061	4	105	5.15E-36	125.917	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2559 - 	CGI_10011481	superfamily	243061	111	212	2.05E-27	102.805	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2559 - 	CGI_10011481	superfamily	243061	211	268	1.44E-17	75.4562	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#2560 - 	CGI_10011482	superfamily	203101	42	142	2.77E-22	88.9535	cl04785	Popeye superfamily	N	 - 	Popeye protein conserved region; The function of Popeye proteins is not well understood. They are predominantly expressed in cardiac and skeletal muscle. This family represents a conserved region which includes three potential transmembrane domains.
Q#2561 - 	CGI_10011483	superfamily	248012	10	90	9.68E-09	52.5801	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2561 - 	CGI_10011483	superfamily	213389	147	316	7.59E-08	50.7507	cl17092	STING_C superfamily	 - 	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#2562 - 	CGI_10012020	superfamily	243072	856	981	1.26E-40	147.53	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2562 - 	CGI_10012020	superfamily	243072	625	750	4.00E-40	145.989	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2562 - 	CGI_10012020	superfamily	243072	955	1080	2.75E-39	143.678	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2562 - 	CGI_10012020	superfamily	243072	691	816	6.67E-39	142.523	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2562 - 	CGI_10012020	superfamily	243072	545	684	3.91E-31	120.181	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2562 - 	CGI_10012020	superfamily	243072	828	859	0.00029369	39.8448	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2562 - 	CGI_10012020	superfamily	247755	39	116	0.00134278	40.143	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2564 - 	CGI_10012022	superfamily	222150	129	154	6.49E-05	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2564 - 	CGI_10012022	superfamily	222150	157	180	0.000225979	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2565 - 	CGI_10012023	superfamily	222150	312	337	0.000245096	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2565 - 	CGI_10012023	superfamily	222150	340	363	0.00424187	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2566 - 	CGI_10012024	superfamily	243034	11	114	1.37E-17	80.1167	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2566 - 	CGI_10012024	superfamily	243058	819	929	8.21E-05	41.9164	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#2566 - 	CGI_10012024	superfamily	221172	363	508	2.16E-23	98.4662	cl13196	UNC45-central superfamily	 - 	 - 	"Myosin-binding striated muscle assembly central; The UNC-45 or small muscle protein 1 of C.elegans is expressed in two forms from different genomic positions in mammals, as a general tissue protein UNC-45a and a specific form Unc-45b expressed only in striated and skeletal muscle. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) domains towards their N-terminal, a UCS domain at the C-terminal that contains a number of Arm repeats pfam00514 and this central region of approximately 400 residues. Both the general form and the muscle form of UNC-45 function in myotube formation through cell fusion. Myofibril formation requires both GC and SM UNC-45, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organised myofibrils. The S. pombe Rng3p, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins. Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90. The exact function of this central region is not known."
Q#2566 - 	CGI_10012024	superfamily	243058	640	749	0.00307374	37.294	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#2567 - 	CGI_10012025	superfamily	241863	7	182	4.96E-25	97.0744	cl00438	Flavodoxin_2 superfamily	 - 	 - 	Flavodoxin-like fold; This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
Q#2568 - 	CGI_10012026	superfamily	243088	8	61	6.75E-06	42.318	cl02563	PX_domain superfamily	N	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#2569 - 	CGI_10012027	superfamily	247057	384	449	2.05E-36	129.786	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#2569 - 	CGI_10012027	superfamily	218123	95	292	2.85E-75	240.293	cl04559	CP2 superfamily	 - 	 - 	CP2 transcription factor; This family represents a conserved region in the CP2 transcription factor family.
Q#2570 - 	CGI_10012028	superfamily	199166	474	662	9.69E-33	126.288	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#2570 - 	CGI_10012028	superfamily	199166	372	523	1.14E-18	85.0716	cl15308	AMN1 superfamily	N	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#2570 - 	CGI_10012028	superfamily	243074	302	343	8.80E-13	64.0649	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#2571 - 	CGI_10012029	superfamily	217210	490	971	4.29E-153	467.525	cl10595	Ald_Xan_dh_C2 superfamily	 - 	 - 	Molybdopterin-binding domain of aldehyde dehydrogenase; Molybdopterin-binding domain of aldehyde dehydrogenase.  
Q#2571 - 	CGI_10012029	superfamily	243326	375	480	8.32E-31	118.39	cl03161	Ald_Xan_dh_C superfamily	 - 	 - 	"Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain.  "
Q#2571 - 	CGI_10012029	superfamily	201981	88	146	2.17E-20	87.536	cl08334	Fer2_2 superfamily	C	 - 	[2Fe-2S] binding domain; [2Fe-2S] binding domain.  
Q#2575 - 	CGI_10011029	superfamily	247068	238	331	9.77E-19	86.2133	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	746	837	8.95E-17	80.4353	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5704	5800	2.97E-16	78.8945	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1286	1386	2.69E-15	76.1981	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	966	1059	4.31E-15	75.4277	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1397	1487	3.76E-14	72.7313	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2158	2239	9.61E-14	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3747	3836	1.08E-13	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3324	3426	1.14E-13	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1193	1274	1.16E-13	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2354	2444	1.87E-13	70.8053	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5812	5899	3.94E-13	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2046	2141	1.21E-12	68.4941	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4470	4562	3.99E-12	66.9533	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1500	1597	6.67E-12	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4269	4354	7.49E-12	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5912	6009	1.00E-11	65.7977	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2252	2345	1.83E-11	65.0273	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3125	3217	2.47E-11	64.6421	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4369	4457	2.67E-11	64.2569	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2913	3008	6.88E-10	60.4049	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3640	3732	9.02E-10	60.0197	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2705	2797	1.33E-09	59.2493	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3434	3523	1.43E-09	59.2493	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	6197	6277	1.94E-09	58.8641	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3232	3312	2.04E-09	58.8641	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5009	5081	2.44E-09	58.4789	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3023	3117	3.42E-09	58.0938	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5493	5589	1.20E-08	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4165	4251	1.90E-08	55.7826	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2808	2886	3.46E-08	55.0122	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	343	434	1.03E-07	53.8566	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3961	4050	1.83E-07	53.0862	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4575	4672	2.55E-07	52.701	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1933	2034	4.21E-07	51.9306	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3535	3627	5.27E-07	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	3858	3942	5.97E-07	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5385	5463	6.46E-07	51.1602	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4779	4870	1.04E-06	50.775	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1723	1815	1.12E-06	50.775	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	2536	2625	1.15E-06	50.3898	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	665	734	2.16E-06	49.6194	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5094	5186	2.22E-06	49.6194	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5599	5690	2.87E-06	49.2342	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1832	1920	2.88E-06	49.2342	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1072	1173	7.67E-06	48.0786	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4060	4151	1.54E-05	46.923	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	41	102	1.64E-05	46.923	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	4883	4978	3.81E-05	45.7674	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	549	637	7.91E-05	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	1639	1708	0.000134035	44.2266	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	446	536	0.00014386	44.2266	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	849	953	0.000365032	42.6858	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	5278	5371	0.000444486	42.6858	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2575 - 	CGI_10011029	superfamily	247068	6074	6178	0.00273014	39.9894	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2576 - 	CGI_10011030	superfamily	241622	988	1051	1.59E-08	53.0781	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#2576 - 	CGI_10011030	superfamily	247725	1119	1216	4.52E-28	111.251	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2576 - 	CGI_10011030	superfamily	221808	541	667	6.36E-20	88.9442	cl15119	Tet_JBP superfamily	C	 - 	"Oxygenase domain of the 2OGFeDO superfamily; A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in various eukaryotes, bacteria and bacteriophages. Members of this family catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids, and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (hmC), or further oxidation to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Metazoan TET proteins contain a cysteine-rich region inserted into the core of the DSBH fold. Vertebrate TET proteins are oncogenes that are mutated in various myeloid cancers. Fungal and algal versions of this family are linked to a predicted transposase and show lineage-specific expansions."
Q#2576 - 	CGI_10011030	superfamily	243142	817	946	6.67E-12	64.5699	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#2577 - 	CGI_10011031	superfamily	204502	20	71	6.23E-22	87.9398	cl11146	GalKase_gal_bdg superfamily	 - 	 - 	"Galactokinase galactose-binding signature; This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry. The function of this domain appears to be to bind galactose, and the domain is normally at the N-terminus of the enzymes, EC:2.7.1.6. This domain is associated with the families GHMP_kinases_C, pfam08544 and GHMP_kinases_N, pfam00288."
Q#2577 - 	CGI_10011031	superfamily	219894	295	378	0.00396558	35.1681	cl08484	GHMP_kinases_C superfamily	 - 	 - 	"GHMP kinases C terminal; This family includes homoserine kinases, galactokinases and mevalonate kinases."
Q#2578 - 	CGI_10011032	superfamily	241563	74	115	1.33E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2579 - 	CGI_10011033	superfamily	241563	75	116	2.46E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2583 - 	CGI_10011037	superfamily	203773	189	384	1.18E-69	228.784	cl18250	PGAP1 superfamily	 - 	 - 	PGAP1-like protein; The sequences found in this family are similar to PGAP1. This is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body.
Q#2584 - 	CGI_10011038	superfamily	241659	188	276	2.63E-23	92.2253	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#2584 - 	CGI_10011038	superfamily	206220	6	67	1.39E-18	78.3871	cl16569	Nudc_N superfamily	 - 	 - 	N-terminal conserved domain of Nudc; The N-terminus of nuclear distribution gene C homolog (NUDC) proteins contains a highly conserved region consisting of a predicted three helix bundle. In the human homolog this segment has been targeted for structure determination by the Joint Center for Structural Genomics. NUDC forms a complex with other NUD proteins and is involved in several cellular division activities. Recently it was shown that NUDC regulates platelet-activating factor (PAF) acetylhydrolase with PAF being a pro-inflammatory secondary lipidic messenger.
Q#2588 - 	CGI_10011043	superfamily	243072	309	358	0.00536599	35.4371	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2591 - 	CGI_10011046	superfamily	243072	301	354	0.00357396	36.2075	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2593 - 	CGI_10011048	superfamily	217293	4	94	3.81E-17	73.4359	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#2595 - 	CGI_10011050	superfamily	217293	32	231	5.68E-33	123.512	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#2595 - 	CGI_10011050	superfamily	202474	238	324	1.53E-06	47.6485	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#2596 - 	CGI_10011051	superfamily	217293	39	234	7.97E-29	111.956	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#2596 - 	CGI_10011051	superfamily	202474	242	326	8.96E-08	51.1153	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#2597 - 	CGI_10011052	superfamily	219000	211	328	2.23E-05	44.9448	cl05717	Drf_FH3 superfamily	C	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#2600 - 	CGI_10022624	superfamily	241583	121	325	3.75E-41	152.913	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#2600 - 	CGI_10022624	superfamily	245321	541	605	1.69E-10	58.7911	cl10507	Disintegrin superfamily	 - 	 - 	Disintegrin; Disintegrin.  
Q#2600 - 	CGI_10022624	superfamily	128778	647	757	0.00125281	38.7851	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#2601 - 	CGI_10022625	superfamily	248019	109	534	5.76E-62	215.905	cl17465	DAGK_cat superfamily	 - 	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#2602 - 	CGI_10022626	superfamily	243035	17	92	2.67E-13	62.7788	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2602 - 	CGI_10022626	superfamily	243035	97	192	1.01E-11	58.0763	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2603 - 	CGI_10022627	superfamily	243035	8	112	1.79E-19	78.4305	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2604 - 	CGI_10022628	superfamily	241568	4	60	1.54E-12	59.0136	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#2605 - 	CGI_10022629	superfamily	241568	6	62	9.14E-09	49.3836	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#2606 - 	CGI_10022630	superfamily	241568	6	57	9.94E-09	49.3836	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#2607 - 	CGI_10022631	superfamily	241568	7	63	2.36E-05	40.1388	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#2608 - 	CGI_10022632	superfamily	248097	45	167	2.70E-16	71.1422	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2609 - 	CGI_10022633	superfamily	248097	209	331	5.59E-15	69.9866	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2609 - 	CGI_10022633	superfamily	248097	97	204	8.06E-11	58.0454	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2610 - 	CGI_10022634	superfamily	248097	177	302	4.34E-14	66.905	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2611 - 	CGI_10022635	superfamily	241758	33	178	3.20E-23	90.507	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#2612 - 	CGI_10022636	superfamily	243092	1251	1537	6.83E-06	48.4852	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2612 - 	CGI_10022636	superfamily	243092	1006	1286	1.69E-05	47.3296	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2612 - 	CGI_10022636	superfamily	247743	481	598	0.00239653	39.1052	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#2613 - 	CGI_10022637	superfamily	241983	480	646	1.85E-23	101.666	cl00614	ADP_ribosyl_GH superfamily	N	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#2613 - 	CGI_10022637	superfamily	243212	809	940	1.90E-19	86.6289	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#2613 - 	CGI_10022637	superfamily	215866	677	786	3.14E-14	71.5876	cl18349	Arrestin_N superfamily	N	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#2613 - 	CGI_10022637	superfamily	241983	290	379	3.50E-11	63.9162	cl00614	ADP_ribosyl_GH superfamily	C	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#2614 - 	CGI_10022638	superfamily	248305	5	334	2.32E-33	129.78	cl17751	Glyco_transf_22 superfamily	 - 	 - 	Alg9-like mannosyltransferase family; Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Q#2615 - 	CGI_10022639	superfamily	243362	184	225	0.00766767	35.4787	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#2617 - 	CGI_10022641	superfamily	245213	570	605	6.63E-09	53.0242	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2617 - 	CGI_10022641	superfamily	245213	607	638	6.30E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2617 - 	CGI_10022641	superfamily	245213	533	568	1.05E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2617 - 	CGI_10022641	superfamily	245213	501	529	0.00142501	37.4562	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2618 - 	CGI_10022642	superfamily	247794	31	448	0	586.448	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#2618 - 	CGI_10022642	superfamily	245206	464	586	0.00047313	41.5196	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#2619 - 	CGI_10022643	superfamily	245206	17	89	0.00016039	41.5196	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#2620 - 	CGI_10022644	superfamily	218109	358	418	4.16E-07	48.0906	cl12292	Gly_transf_sug superfamily	N	 - 	"Glycosyltransferase sugar-binding region containing DXD motif; The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases."
Q#2620 - 	CGI_10022644	superfamily	217539	385	463	0.000723852	39.9989	cl18414	Nucleotid_trans superfamily	NC	 - 	Nucleotide-diphospho-sugar transferase; Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases.
Q#2621 - 	CGI_10022645	superfamily	241832	11	74	5.94E-13	60.785	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#2622 - 	CGI_10022646	superfamily	241632	19	379	9.84E-121	386.993	cl00137	SERPIN superfamily	 - 	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#2622 - 	CGI_10022646	superfamily	247068	1236	1332	7.71E-29	113.948	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	1027	1125	1.36E-26	107.399	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	1446	1548	2.32E-26	106.629	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	1138	1229	5.60E-21	91.2209	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	504	581	3.20E-20	88.9097	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	691	821	1.67E-17	80.8205	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	1341	1438	4.06E-17	79.6649	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	932	1002	9.62E-10	58.0938	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	1557	1644	1.21E-09	57.7086	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	832	911	1.23E-05	45.7674	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2622 - 	CGI_10022646	superfamily	247068	605	677	1.49E-05	45.3822	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2623 - 	CGI_10022647	superfamily	241632	19	378	1.20E-132	387.379	cl00137	SERPIN superfamily	 - 	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#2624 - 	CGI_10022648	superfamily	241632	19	378	7.68E-132	385.067	cl00137	SERPIN superfamily	 - 	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#2625 - 	CGI_10022649	superfamily	241563	73	112	0.000138132	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2626 - 	CGI_10022650	superfamily	110440	163	187	0.00451422	33.5353	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2627 - 	CGI_10022651	superfamily	217252	364	476	6.97E-36	129.222	cl08372	Pyr_redox_dim superfamily	 - 	 - 	"Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases."
Q#2627 - 	CGI_10022651	superfamily	215691	188	268	2.92E-13	65.685	cl15766	Pyr_redox superfamily	 - 	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#2627 - 	CGI_10022651	superfamily	183782	6	53	4.58E-05	44.5039	cl18137	PRK12834 superfamily	C	 - 	putative FAD-binding dehydrogenase; Reviewed
Q#2627 - 	CGI_10022651	superfamily	248054	149	218	0.000719235	39.5931	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#2629 - 	CGI_10022653	superfamily	110440	314	340	0.00646889	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2632 - 	CGI_10022656	superfamily	241574	90	291	1.51E-20	87.2561	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#2635 - 	CGI_10022659	superfamily	207637	73	145	7.48E-12	57.9331	cl02541	CIDE_N superfamily	 - 	 - 	"CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein."
Q#2637 - 	CGI_10022661	superfamily	218284	1	61	3.51E-09	48.7899	cl04786	SOUL superfamily	N	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#2638 - 	CGI_10022662	superfamily	243092	138	290	0.00958899	36.1588	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2640 - 	CGI_10022664	superfamily	245596	1	90	3.94E-27	101.251	cl11394	Glyco_tranf_GTA_type superfamily	NC	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#2641 - 	CGI_10022665	superfamily	217473	105	328	9.42E-27	110.532	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#2644 - 	CGI_10022668	superfamily	147446	3	79	2.15E-32	109.068	cl05015	UPF0197 superfamily	 - 	 - 	Uncharacterized protein family (UPF0197); This family of proteins is functionally uncharacterized.
Q#2645 - 	CGI_10022669	superfamily	247736	73	122	3.58E-10	52.6632	cl17182	NAT_SF superfamily	N	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#2646 - 	CGI_10022670	superfamily	247736	115	184	7.56E-11	57.2856	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#2648 - 	CGI_10022672	superfamily	247727	177	273	4.78E-14	67.455	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#2649 - 	CGI_10022673	superfamily	215731	59	103	0.00215236	34.8813	cl08245	Gln-synt_C superfamily	N	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#2650 - 	CGI_10022674	superfamily	215731	75	108	0.000104956	38.7333	cl08245	Gln-synt_C superfamily	NC	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#2651 - 	CGI_10007687	superfamily	245226	498	546	5.34E-07	48.4509	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#2654 - 	CGI_10007690	superfamily	222150	272	295	7.21E-06	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2654 - 	CGI_10007690	superfamily	222150	242	269	0.000911481	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2654 - 	CGI_10007690	superfamily	246975	288	308	0.00503953	34.2449	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#2656 - 	CGI_10007692	superfamily	241754	13	721	0	812.267	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#2656 - 	CGI_10007692	superfamily	210118	747	769	0.000535612	39.2311	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#2659 - 	CGI_10006128	superfamily	218286	508	809	8.03E-99	312.486	cl04794	Vps16_C superfamily	 - 	 - 	"Vps16, C-terminal region; This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport. The role of VPS16 in this complex is not known."
Q#2661 - 	CGI_10006130	superfamily	247725	148	280	1.57E-26	101.646	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2662 - 	CGI_10006131	superfamily	245201	213	406	9.56E-41	146.613	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2662 - 	CGI_10006131	superfamily	245309	39	117	2.34E-07	48.6444	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#2663 - 	CGI_10006132	superfamily	243100	224	285	8.56E-09	51.0255	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#2664 - 	CGI_10006133	superfamily	245213	52	88	9.85E-06	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2664 - 	CGI_10006133	superfamily	245213	10	45	3.78E-05	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2667 - 	CGI_10006138	superfamily	241584	728	821	1.11E-09	57.1211	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2667 - 	CGI_10006138	superfamily	241584	949	1050	1.49E-07	50.5727	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2667 - 	CGI_10006138	superfamily	243035	5	115	1.05E-06	48.385	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2667 - 	CGI_10006138	superfamily	241584	1059	1149	0.000221568	40.9427	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2667 - 	CGI_10006138	superfamily	245814	632	714	3.02E-15	73.1086	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2667 - 	CGI_10006138	superfamily	245814	526	612	3.31E-13	67.1452	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2667 - 	CGI_10006138	superfamily	245814	167	232	1.03E-09	57.2248	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2667 - 	CGI_10006138	superfamily	245814	244	321	3.62E-09	55.6392	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2667 - 	CGI_10006138	superfamily	245814	373	446	1.51E-08	53.6633	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2667 - 	CGI_10006138	superfamily	245814	463	512	1.32E-05	44.32	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2669 - 	CGI_10008263	superfamily	241758	5	151	1.83E-26	97.8258	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#2670 - 	CGI_10008264	superfamily	241758	26	111	1.52E-12	59.691	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#2671 - 	CGI_10008265	superfamily	241758	7	138	9.17E-18	74.7138	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#2672 - 	CGI_10008266	superfamily	110440	54	80	0.00896311	29.6833	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2673 - 	CGI_10008267	superfamily	241758	160	209	3.39E-14	66.2394	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#2674 - 	CGI_10008268	superfamily	241758	825	874	5.25E-13	67.395	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#2675 - 	CGI_10008269	superfamily	222324	17	83	2.58E-13	60.4834	cl16352	zf-3CxxC superfamily	 - 	 - 	Zinc-binding domain; This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue.
Q#2676 - 	CGI_10008270	superfamily	241845	110	274	6.34E-39	138.238	cl00407	tRNA_m1G_MT superfamily	 - 	 - 	"tRNA (Guanine-1)-methyltransferase; This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyzes the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA."
Q#2677 - 	CGI_10008271	superfamily	243072	300	424	9.50E-37	137.9	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2677 - 	CGI_10008271	superfamily	243072	232	358	1.47E-35	134.819	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2677 - 	CGI_10008271	superfamily	243072	1267	1394	1.59E-35	134.433	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2677 - 	CGI_10008271	superfamily	243072	1374	1496	1.66E-30	120.181	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2677 - 	CGI_10008271	superfamily	243072	1436	1562	2.46E-30	119.411	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2677 - 	CGI_10008271	superfamily	243072	470	621	6.32E-29	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2677 - 	CGI_10008271	superfamily	243072	142	291	1.85E-26	108.24	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2677 - 	CGI_10008271	superfamily	247799	1895	1956	2.99E-14	71.0519	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#2677 - 	CGI_10008271	superfamily	243072	1238	1270	1.23E-05	45.2376	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2678 - 	CGI_10008272	superfamily	243175	146	255	3.30E-32	116.093	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#2678 - 	CGI_10008272	superfamily	241832	58	131	4.45E-27	100.758	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#2679 - 	CGI_10008273	superfamily	246598	351	507	3.08E-97	294.118	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#2679 - 	CGI_10008273	superfamily	117535	93	182	0.000270219	39.4449	cl07540	DUF1873 superfamily	 - 	 - 	Domain of unknown function (DUF1873); This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It has no known function.
Q#2680 - 	CGI_10008274	superfamily	243095	23	200	9.01E-38	140.675	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#2680 - 	CGI_10008274	superfamily	247637	849	937	4.43E-16	79.2002	cl16912	MDR superfamily	C	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#2681 - 	CGI_10008275	superfamily	247742	72	396	1.02E-145	421.742	cl17188	enolase_like superfamily	 - 	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#2682 - 	CGI_10008276	superfamily	247637	8	353	1.06E-101	306.083	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#2683 - 	CGI_10008277	superfamily	241573	10	322	4.08E-103	320.433	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#2683 - 	CGI_10008277	superfamily	241653	341	484	9.92E-40	143.208	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#2685 - 	CGI_10008279	superfamily	245864	13	447	3.45E-114	346.188	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#2688 - 	CGI_10003022	superfamily	245814	103	190	1.50E-15	68.6262	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2694 - 	CGI_10020619	superfamily	247856	140	189	3.08E-05	39.8385	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2695 - 	CGI_10020620	superfamily	245213	434	471	4.18E-08	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	512	548	2.64E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	357	394	5.05E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	589	625	8.40E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	319	355	8.63E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	473	510	5.98E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	706	744	1.71E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	822	858	6.82E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	396	431	6.97E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	746	781	0.00012265	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	627	662	0.000804226	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	784	819	0.00097964	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	281	317	0.00258309	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2695 - 	CGI_10020620	superfamily	245213	665	704	0.00328733	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2696 - 	CGI_10020621	superfamily	241750	48	427	3.18E-176	500.633	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#2698 - 	CGI_10020623	superfamily	243409	36	144	5.80E-23	90.7185	cl03389	RNase_P_p30 superfamily	 - 	 - 	RNase P subunit p30; This protein is part of the RNase P complex that is involved in tRNA maturation.
Q#2700 - 	CGI_10020625	superfamily	241640	125	398	1.61E-74	234.093	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#2701 - 	CGI_10020626	superfamily	241584	273	356	2.52E-14	69.8327	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2701 - 	CGI_10020626	superfamily	241584	369	462	7.23E-14	68.2919	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2701 - 	CGI_10020626	superfamily	241584	171	262	1.25E-13	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2701 - 	CGI_10020626	superfamily	241584	467	563	8.27E-07	47.4911	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2702 - 	CGI_10020627	superfamily	241574	84	280	1.42E-90	282.167	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#2702 - 	CGI_10020627	superfamily	241574	340	566	1.37E-48	170.074	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#2703 - 	CGI_10020628	superfamily	243064	23	150	9.88E-31	110.911	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#2704 - 	CGI_10020629	superfamily	243064	23	150	8.34E-35	121.697	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#2705 - 	CGI_10020630	superfamily	243092	205	512	8.35E-59	197.943	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2705 - 	CGI_10020630	superfamily	128914	40	90	3.45E-05	41.7878	cl15352	CTLH superfamily	 - 	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#2705 - 	CGI_10020630	superfamily	199226	5	38	0.000725805	37.414	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#2706 - 	CGI_10020631	superfamily	247736	39	98	2.41E-06	42.6481	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#2706 - 	CGI_10020631	superfamily	247736	138	186	0.00616182	34.5069	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#2707 - 	CGI_10020632	superfamily	241563	116	158	6.07E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2707 - 	CGI_10020632	superfamily	110440	517	543	0.00067231	37.7725	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2707 - 	CGI_10020632	superfamily	128778	154	275	0.000927335	38.3999	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#2709 - 	CGI_10020634	superfamily	247723	40	117	1.10E-53	166.568	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2710 - 	CGI_10020635	superfamily	248305	12	453	4.42E-39	147.499	cl17751	Glyco_transf_22 superfamily	 - 	 - 	Alg9-like mannosyltransferase family; Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Q#2711 - 	CGI_10020636	superfamily	201217	259	306	6.65E-09	52.9132	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2711 - 	CGI_10020636	superfamily	201217	208	255	1.07E-08	52.1428	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2711 - 	CGI_10020636	superfamily	201217	106	154	2.58E-07	48.2908	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2711 - 	CGI_10020636	superfamily	201217	157	204	1.51E-06	45.9796	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2711 - 	CGI_10020636	superfamily	201217	309	360	3.27E-06	45.2092	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2711 - 	CGI_10020636	superfamily	201217	54	102	8.42E-06	43.6684	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2711 - 	CGI_10020636	superfamily	205718	39	67	8.33E-05	40.5514	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2712 - 	CGI_10020637	superfamily	242889	303	402	6.48E-20	84.5769	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#2714 - 	CGI_10020639	superfamily	247740	32	262	2.87E-99	300.565	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#2715 - 	CGI_10020640	superfamily	218802	8	147	4.71E-40	142.115	cl05462	DUF862 superfamily	 - 	 - 	"PPPDE putative peptidase domain; The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)."
Q#2716 - 	CGI_10020641	superfamily	243092	464	726	6.65E-61	210.654	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2716 - 	CGI_10020641	superfamily	243092	181	494	1.77E-46	169.823	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2716 - 	CGI_10020641	superfamily	204007	738	873	1.64E-56	192.782	cl07300	Utp13 superfamily	 - 	 - 	Utp13 specific WD40 associated domain; Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome. Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end.
Q#2717 - 	CGI_10020642	superfamily	247792	19	60	3.08E-08	49.7516	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2719 - 	CGI_10020644	superfamily	241546	212	307	1.72E-24	100.428	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#2720 - 	CGI_10020645	superfamily	247792	139	192	0.00019315	37.8104	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2722 - 	CGI_10020647	superfamily	247684	29	248	1.20E-62	204.048	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#2729 - 	CGI_10019692	superfamily	215647	279	487	4.73E-31	120.791	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#2729 - 	CGI_10019692	superfamily	243029	210	265	1.94E-11	60.4421	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#2729 - 	CGI_10019692	superfamily	241557	43	90	3.94E-07	48.6684	cl00022	YbaK_like superfamily	C	 - 	"YbaK-like.  The YbaK family of deacylase domains includes the INS amino acid-editing domain of  the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX.  The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation.  Organisms whose ProRS lacks the INS domain express an INS homolog in trans (e.g. YbaK, ProX, or PrdX)."
Q#2733 - 	CGI_10019696	superfamily	247723	105	183	1.66E-43	146.338	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2733 - 	CGI_10019696	superfamily	247723	26	96	8.44E-41	138.923	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2735 - 	CGI_10019698	superfamily	238191	74	594	6.82E-108	336.612	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#2737 - 	CGI_10019700	superfamily	241600	113	253	7.96E-47	157.017	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2737 - 	CGI_10019700	superfamily	241619	17	78	0.00456656	34.0949	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#2738 - 	CGI_10019702	superfamily	241600	3	216	2.67E-76	231.36	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#2739 - 	CGI_10019703	superfamily	110440	237	263	0.00258211	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#2740 - 	CGI_10019704	superfamily	247809	640	811	1.94E-28	113.91	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#2741 - 	CGI_10019705	superfamily	241622	44	125	3.45E-24	90.7038	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#2742 - 	CGI_10019706	superfamily	242120	23	222	2.40E-92	273.25	cl00821	Ribosomal_S3Ae superfamily	 - 	 - 	Ribosomal S3Ae family; Ribosomal S3Ae family.  
Q#2743 - 	CGI_10019707	superfamily	242120	60	264	1.40E-96	285.961	cl00821	Ribosomal_S3Ae superfamily	 - 	 - 	Ribosomal S3Ae family; Ribosomal S3Ae family.  
Q#2745 - 	CGI_10019709	superfamily	245227	62	476	0	653.501	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#2746 - 	CGI_10019710	superfamily	243066	457	544	4.66E-08	53.8488	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#2746 - 	CGI_10019710	superfamily	210118	2737	2755	0.00463737	37.6903	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#2747 - 	CGI_10019711	superfamily	245213	646	675	0.00217179	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2747 - 	CGI_10019711	superfamily	234316	2427	2477	4.00E-05	44.398	cl14012	Rhs_assc_core superfamily	C	 - 	"RHS repeat-associated core domain; This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (pfam01839) class, and an RHS repeat (pfam05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain."
Q#2747 - 	CGI_10019711	superfamily	248053	936	1010	0.000254889	41.8937	cl17499	Peptidase_M14NE-CP-C_like superfamily	 - 	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#2747 - 	CGI_10019711	superfamily	219677	815	845	0.00217937	38.5728	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#2747 - 	CGI_10019711	superfamily	245826	1699	1735	0.00741247	37.2809	cl11982	RHS_repeat superfamily	 - 	 - 	RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be involved in ligand binding. Note that this model may not find all the repeats in a protein and that it covers two RHS repeats.
Q#2748 - 	CGI_10019712	superfamily	247692	260	619	2.61E-52	184.262	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#2748 - 	CGI_10019712	superfamily	247692	107	283	4.31E-06	48.3449	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#2749 - 	CGI_10019713	superfamily	217181	103	189	5.75E-41	141.264	cl18395	Pirin superfamily	 - 	 - 	"Pirin; This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homologue of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily."
Q#2749 - 	CGI_10019713	superfamily	203319	242	349	1.91E-34	123.45	cl05342	Pirin_C superfamily	 - 	 - 	Pirin C-terminal cupin domain; This region is found the C-terminal half of the Pirin protein.
Q#2750 - 	CGI_10019714	superfamily	217181	33	116	1.62E-32	116.996	cl18395	Pirin superfamily	 - 	 - 	"Pirin; This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homologue of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily."
Q#2750 - 	CGI_10019714	superfamily	203319	169	276	7.90E-30	109.583	cl05342	Pirin_C superfamily	 - 	 - 	Pirin C-terminal cupin domain; This region is found the C-terminal half of the Pirin protein.
Q#2751 - 	CGI_10019715	superfamily	247792	13	60	2.96E-06	45.1292	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2751 - 	CGI_10019715	superfamily	241563	151	188	0.000122255	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2751 - 	CGI_10019715	superfamily	128778	213	318	0.000479627	39.1703	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#2752 - 	CGI_10019716	superfamily	248012	16	151	5.86E-20	81.2156	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2753 - 	CGI_10019717	superfamily	248012	16	155	8.01E-20	80.8304	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2755 - 	CGI_10019719	superfamily	248012	16	155	6.24E-18	75.8228	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2756 - 	CGI_10010239	superfamily	246664	19	420	4.18E-132	391.553	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#2757 - 	CGI_10010240	superfamily	246664	315	697	4.45E-132	402.338	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#2757 - 	CGI_10010240	superfamily	246664	214	256	5.63E-06	48.0754	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#2760 - 	CGI_10010243	superfamily	199166	118	317	5.63E-23	95.472	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#2760 - 	CGI_10010243	superfamily	243074	29	72	1.14E-12	62.5241	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#2760 - 	CGI_10010243	superfamily	199166	331	386	0.00137675	38.4624	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#2761 - 	CGI_10010244	superfamily	243092	327	643	2.81E-19	87.7756	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2761 - 	CGI_10010244	superfamily	151977	101	131	1.39E-07	48.9622	cl13056	Dynein_IC2 superfamily	 - 	 - 	"Cytoplasmic dynein 1 intermediate chain 2; Intermediate chain IC 2 forms part of the complex cytoplasmic dynein 1 along with a heavy chain (HC), two light intermediate chains (LICs) and three light chains (LCs). The complex is responsible for hydrolysing ATP to generate force toward the minus end of microtubules. IC binds to the HC via the N terminal binding domain on the HC and ICs contain binding sites for the LCs. The ICs are responsible for binding to kinetochores and the Golgi apparatus through an interaction with the p150Glued subunit of dynactin which is another complex."
Q#2762 - 	CGI_10010245	superfamily	243035	77	204	7.64E-29	110.787	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2762 - 	CGI_10010245	superfamily	243035	229	331	1.08E-17	79.5861	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2762 - 	CGI_10010245	superfamily	243035	358	430	1.84E-07	49.5406	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2762 - 	CGI_10010245	superfamily	243035	40	75	7.60E-06	44.6562	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2763 - 	CGI_10010246	superfamily	243035	89	203	4.03E-33	124.269	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2763 - 	CGI_10010246	superfamily	243035	378	492	2.79E-22	93.4533	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2763 - 	CGI_10010246	superfamily	243035	227	352	1.12E-29	115.094	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2763 - 	CGI_10010246	superfamily	243035	527	629	1.05E-24	100.143	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2763 - 	CGI_10010246	superfamily	243035	651	756	1.27E-24	100.457	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2763 - 	CGI_10010246	superfamily	243035	4	53	5.35E-09	54.6095	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2764 - 	CGI_10010247	superfamily	243035	89	142	3.96E-13	61.847	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2765 - 	CGI_10010248	superfamily	243035	130	200	7.25E-06	42.2218	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2765 - 	CGI_10010248	superfamily	243035	11	120	1.56E-11	57.995	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2766 - 	CGI_10010249	superfamily	241607	36	61	0.00470299	30.3402	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#2767 - 	CGI_10010250	superfamily	222269	74	285	1.05E-34	129.751	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#2769 - 	CGI_10010252	superfamily	246723	7	505	0	598.781	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#2771 - 	CGI_10010254	superfamily	243095	300	514	1.57E-74	239.94	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#2772 - 	CGI_10010255	superfamily	241641	98	137	0.000242483	38.2137	cl00150	TY superfamily	C	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#2773 - 	CGI_10010256	superfamily	245819	153	340	5.23E-47	168.141	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#2774 - 	CGI_10010257	superfamily	247692	198	547	2.40E-45	163.616	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#2774 - 	CGI_10010257	superfamily	247692	49	240	2.93E-12	67.6708	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#2775 - 	CGI_10010258	superfamily	247058	51	237	1.00E-37	133.455	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#2777 - 	CGI_10002431	superfamily	241563	62	100	4.06E-05	41.1188	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2777 - 	CGI_10002431	superfamily	241563	8	53	0.00436691	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2780 - 	CGI_10002434	superfamily	245596	104	318	6.08E-113	329.543	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#2784 - 	CGI_10019723	superfamily	248054	54	102	0.00216193	36.296	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#2785 - 	CGI_10019724	superfamily	247724	56	176	1.12E-11	59.3436	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2789 - 	CGI_10019729	superfamily	191128	47	143	1.70E-10	53.6968	cl04846	Ninjurin superfamily	 - 	 - 	Ninjurin; Ninjurin (nerve injury-induced protein) is involved in nerve regeneration and in the formation and function in some tissues.
Q#2790 - 	CGI_10019730	superfamily	191128	75	112	7.35E-05	38.674	cl04846	Ninjurin superfamily	C	 - 	Ninjurin; Ninjurin (nerve injury-induced protein) is involved in nerve regeneration and in the formation and function in some tissues.
Q#2791 - 	CGI_10019731	superfamily	241580	71	148	1.54E-48	161.568	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#2793 - 	CGI_10019733	superfamily	216112	675	1023	7.13E-112	354.295	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#2795 - 	CGI_10019735	superfamily	219619	290	342	1.21E-17	78.0183	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#2795 - 	CGI_10019735	superfamily	219619	432	509	7.93E-13	64.1511	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#2796 - 	CGI_10019736	superfamily	202662	235	271	0.00696015	35.6106	cl18231	B3_4 superfamily	NC	 - 	B3/4 domain; This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.
Q#2798 - 	CGI_10019738	superfamily	241659	146	227	6.39E-13	61.3819	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#2798 - 	CGI_10019738	superfamily	241659	41	119	3.15E-06	43.2775	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#2801 - 	CGI_10019741	superfamily	241563	75	115	8.24E-08	49.4	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#2801 - 	CGI_10019741	superfamily	217754	119	233	4.62E-05	42.233	cl04284	RasGAP_C superfamily	C	 - 	RasGAP C-terminus; RasGAP C-terminus.  
Q#2803 - 	CGI_10019743	superfamily	243250	357	592	1.63E-114	355.033	cl02959	Glyco_hydro_9 superfamily	C	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#2803 - 	CGI_10019743	superfamily	243250	590	713	2.83E-29	120.446	cl02959	Glyco_hydro_9 superfamily	N	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#2803 - 	CGI_10019743	superfamily	248312	59	202	1.07E-08	53.9052	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#2804 - 	CGI_10019744	superfamily	245864	48	346	3.83E-40	147.81	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#2806 - 	CGI_10019746	superfamily	216566	1052	1151	0.00110689	40.6337	cl18370	Peptidase_M23 superfamily	 - 	 - 	"Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Escherichia coli murein hydrolase activator NlpD, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown."
Q#2807 - 	CGI_10019747	superfamily	203136	103	223	9.96E-10	55.4284	cl04867	LRAT superfamily	 - 	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#2807 - 	CGI_10019747	superfamily	203136	354	396	0.0012	37.324	cl04867	LRAT superfamily	N	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#2808 - 	CGI_10019748	superfamily	244943	21	206	8.26E-51	166.181	cl08415	TPK superfamily	 - 	 - 	"Thiamine pyrophosphokinase; Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis."
Q#2809 - 	CGI_10019749	superfamily	217882	489	783	6.76E-115	353.896	cl11712	ORC2 superfamily	 - 	 - 	Origin recognition complex subunit 2; All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. The function of ORC is reviewed in.
Q#2809 - 	CGI_10019749	superfamily	242406	60	203	1.48E-17	80.7133	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#2810 - 	CGI_10019750	superfamily	220692	59	364	2.14E-25	103.823	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#2811 - 	CGI_10004417	superfamily	244307	1505	1968	0	682.961	cl06123	DHR2_DOCK superfamily	 - 	 - 	"Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins; DOCK proteins comprise a family of atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. They are also called the CZH (CED-5, Dock180, and MBC-zizimin homology) family, after the first family members identified. Dock180 was first isolated as a binding partner for the adaptor protein Crk. The Caenorhabditis elegans protein, Ced-5, is essential for cell migration and phagocytosis, while the Drosophila ortholog, Myoblast city (MBC), is necessary for myoblast fusion and dorsal closure. DOCKs are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1 (or Dock180), 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1, and DHR-2 (also called CZH2 or Docker). This alignment model represents the DHR-2 domain of DOCK proteins, which contains the catalytic GEF activity for Rac and/or Cdc42."
Q#2811 - 	CGI_10004417	superfamily	246669	540	677	1.44E-65	222.228	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#2811 - 	CGI_10004417	superfamily	221285	65	146	2.14E-13	68.917	cl13339	DUF3398 superfamily	 - 	 - 	Domain of unknown function (DUF3398); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 100 amino acids in length.
Q#2812 - 	CGI_10004418	superfamily	245201	33	403	0	722.332	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2812 - 	CGI_10004418	superfamily	241566	1076	1122	7.29E-11	59.8132	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#2812 - 	CGI_10004418	superfamily	247725	1044	1088	1.81E-07	50.8481	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2812 - 	CGI_10004418	superfamily	149849	877	943	0.00133433	38.6283	cl07487	Rho_Binding superfamily	 - 	 - 	"Rho Binding; Rho Binding Domain is responsible for the recognition and binding of Rho binding domain-containing proteins (such as ROCK) to Rho, resulting in activation of the GTPase which in turn modulates the phosphorylation of various signalling proteins. This domain is within an amphipathic alpha-helical coiled-coil and interacts with Rho through predominantly hydrophobic interactions."
Q#2813 - 	CGI_10004419	superfamily	241862	200	349	1.13E-21	91.6488	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#2816 - 	CGI_10007066	superfamily	248012	7	75	0.00377584	34.2212	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#2817 - 	CGI_10007067	superfamily	217740	29	183	7.70E-12	60.4529	cl18427	Scramblase superfamily	C	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#2818 - 	CGI_10007068	superfamily	247856	68	123	7.46E-05	38.6829	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2821 - 	CGI_10007071	superfamily	247723	241	309	1.25E-36	133.226	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2821 - 	CGI_10007071	superfamily	207717	162	236	9.64E-26	102.133	cl02755	LAM superfamily	 - 	 - 	"LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes."
Q#2822 - 	CGI_10007072	superfamily	241706	22	102	2.77E-48	151.533	cl00229	eIF1_SUI1_like superfamily	 - 	 - 	"Eukaryotic initiation factor 1 and related proteins; Members of the eIF1/SUI1 (eukaryotic initiation factor 1) family are found in eukaryotes, archaea, and some bacteria; eukaryotic members are understood to play an important role in accurate initiator codon recognition during translation initiation. eIF1 interacts with 18S rRNA in the 40S ribosomal subunit during eukaryotic translation initiation. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown. The function of non-eukaryotic family members is also unclear."
Q#2824 - 	CGI_10007074	superfamily	241647	1288	1316	1.37E-07	50.219	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#2824 - 	CGI_10007074	superfamily	243091	484	607	2.12E-40	147.481	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#2824 - 	CGI_10007074	superfamily	149349	1355	1443	5.69E-22	93.0782	cl07026	SRI superfamily	 - 	 - 	"SRI (Set2 Rpb1 interacting) domain; The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation."
Q#2824 - 	CGI_10007074	superfamily	197795	432	483	2.26E-20	87.455	cl02673	AWS superfamily	 - 	 - 	associated with SET domains; subdomain of PRESET
Q#2824 - 	CGI_10007074	superfamily	214703	608	624	0.000167436	41.2368	cl02636	PostSET superfamily	 - 	 - 	Cysteine-rich motif following a subset of SET domains; Cysteine-rich motif following a subset of SET domains.  
Q#2825 - 	CGI_10007075	superfamily	247750	44	289	5.67E-71	224.664	cl17196	E1_enzyme_family superfamily	 - 	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#2826 - 	CGI_10007076	superfamily	222431	338	426	1.52E-21	88.8185	cl16447	RPAP3_C superfamily	 - 	 - 	Potential Monad-binding region of RPAP3; This domain is found at the C-terminus of RNA-polymerase II-associated proteins. These proteins bind to Monad and are involved in regulating apoptosis. They contain TPR-repeats towards the N_terminus.
Q#2828 - 	CGI_10007078	superfamily	221630	24	91	9.20E-07	42.3982	cl13918	CWC25 superfamily	 - 	 - 	"Pre-mRNA splicing factor; This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with pfam10197. There is a single completely conserved residue Y that may be functionally important. Cwc25 has been identified to associate with pre-mRNA splicing factor Cef1/Ntc85, a component of the Prp19-associated complex (NTC) involved in spliceosome activation. Cwc25 is neither tightly associated with NTC nor required for spliceosome activation, but is required for the first catalytic reaction."
Q#2837 - 	CGI_10009832	superfamily	245213	294	332	3.29E-08	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2837 - 	CGI_10009832	superfamily	245213	525	560	5.96E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2837 - 	CGI_10009832	superfamily	245213	448	484	1.21E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2837 - 	CGI_10009832	superfamily	245213	412	445	6.38E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2837 - 	CGI_10009832	superfamily	245213	494	521	0.000128544	40.6978	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2837 - 	CGI_10009832	superfamily	245213	335	369	0.000293233	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2837 - 	CGI_10009832	superfamily	245213	377	407	0.000719449	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2837 - 	CGI_10009832	superfamily	219501	28	104	2.31E-19	83.9189	cl06622	MNNL superfamily	 - 	 - 	N terminus of Notch ligand; This entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins.
Q#2840 - 	CGI_10009835	superfamily	201526	50	123	8.99E-27	98.7644	cl09522	Synaptobrevin superfamily	 - 	 - 	Synaptobrevin; Synaptobrevin.  
Q#2841 - 	CGI_10009836	superfamily	241874	51	463	0	550.356	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2841 - 	CGI_10009836	superfamily	241874	12	57	9.01E-16	78.8718	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2841 - 	CGI_10009836	superfamily	245010	467	536	2.35E-05	43.1348	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#2841 - 	CGI_10009836	superfamily	241874	520	563	0.0025599	39.1334	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2842 - 	CGI_10009837	superfamily	248458	52	236	1.05E-05	46.5381	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#2842 - 	CGI_10009837	superfamily	247913	428	609	8.75E-29	120.656	cl17359	PTR2 superfamily	N	 - 	POT family; The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters.
Q#2843 - 	CGI_10009838	superfamily	243034	551	650	2.64E-21	90.5171	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2843 - 	CGI_10009838	superfamily	243034	619	718	2.26E-17	78.9611	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2843 - 	CGI_10009838	superfamily	243034	59	166	4.98E-05	42.3672	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2843 - 	CGI_10009838	superfamily	243034	440	581	0.000235471	40.4412	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#2844 - 	CGI_10009839	superfamily	247723	392	473	4.28E-39	137.31	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2844 - 	CGI_10009839	superfamily	247723	10	82	9.28E-31	113.483	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2845 - 	CGI_10009840	superfamily	241578	693	859	3.18E-13	69.517	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#2845 - 	CGI_10009840	superfamily	246031	319	440	3.66E-20	89.5212	cl12567	Beta-Casp superfamily	 - 	 - 	Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.
Q#2846 - 	CGI_10009841	superfamily	218912	51	139	1.62E-05	43.7879	cl18485	COG2 superfamily	N	 - 	"COG (conserved oligomeric Golgi) complex component, COG2; The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function. The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficing proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs."
Q#2847 - 	CGI_10009842	superfamily	241646	462	506	3.46E-06	44.7483	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#2848 - 	CGI_10001210	superfamily	243077	7	59	3.48E-15	64.4889	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#2849 - 	CGI_10015052	superfamily	248097	82	201	5.95E-21	84.6242	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#2850 - 	CGI_10015053	superfamily	216456	474	576	8.40E-22	93.5422	cl03182	RYDR_ITPR superfamily	C	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#2850 - 	CGI_10015053	superfamily	197746	112	166	1.21E-05	43.4839	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#2850 - 	CGI_10015053	superfamily	197746	310	338	0.00206054	36.5503	cl02624	MIR superfamily	C	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#2851 - 	CGI_10015054	superfamily	241599	484	532	3.25E-10	56.4829	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2851 - 	CGI_10015054	superfamily	241599	395	453	2.38E-08	51.0901	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2852 - 	CGI_10015055	superfamily	241599	482	530	9.32E-11	58.0237	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2852 - 	CGI_10015055	superfamily	241599	393	451	1.85E-08	51.4753	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#2853 - 	CGI_10015056	superfamily	216456	610	788	4.35E-50	178.286	cl03182	RYDR_ITPR superfamily	 - 	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#2853 - 	CGI_10015056	superfamily	216456	1	90	1.76E-25	107.024	cl03182	RYDR_ITPR superfamily	N	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#2854 - 	CGI_10015057	superfamily	218109	144	192	1.47E-06	45.3942	cl12292	Gly_transf_sug superfamily	N	 - 	"Glycosyltransferase sugar-binding region containing DXD motif; The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases."
Q#2855 - 	CGI_10015058	superfamily	218109	144	192	1.40E-06	45.3942	cl12292	Gly_transf_sug superfamily	N	 - 	"Glycosyltransferase sugar-binding region containing DXD motif; The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases."
Q#2856 - 	CGI_10015059	superfamily	245847	24	143	7.56E-10	53.3294	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#2857 - 	CGI_10015060	superfamily	247755	1	167	5.92E-97	311.539	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2857 - 	CGI_10015060	superfamily	247755	1070	1142	3.68E-36	138.97	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2857 - 	CGI_10015060	superfamily	244201	517	634	2.77E-28	111.939	cl05797	SMC_hinge superfamily	 - 	 - 	SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.
Q#2857 - 	CGI_10015060	superfamily	243054	822	931	0.000520825	41.6624	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#2857 - 	CGI_10015060	superfamily	245835	671	848	0.000893023	41.1849	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#2860 - 	CGI_10015063	superfamily	194414	135	181	1.76E-08	51.5113	cl02684	zf-DBF superfamily	 - 	 - 	DBF zinc finger; This domain is predicted to bind metal ions and is often found associated with pfam00533 and pfam02178.
Q#2861 - 	CGI_10015064	superfamily	241750	30	297	4.44E-85	258.272	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#2862 - 	CGI_10015065	superfamily	246908	115	214	1.63E-47	161.211	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#2862 - 	CGI_10015065	superfamily	247683	54	106	2.57E-23	93.0308	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#2862 - 	CGI_10015065	superfamily	245201	228	485	7.41E-154	442.145	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2868 - 	CGI_10013626	superfamily	248312	21	159	6.32E-05	40.0293	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#2870 - 	CGI_10013628	superfamily	247755	72	126	2.07E-16	72.5376	cl17201	ABC_ATPase superfamily	NC	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#2872 - 	CGI_10013630	superfamily	245206	2	262	9.33E-124	356.46	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#2873 - 	CGI_10013631	superfamily	247724	19	183	1.22E-115	333.508	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2874 - 	CGI_10013632	superfamily	248458	43	414	1.14E-18	85.4433	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#2875 - 	CGI_10013633	superfamily	147195	6	83	3.48E-45	154.626	cl04835	NCD1 superfamily	 - 	 - 	"NAB conserved region 1 (NCD1); Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription factors. This region consists of the N-terminal NAB conserved region 1, which interacts with the EGR1 inhibitory domain (R1). It may also mediate multimerisation."
Q#2875 - 	CGI_10013633	superfamily	218320	213	311	3.24E-35	129.677	cl04836	NCD2 superfamily	N	 - 	"NAB conserved region 2 (NCD2); Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription factors. This family consists of NAB conserved region 2, near the C-terminus of the protein. It is necessary for transcriptional repression by the Nab proteins. It is also required for transcription activation by Nab proteins at Nab-activated promoters."
Q#2877 - 	CGI_10013635	superfamily	247724	76	270	3.61E-95	299.794	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2877 - 	CGI_10013635	superfamily	247725	518	593	1.25E-38	140.919	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2877 - 	CGI_10013635	superfamily	243072	913	972	2.54E-12	65.4826	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2877 - 	CGI_10013635	superfamily	243047	759	867	1.48E-49	172.034	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#2877 - 	CGI_10013635	superfamily	247725	679	739	4.88E-18	81.9833	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#2879 - 	CGI_10013637	superfamily	243088	39	165	1.46E-62	200.287	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#2879 - 	CGI_10013637	superfamily	245835	186	430	6.95E-86	263.477	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#2881 - 	CGI_10013639	superfamily	248422	2023	2199	3.06E-05	46.9305	cl17868	CHAT superfamily	 - 	 - 	CHAT domain; These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins.
Q#2882 - 	CGI_10013640	superfamily	241750	24	360	1.11E-97	296.037	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#2883 - 	CGI_10013641	superfamily	241596	107	163	1.64E-14	64.9279	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#2884 - 	CGI_10013642	superfamily	247724	50	282	4.45E-149	422.725	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2884 - 	CGI_10013642	superfamily	247063	276	351	6.35E-40	137.226	cl15768	TGS superfamily	 - 	 - 	"The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role."
Q#2885 - 	CGI_10013643	superfamily	220774	38	305	2.68E-15	78.8201	cl11118	EIF4E-T superfamily	C	 - 	"Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E; EIF4E-T is the transporter protein for shuttling the mRNA cap-binding protein EIF4E protein, targeting it for nuclear import. EIF4E-T contains several key binding domains including two functional leucine-rich NESs (nuclear export signals) between residues 438-447 and 613-638 in the human protein. The other two binding domains are an EIF4E-binding site, between residues 27-42 in Q9EST3, and a bipartite NLS (nuclear localisation signals) between 194-211, and these lie in family EIF4E-T_N. EIF4E is the eukaryotic translation initiation factor 4E that is the rate-limiting factor for cap-dependent translation initiation."
Q#2887 - 	CGI_10013645	superfamily	247723	153	236	3.48E-43	149.329	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2887 - 	CGI_10013645	superfamily	247792	257	299	1.17E-08	51.6776	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2887 - 	CGI_10013645	superfamily	245220	312	374	4.18E-24	96.3198	cl09957	zf-UBP superfamily	 - 	 - 	Zn-finger in ubiquitin-hydrolases and other protein; Zn-finger in ubiquitin-hydrolases and other protein.  
Q#2889 - 	CGI_10013647	superfamily	241550	31	325	3.58E-120	351.834	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#2893 - 	CGI_10003928	superfamily	247692	78	417	1.14E-120	361.172	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#2894 - 	CGI_10003929	superfamily	247692	1	92	1.75E-17	76.2804	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#2895 - 	CGI_10006473	superfamily	247068	39	138	6.22E-31	113.562	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2895 - 	CGI_10006473	superfamily	247068	146	244	2.35E-19	81.5909	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2895 - 	CGI_10006473	superfamily	247068	266	326	8.36E-07	46.1526	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2895 - 	CGI_10006473	superfamily	247068	5	31	9.32E-05	39.9894	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2896 - 	CGI_10006474	superfamily	247907	302	462	5.47E-28	113.667	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2896 - 	CGI_10006474	superfamily	247907	526	674	1.40E-15	77.0732	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#2896 - 	CGI_10006474	superfamily	238012	830	877	2.49E-13	67.7646	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#2896 - 	CGI_10006474	superfamily	245213	216	251	5.83E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2896 - 	CGI_10006474	superfamily	245213	486	519	7.14E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2896 - 	CGI_10006474	superfamily	245213	703	732	0.00245632	38.3866	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#2896 - 	CGI_10006474	superfamily	215647	1302	1532	4.10E-52	186.66	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#2896 - 	CGI_10006474	superfamily	221370	957	1189	9.42E-16	78.9525	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#2896 - 	CGI_10006474	superfamily	243146	2385	2430	3.61E-11	61.5234	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2896 - 	CGI_10006474	superfamily	243086	1216	1288	1.33E-09	56.9998	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#2896 - 	CGI_10006474	superfamily	243146	2346	2396	9.21E-06	45.6271	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2896 - 	CGI_10006474	superfamily	243029	886	942	0.000564606	40.7969	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#2896 - 	CGI_10006474	superfamily	243146	2544	2581	0.00366625	38.0262	cl02701	Kelch_3 superfamily	C	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#2903 - 	CGI_10005476	superfamily	220679	16	182	8.08E-41	138.614	cl18567	Methyltransf_16 superfamily	 - 	 - 	Putative methyltransferase; Putative methyltransferase.  
Q#2904 - 	CGI_10005477	superfamily	247723	22	117	4.08E-13	65.8943	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#2904 - 	CGI_10005477	superfamily	242788	133	228	3.07E-05	43.1113	cl01936	Rad52_Rad22 superfamily	N	 - 	"Rad52/22 family double-strand break repair protein; The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52. These proteins contain two helix-hairpin-helix motifs."
Q#2905 - 	CGI_10005478	superfamily	241802	1900	2212	2.72E-75	255.89	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#2905 - 	CGI_10005478	superfamily	207662	163	222	7.59E-07	49.3834	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#2911 - 	CGI_10005484	superfamily	241559	24	128	5.19E-22	93.9147	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#2911 - 	CGI_10005484	superfamily	241559	141	236	2.59E-14	71.5731	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#2911 - 	CGI_10005484	superfamily	241559	243	335	6.20E-09	55.3947	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#2911 - 	CGI_10005484	superfamily	216033	775	855	1.35E-17	80.4556	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#2911 - 	CGI_10005484	superfamily	216033	1216	1301	5.34E-17	78.9148	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#2911 - 	CGI_10005484	superfamily	216033	1315	1400	4.44E-15	73.1368	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#2911 - 	CGI_10005484	superfamily	216033	1124	1207	1.34E-13	68.8996	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#2911 - 	CGI_10005484	superfamily	216033	546	628	1.32E-12	66.2032	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#2911 - 	CGI_10005484	superfamily	216033	858	954	2.60E-09	56.188	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#2911 - 	CGI_10005484	superfamily	216033	704	765	3.96E-05	43.4764	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#2913 - 	CGI_10005486	superfamily	203591	83	216	9.59E-29	110.154	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#2915 - 	CGI_10012147	superfamily	201217	12	61	7.22E-10	49.4464	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#2916 - 	CGI_10012148	superfamily	243092	31	329	5.07E-57	196.017	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#2916 - 	CGI_10012148	superfamily	221242	366	666	6.36E-59	202.381	cl13285	DUF3337 superfamily	 - 	 - 	Domain of unknown function (DUF3337); This family of proteins are functionally uncharacterized. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length.
Q#2918 - 	CGI_10012150	superfamily	245206	33	320	2.33E-107	318.068	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#2919 - 	CGI_10012151	superfamily	245206	32	321	1.81E-109	323.075	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#2920 - 	CGI_10012152	superfamily	241913	173	245	2.25E-09	53.3789	cl00509	hot_dog superfamily	C	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#2923 - 	CGI_10012155	superfamily	219996	120	172	0.000878434	37.0528	cl07379	Gon7 superfamily	N	 - 	Gon7 family; In S. cerevisiae Gon7 is a member of the KEOPS protein complex. A protein complex proposed to be involved in transcription and promoting telomere uncapping and telomere elongation.
Q#2924 - 	CGI_10012156	superfamily	247856	106	167	6.10E-12	57.5577	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2924 - 	CGI_10012156	superfamily	247856	33	89	0.00198429	34.0605	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#2925 - 	CGI_10012157	superfamily	241868	1393	1565	9.86E-21	92.5686	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#2926 - 	CGI_10012158	superfamily	245201	373	589	3.40E-34	132.746	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#2926 - 	CGI_10012158	superfamily	216276	204	280	1.47E-06	48.3131	cl15639	Activin_recp superfamily	 - 	 - 	"Activin types I and II receptor domain; This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box."
Q#2926 - 	CGI_10012158	superfamily	216276	35	103	1.08E-05	45.6167	cl15639	Activin_recp superfamily	 - 	 - 	"Activin types I and II receptor domain; This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box."
Q#2927 - 	CGI_10012159	superfamily	243179	136	240	5.67E-29	107.434	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#2929 - 	CGI_10006832	superfamily	247068	64	150	0.000669757	37.7258	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#2930 - 	CGI_10006833	superfamily	247639	47	290	6.29E-42	147.608	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#2931 - 	CGI_10006834	superfamily	217390	174	313	3.26E-05	42.1617	cl18407	TPT superfamily	 - 	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#2933 - 	CGI_10006836	superfamily	219910	3	129	2.09E-10	53.7735	cl07253	DUF1761 superfamily	 - 	 - 	Protein of unknown function (DUF1761); Family of conserved fungal and bacterial membrane proteins with unknown function.
Q#2934 - 	CGI_10006837	superfamily	247724	14	176	7.20E-102	293.571	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2935 - 	CGI_10000237	superfamily	247724	3	177	3.32E-131	368.432	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#2936 - 	CGI_10000218	superfamily	222150	67	92	0.00018971	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2937 - 	CGI_10018525	superfamily	245206	4	274	6.29E-104	304.93	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#2940 - 	CGI_10018528	superfamily	245225	167	533	4.61E-28	115.803	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#2942 - 	CGI_10018530	superfamily	247675	248	312	0.00681797	36.1625	cl17011	Arginase_HDAC superfamily	C	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#2943 - 	CGI_10018531	superfamily	191913	61	164	9.72E-09	52.7203	cl07876	NIPSNAP superfamily	C	 - 	NIPSNAP; Members of this family include many hypothetical proteins. It also includes members of the NIPSNAP family which have putative roles in vesicular transport. This domain is often found in duplicate.
Q#2945 - 	CGI_10018533	superfamily	222150	880	905	0.0035342	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#2946 - 	CGI_10018534	superfamily	220249	158	220	5.06E-10	53.3781	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#2947 - 	CGI_10018535	superfamily	245595	103	396	5.07E-164	465.072	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#2947 - 	CGI_10018535	superfamily	216944	34	84	4.31E-08	49.8883	cl03496	Propep_M14 superfamily	N	 - 	"Carboxypeptidase activation peptide; Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme."
Q#2949 - 	CGI_10018537	superfamily	241750	62	274	2.39E-44	154.428	cl00281	metallo-dependent_hydrolases superfamily	C	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#2952 - 	CGI_10018540	superfamily	220390	52	218	6.12E-42	142.794	cl10748	Peptidase_M76 superfamily	 - 	 - 	Peptidase M76 family; This is a family of metalloproteases. Proteins in this family are also annotated as Ku70-binding proteins.
Q#2953 - 	CGI_10018541	superfamily	243035	84	178	1.05E-06	49.5406	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2953 - 	CGI_10018541	superfamily	215647	2390	2603	6.05E-47	171.638	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#2953 - 	CGI_10018541	superfamily	243086	2307	2351	5.65E-10	58.1554	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#2955 - 	CGI_10018543	superfamily	243072	15	139	7.75E-14	64.327	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2956 - 	CGI_10018544	superfamily	243072	89	218	2.09E-16	75.883	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2956 - 	CGI_10018544	superfamily	243072	308	444	8.25E-15	71.2606	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2956 - 	CGI_10018544	superfamily	243072	159	299	3.99E-12	63.5566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2961 - 	CGI_10018549	superfamily	245598	531	864	2.54E-144	432.14	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#2961 - 	CGI_10018549	superfamily	243072	341	461	2.56E-26	105.929	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2961 - 	CGI_10018549	superfamily	243072	200	327	1.44E-19	86.2834	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#2964 - 	CGI_10018553	superfamily	217895	21	134	1.52E-05	44.1711	cl04401	CD20 superfamily	 - 	 - 	"CD20-like family; This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton."
Q#2965 - 	CGI_10018554	superfamily	243035	173	262	8.64E-19	79.2009	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2965 - 	CGI_10018554	superfamily	198867	5	45	2.11E-07	47.3361	cl06652	BACK superfamily	N	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#2967 - 	CGI_10018556	superfamily	243035	78	186	9.69E-21	83.4381	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#2969 - 	CGI_10002834	superfamily	241609	505	581	8.28E-24	95.9079	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#2969 - 	CGI_10002834	superfamily	241571	371	499	3.17E-07	48.5627	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#2969 - 	CGI_10002834	superfamily	241583	139	321	9.79E-40	143.095	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#2970 - 	CGI_10001618	superfamily	220714	54	180	1.45E-68	211.343	cl11024	Kin17_mid superfamily	 - 	 - 	"Domain of Kin17 curved DNA-binding protein; Kin17_mid is the conserved central 169 residue region of a family of Kin17 proteins. Towards the N-terminal end there is a zinc-finger domain, and in human and mouse members there is a RecA-like domain further downstream. The Kin17 protein in humans forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle."
Q#2970 - 	CGI_10001618	superfamily	217505	181	291	2.35E-46	162.414	cl04021	Serinc superfamily	N	 - 	Serine incorporator (Serinc); This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid. Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis.
Q#2970 - 	CGI_10001618	superfamily	205121	28	52	0.00456817	34.0168	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#2971 - 	CGI_10001619	superfamily	247792	84	140	5.24E-11	54.5743	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#2973 - 	CGI_10000768	superfamily	244363	293	378	6.33E-28	108.236	cl06336	Commd superfamily	N	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#2976 - 	CGI_10004388	superfamily	245814	351	420	5.73E-12	62.5067	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2976 - 	CGI_10004388	superfamily	245814	628	667	1.85E-05	43.1644	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2976 - 	CGI_10004388	superfamily	245814	142	224	8.05E-05	41.3369	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#2984 - 	CGI_10004370	superfamily	243905	74	172	0.000111646	39.4778	cl04855	BLUF superfamily	 - 	 - 	Sensors of blue-light using FAD; The BLUF domain has been shown to bind FAD in the AppA protein. AppA is involved in the repression of photosynthesis genes in response to blue-light.
Q#2985 - 	CGI_10004371	superfamily	242793	160	335	3.11E-63	204.209	cl01947	MT-A70 superfamily	 - 	 - 	"MT-A70; MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A methyl-transferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs."
Q#2986 - 	CGI_10004372	superfamily	192535	42	226	0.000129325	42.1978	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#2988 - 	CGI_10013747	superfamily	246669	5	114	1.88E-66	217.56	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#2989 - 	CGI_10013748	superfamily	241610	1082	1135	1.01E-16	78.4458	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#2989 - 	CGI_10013748	superfamily	241610	362	413	5.79E-10	58.8006	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#2989 - 	CGI_10013748	superfamily	215827	1385	1558	9.12E-29	118.34	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#2989 - 	CGI_10013748	superfamily	243065	3904	4063	3.11E-28	115.192	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#2989 - 	CGI_10013748	superfamily	215827	562	720	4.52E-25	107.554	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#2989 - 	CGI_10013748	superfamily	244710	4104	4174	2.72E-19	86.6753	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#2989 - 	CGI_10013748	superfamily	248289	3541	3595	7.72E-10	58.5895	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3851	3908	5.33E-08	53.1967	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2326	2380	1.24E-07	52.0411	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3426	3482	1.59E-07	51.6559	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3310	3366	9.21E-07	49.7299	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2090	2141	1.52E-06	48.9595	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2971	3025	1.83E-06	48.5743	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2564	2620	5.62E-06	47.4187	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3656	3716	6.98E-06	47.0335	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2444	2501	8.08E-06	46.6483	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	1927	1978	1.19E-05	46.2631	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2505	2561	5.10E-05	44.3371	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2625	2681	6.49E-05	43.9519	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2383	2441	0.000113229	43.1815	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3029	3080	0.000433749	41.6407	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2855	2909	0.000471008	41.6407	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3083	3137	0.000561923	41.2555	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2741	2795	0.000563578	41.2555	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2266	2323	0.000590722	41.2555	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	1982	2039	0.00105333	40.4851	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3253	3307	0.00172277	39.7147	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	2798	2852	0.00486648	38.5591	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3791	3843	0.00524871	38.1739	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3140	3184	0.00660302	38.1739	cl17735	VWC superfamily	C	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2989 - 	CGI_10013748	superfamily	248289	3598	3653	0.00675819	37.7887	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#2990 - 	CGI_10013749	superfamily	243058	250	347	4.77E-08	50.3907	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#2991 - 	CGI_10013750	superfamily	241574	285	514	2.63E-119	354.585	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#2991 - 	CGI_10013750	superfamily	197431	95	155	6.08E-05	42.7964	cl06408	UP_III_II superfamily	NC	 - 	"Uroplakin IIIb, IIIa and II; Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb,  UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains separating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers; six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis."
Q#2992 - 	CGI_10013751	superfamily	241584	459	575	7.61E-09	54.0395	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2992 - 	CGI_10013751	superfamily	241584	346	452	2.26E-06	46.7207	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2992 - 	CGI_10013751	superfamily	241584	264	328	0.000703024	39.0167	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2992 - 	CGI_10013751	superfamily	242406	676	817	1.92E-19	86.4913	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#2993 - 	CGI_10013752	superfamily	241554	47	187	2.02E-60	199.92	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#2993 - 	CGI_10013752	superfamily	247069	342	478	1.84E-21	92.063	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#2994 - 	CGI_10013753	superfamily	218702	100	147	0.000523408	36.111	cl05324	Dimer_Tnp_hAT superfamily	N	 - 	hAT family dimerisation domain; This dimerisation domain is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation domain forms extremely stable dimers in vitro.
Q#2995 - 	CGI_10013754	superfamily	241874	77	617	0	824.986	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#2996 - 	CGI_10013755	superfamily	241570	240	361	2.62E-15	73.129	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#2996 - 	CGI_10013755	superfamily	241570	140	220	1.04E-05	44.6242	cl00047	CAP_ED superfamily	N	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#2998 - 	CGI_10013757	superfamily	241584	210	302	2.68E-08	50.5727	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#2998 - 	CGI_10013757	superfamily	245814	88	178	4.04E-08	50.1965	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3000 - 	CGI_10013759	superfamily	110440	356	383	0.00356022	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#3002 - 	CGI_10013761	superfamily	243092	2	233	3.12E-28	108.962	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3003 - 	CGI_10004662	superfamily	243072	479	604	4.84E-25	100.921	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3003 - 	CGI_10004662	superfamily	243072	378	505	2.09E-09	55.4674	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3003 - 	CGI_10004662	superfamily	241568	253	298	5.56E-06	44.376	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#3005 - 	CGI_10004664	superfamily	215754	39	117	4.23E-15	68.434	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#3005 - 	CGI_10004664	superfamily	215754	240	275	5.45E-09	51.8704	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#3006 - 	CGI_10004665	superfamily	243082	336	723	2.95E-141	436.303	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#3010 - 	CGI_10017878	superfamily	248458	50	135	8.87E-06	45.3825	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#3011 - 	CGI_10017879	superfamily	243035	279	386	9.35E-14	68.4153	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3011 - 	CGI_10017879	superfamily	241619	177	228	9.44E-06	43.9977	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#3011 - 	CGI_10017879	superfamily	243035	56	146	3.49E-05	42.607	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3012 - 	CGI_10017880	superfamily	241568	379	413	0.00023178	39.3684	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#3013 - 	CGI_10017881	superfamily	247755	940	1167	1.08E-121	379.145	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#3013 - 	CGI_10017881	superfamily	247755	312	501	1.01E-101	323.267	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#3013 - 	CGI_10017881	superfamily	216049	104	228	7.87E-20	90.8082	cl18356	ABC_membrane superfamily	NC	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#3013 - 	CGI_10017881	superfamily	216049	606	894	1.65E-15	77.3262	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#3014 - 	CGI_10017882	superfamily	243555	20	209	3.96E-20	86.6762	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#3016 - 	CGI_10017884	superfamily	110204	679	882	1.97E-91	289.875	cl03127	Lysyl_oxidase superfamily	 - 	 - 	Lysyl oxidase; Lysyl oxidase.  
Q#3016 - 	CGI_10017884	superfamily	243061	26	131	2.00E-31	119.369	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#3016 - 	CGI_10017884	superfamily	243061	585	674	4.25E-18	81.2342	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#3017 - 	CGI_10017885	superfamily	241782	12	457	0	686.395	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#3018 - 	CGI_10017886	superfamily	192535	55	287	0.000220122	41.0422	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#3019 - 	CGI_10017887	superfamily	247639	17	267	2.64E-35	129.118	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#3021 - 	CGI_10017889	superfamily	245213	308	344	2.24E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	458	493	6.23E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	232	267	1.54E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	571	607	4.03E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	271	306	7.36E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	346	382	8.95E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	118	154	0.000135894	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	195	230	0.000328151	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	609	645	0.000898978	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	810	844	0.00270787	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	536	569	0.00373293	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	245213	421	455	0.00438224	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3021 - 	CGI_10017889	superfamily	243035	1135	1263	0.00764245	36.829	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3022 - 	CGI_10017890	superfamily	247792	11	58	9.94E-06	43.9736	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3022 - 	CGI_10017890	superfamily	128778	205	330	1.78E-06	46.8743	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#3022 - 	CGI_10017890	superfamily	243109	545	739	6.44E-06	45.7369	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#3022 - 	CGI_10017890	superfamily	241563	159	197	0.00602615	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3023 - 	CGI_10017891	superfamily	192535	68	345	9.05E-06	45.6646	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#3032 - 	CGI_10017900	superfamily	242406	4	113	6.37E-08	47.9713	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#3034 - 	CGI_10004732	superfamily	245864	33	424	2.00E-92	289.178	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3035 - 	CGI_10004733	superfamily	241758	133	232	2.06E-12	61.2318	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#3035 - 	CGI_10004733	superfamily	241758	111	143	1.93E-09	53.1426	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#3036 - 	CGI_10004734	superfamily	241758	7	143	4.48E-22	86.2698	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#3040 - 	CGI_10004738	superfamily	110440	253	280	0.000518405	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#3042 - 	CGI_10006049	superfamily	241629	294	420	9.95E-39	137.858	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#3042 - 	CGI_10006049	superfamily	241629	36	135	2.55E-27	105.673	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#3042 - 	CGI_10006049	superfamily	241629	136	214	6.23E-19	82.6808	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#3042 - 	CGI_10006049	superfamily	241629	216	293	2.31E-15	72.7588	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#3044 - 	CGI_10006051	superfamily	243555	24	211	1.03E-17	79.3574	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#3046 - 	CGI_10005689	superfamily	241902	32	118	5.16E-32	112.202	cl00493	trimeric_dUTPase superfamily	 - 	 - 	"Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA.  It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface."
Q#3048 - 	CGI_10005691	superfamily	247794	5	135	1.62E-37	131.875	cl17240	FDH_GDH_like superfamily	NC	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#3049 - 	CGI_10005692	superfamily	243072	203	343	1.93E-09	57.0082	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3049 - 	CGI_10005692	superfamily	201924	104	157	4.43E-05	42.5169	cl03316	Cauli_VI superfamily	 - 	 - 	"Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner."
Q#3049 - 	CGI_10005692	superfamily	243175	1010	1078	0.00120207	38.5588	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#3049 - 	CGI_10005692	superfamily	243125	23	46	0.00217932	37.3838	cl02649	LEM superfamily	N	 - 	"LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins; The family corresponds to a group of inner nuclear membrane proteins containing LEM domain. Emerin occurs in four phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy. Emerin interacts with A-type and B-type lamins. Man1, also termed LEM domain-containing protein 3 (LEMD3) is an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and post-mitotic reassembly. Some LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are non-membrane nuclear polypeptides. This family also contains LEM domain-containing protein LEMP-1 and LEM2. LEMP-1, also termed cancer/testis antigen 50 (CT50), is encoded by LEMD1, a novel testis-specific gene expressed in colorectal cancers. LEMP-1 may function as a cancer-testis antigen for immunotherapy of colorectal carcinoma (CRC). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization while its binding to lamin C plays an important role in the organization of lamin A/C complexes. Some uncharacterized LEM domain-containing proteins are also included in this family. Unlike other family members, these harbor an ankyrin repeat region that may mediate protein-protein interactions."
Q#3050 - 	CGI_10005693	superfamily	220736	425	563	3.62E-21	89.6762	cl11068	PTEN_C2 superfamily	 - 	 - 	"C2 domain of PTEN tumour-suppressor protein; This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane."
Q#3050 - 	CGI_10005693	superfamily	241574	320	418	4.25E-08	52.0685	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#3051 - 	CGI_10005694	superfamily	247986	381	474	1.48E-10	60.8498	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#3051 - 	CGI_10005694	superfamily	245225	20	377	8.51E-45	165.946	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#3051 - 	CGI_10005694	superfamily	197504	587	685	9.14E-23	95.8192	cl18192	PBPe superfamily	C	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#3052 - 	CGI_10005695	superfamily	247986	176	262	1.94E-12	67.013	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#3052 - 	CGI_10005695	superfamily	197504	375	511	5.80E-45	159.762	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#3052 - 	CGI_10005695	superfamily	245225	15	114	4.12E-23	101.618	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#3052 - 	CGI_10005695	superfamily	245746	903	963	3.18E-19	83.8138	cl11668	Lig_chan-Glu_bd superfamily	 - 	 - 	"Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060."
Q#3052 - 	CGI_10005695	superfamily	245225	611	816	6.19E-16	79.6617	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#3052 - 	CGI_10005695	superfamily	197504	940	1028	3.69E-12	65.0033	cl18192	PBPe superfamily	C	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#3053 - 	CGI_10015136	superfamily	177822	88	269	5.83E-23	95.3721	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#3054 - 	CGI_10015137	superfamily	245201	1	123	2.93E-21	87.6773	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#3055 - 	CGI_10015138	superfamily	246681	322	362	8.77E-18	80.6176	cl14643	SRPBCC superfamily	N	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#3055 - 	CGI_10015138	superfamily	241571	148	257	0.00229936	36.2363	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#3056 - 	CGI_10015139	superfamily	242406	4	105	2.04E-13	63.3793	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#3057 - 	CGI_10015140	superfamily	222150	176	201	0.000666476	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3057 - 	CGI_10015140	superfamily	222150	148	173	0.00241065	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3057 - 	CGI_10015140	superfamily	246975	135	156	0.00789461	33.0893	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#3058 - 	CGI_10015142	superfamily	221744	56	314	1.31E-28	113.685	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#3059 - 	CGI_10015143	superfamily	245596	190	424	3.35E-87	271.895	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#3059 - 	CGI_10015143	superfamily	245596	20	161	7.73E-50	174.054	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#3062 - 	CGI_10015146	superfamily	243034	60	156	2.45E-09	53.1528	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#3063 - 	CGI_10015147	superfamily	222258	196	374	1.89E-09	56.4223	cl18656	AAA_30 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#3063 - 	CGI_10015147	superfamily	222209	494	578	0.00405544	36.2249	cl18648	UvrD_C_2 superfamily	 - 	 - 	Family description; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Q#3065 - 	CGI_10015149	superfamily	243050	32	90	9.49E-15	70.9114	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#3065 - 	CGI_10015149	superfamily	247916	471	539	1.28E-06	47.3775	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#3066 - 	CGI_10015150	superfamily	118278	230	464	2.55E-133	403.874	cl10730	Membralin superfamily	N	 - 	"Tumour-associated protein; Membralin is evolutionarily highly conserved; though it seems to represent a unique protein family. The protein appears to contain several transmembrane regions. In humans it is expressed in certain cancers, particularly ovarian cancers. Membralin-like gene homologues have been identified in plants including grape, cotton and tomato."
Q#3066 - 	CGI_10015150	superfamily	118278	19	137	1.10E-33	133.464	cl10730	Membralin superfamily	C	 - 	"Tumour-associated protein; Membralin is evolutionarily highly conserved; though it seems to represent a unique protein family. The protein appears to contain several transmembrane regions. In humans it is expressed in certain cancers, particularly ovarian cancers. Membralin-like gene homologues have been identified in plants including grape, cotton and tomato."
Q#3068 - 	CGI_10015152	superfamily	247743	225	367	5.21E-28	111.084	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3068 - 	CGI_10015152	superfamily	247743	477	644	6.26E-28	111.084	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3068 - 	CGI_10015152	superfamily	216993	23	103	5.48E-11	59.8813	cl15641	CDC48_N superfamily	 - 	 - 	"Cell division protein 48 (CDC48), N-terminal domain; This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain."
Q#3068 - 	CGI_10015152	superfamily	244926	128	181	8.79E-09	52.9866	cl08380	CDC48_2 superfamily	 - 	 - 	"Cell division protein 48 (CDC48), domain 2; This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain."
Q#3068 - 	CGI_10015152	superfamily	204202	713	756	0.000695977	38.7757	cl07827	Vps4_C superfamily	 - 	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#3069 - 	CGI_10015153	superfamily	192997	458	587	4.49E-35	132.32	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#3071 - 	CGI_10015155	superfamily	246723	19	615	0	922.337	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#3072 - 	CGI_10015156	superfamily	246723	33	495	0	703.158	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#3074 - 	CGI_10015158	superfamily	215647	96	246	7.98E-33	120.406	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#3074 - 	CGI_10015158	superfamily	243029	6	77	2.14E-18	76.6205	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#3075 - 	CGI_10015159	superfamily	243179	64	155	0.00407519	34.4308	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#3077 - 	CGI_10005107	superfamily	243035	290	390	0.000618848	39.5254	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3077 - 	CGI_10005107	superfamily	246918	214	276	1.35E-08	52.9743	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3077 - 	CGI_10005107	superfamily	246918	1000	1056	2.96E-08	52.2039	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3078 - 	CGI_10005108	superfamily	243035	484	618	1.40E-05	43.7626	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3079 - 	CGI_10005109	superfamily	241638	133	260	7.58E-16	71.2452	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#3080 - 	CGI_10005110	superfamily	241638	53	184	1.89E-17	75.074	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#3082 - 	CGI_10002691	superfamily	241584	426	521	6.85E-08	50.5727	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3082 - 	CGI_10002691	superfamily	241584	318	415	2.15E-06	45.9503	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3082 - 	CGI_10002691	superfamily	241584	267	305	0.00122574	37.4759	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3085 - 	CGI_10002767	superfamily	247725	14	68	6.22E-06	44.637	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3087 - 	CGI_10003891	superfamily	245864	33	250	2.10E-18	82.7114	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3088 - 	CGI_10003892	superfamily	245864	302	638	6.58E-58	203.279	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3089 - 	CGI_10003151	superfamily	245847	294	362	9.30E-05	40.9488	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#3091 - 	CGI_10003047	superfamily	110440	453	479	3.43E-05	41.2393	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#3091 - 	CGI_10003047	superfamily	241563	35	77	0.000111398	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3094 - 	CGI_10002912	superfamily	247097	86	122	0.00020734	37.4306	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#3099 - 	CGI_10002857	superfamily	242406	1	63	0.00226091	34.8745	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#3101 - 	CGI_10007352	superfamily	241874	88	381	6.63E-82	269.351	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#3101 - 	CGI_10007352	superfamily	241874	458	578	2.25E-31	126.827	cl00456	SLC5-6-like_sbd superfamily	NC	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#3101 - 	CGI_10007352	superfamily	241874	358	406	0.000422618	41.6978	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#3102 - 	CGI_10007353	superfamily	243035	97	196	1.08E-21	86.1345	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3102 - 	CGI_10007353	superfamily	243035	7	98	6.75E-19	78.8157	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3103 - 	CGI_10007354	superfamily	219000	339	451	1.12E-35	135.467	cl05717	Drf_FH3 superfamily	C	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#3103 - 	CGI_10007354	superfamily	219001	103	324	9.78E-18	82.7419	cl05720	Drf_GBD superfamily	 - 	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#3104 - 	CGI_10007355	superfamily	245815	2	259	8.24E-165	467.937	cl11961	ALDH-SF superfamily	N	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#3106 - 	CGI_10007357	superfamily	216209	142	350	0.00125115	42.2379	cl15638	Mononeg_RNA_pol superfamily	C	 - 	"Mononegavirales RNA dependent RNA polymerase; Members of the Mononegavirales including the Paramyxoviridae, like other non-segmented negative strand RNA viruses, have an RNA-dependent RNA polymerase composed of two subunits, a large protein L and a phosphoprotein P. This is a protein family of the L protein. The L protein confers the RNA polymerase activity on the complex. The P protein acts as a transcription factor."
Q#3108 - 	CGI_10007359	superfamily	243077	66	114	1.08E-10	57.1701	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#3108 - 	CGI_10007359	superfamily	244850	218	282	7.91E-17	74.5711	cl08096	DUF1992 superfamily	 - 	 - 	Domain of unknown function (DUF1992); This family of proteins are functionally uncharacterized.
Q#3109 - 	CGI_10007360	superfamily	247684	2	64	1.45E-17	74.6211	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3110 - 	CGI_10013932	superfamily	247725	9	109	0.000268604	39.8343	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3111 - 	CGI_10013933	superfamily	247725	26	171	1.96E-40	144.921	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3113 - 	CGI_10013935	superfamily	247725	41	198	2.04E-15	74.8145	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3115 - 	CGI_10013937	superfamily	242565	215	283	0.00369176	35.6326	cl01535	Repair_PSII superfamily	N	 - 	"Repair protein; In plants, this domain plays a role in the photosystem II (PSII) repair cycle. It may be involved in the regulation of synthesis/degradation of the D1 protein of the PSII core and in the assembly of PSII monomers into dimers in the grana stacks. Its function in other organisms is unknown."
Q#3116 - 	CGI_10013938	superfamily	192718	6	163	5.42E-36	125.059	cl12725	DUF2962 superfamily	 - 	 - 	Protein of unknown function (DUF2962); This eukaryotic family of proteins has no known function.
Q#3120 - 	CGI_10013942	superfamily	128469	278	393	1.43E-09	55.5392	cl17971	VPS9 superfamily	 - 	 - 	Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
Q#3121 - 	CGI_10013943	superfamily	247792	950	990	9.02E-09	53.2184	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3122 - 	CGI_10013944	superfamily	219619	215	265	1.44E-06	44.8912	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#3123 - 	CGI_10013945	superfamily	243072	136	260	2.46E-33	126.344	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3123 - 	CGI_10013945	superfamily	243072	235	400	2.46E-15	74.3422	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3124 - 	CGI_10013946	superfamily	246597	8	300	0	684.477	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#3125 - 	CGI_10013947	superfamily	246597	508	791	1.46E-64	219.097	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#3125 - 	CGI_10013947	superfamily	247856	253	281	0.00657909	35.502	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3128 - 	CGI_10013950	superfamily	215731	54	320	8.43E-28	113.077	cl08245	Gln-synt_C superfamily	 - 	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#3128 - 	CGI_10013950	superfamily	215731	456	719	3.01E-25	105.758	cl08245	Gln-synt_C superfamily	 - 	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#3129 - 	CGI_10013951	superfamily	215731	54	320	7.81E-27	106.528	cl08245	Gln-synt_C superfamily	 - 	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#3130 - 	CGI_10013952	superfamily	241554	22	89	1.06E-26	97.7263	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#3132 - 	CGI_10004136	superfamily	241622	2	76	1.34E-13	61.0434	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#3135 - 	CGI_10004139	superfamily	247792	48	94	2.69E-08	50.1368	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3136 - 	CGI_10004140	superfamily	247743	214	338	2.57E-07	50.276	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3136 - 	CGI_10004140	superfamily	248006	876	917	0.00501484	36.0099	cl17452	TPR_10 superfamily	 - 	 - 	Tetratricopeptide repeat; Tetratricopeptide repeat.  
Q#3136 - 	CGI_10004140	superfamily	243034	796	903	0.00540339	36.204	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#3138 - 	CGI_10003578	superfamily	219797	20	55	3.77E-06	43.4582	cl09596	ACC_central superfamily	N	 - 	"Acetyl-CoA carboxylase, central region; The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyzes the rate-limiting step in this process."
Q#3140 - 	CGI_10003580	superfamily	217473	177	324	1.12E-23	101.288	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#3144 - 	CGI_10024751	superfamily	243092	104	400	2.05E-22	98.176	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3144 - 	CGI_10024751	superfamily	243092	480	585	2.01E-06	48.8704	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3145 - 	CGI_10024752	superfamily	216686	65	249	3.49E-46	156.329	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#3146 - 	CGI_10024753	superfamily	247924	138	188	5.38E-15	67.5891	cl17370	PEMT superfamily	C	 - 	Phospholipid methyltransferase; The S. cerevisiae phospholipid methyltransferase (EC:2.1.1.16) has a broad substrate specificity of unsaturated phospholipids.
Q#3150 - 	CGI_10024757	superfamily	247741	72	305	6.24E-42	148.227	cl17187	Aldolase_Class_I superfamily	 - 	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#3152 - 	CGI_10024759	superfamily	217830	7	134	2.16E-63	199.869	cl08410	Autophagy_N superfamily	 - 	 - 	"Autophagocytosis associated protein (Atg3), N-terminal domain; Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the lysosome/vacuole. Atg3 is a ubiquitin like modifier that is topologically similar to the canonical E2 enzyme. It catalyzes the conjugation of Atg8 and phosphatidylethanolamine."
Q#3152 - 	CGI_10024759	superfamily	202841	212	273	2.27E-30	110.388	cl08411	Autophagy_act_C superfamily	 - 	 - 	"Autophagocytosis associated protein, active-site domain; Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex."
Q#3152 - 	CGI_10024759	superfamily	150967	294	318	5.87E-10	53.6928	cl11047	Autophagy_Cterm superfamily	 - 	 - 	Autophagocytosis associated protein C-terminal; Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex. It carries a highly characteristic conserved FLKF sequence motif.
Q#3153 - 	CGI_10024760	superfamily	246669	1705	1835	1.28E-65	220.613	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3153 - 	CGI_10024760	superfamily	246669	228	381	2.68E-62	211.723	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3153 - 	CGI_10024760	superfamily	246669	1470	1593	3.46E-57	196.232	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3153 - 	CGI_10024760	superfamily	246669	64	174	4.56E-56	192.406	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3153 - 	CGI_10024760	superfamily	246669	967	1084	3.13E-55	190.832	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3153 - 	CGI_10024760	superfamily	149289	151	222	6.29E-30	115.846	cl06959	FerI superfamily	 - 	 - 	FerI (NUC094) domain; This domain is present in proteins of the Ferlin family. It is often located between two C2 domains.
Q#3153 - 	CGI_10024760	superfamily	116739	614	691	1.83E-23	97.5684	cl06958	FerB superfamily	 - 	 - 	FerB (NUC096) domain; This is central domain B in proteins of the Ferlin family.
Q#3153 - 	CGI_10024760	superfamily	214777	708	764	1.43E-09	56.7644	cl02740	DysFN superfamily	 - 	 - 	"Dysferlin domain, N-terminal region; Domain of unknown function present in yeast peroxisomal proteins, dysferlin, myoferlin and hypothetical proteins. Due to an insertion of a dysferlin domain within a second dysferlin domain we have chosen to predict these domains in two parts: the N-terminal region and the C-terminal region."
Q#3153 - 	CGI_10024760	superfamily	149301	521	587	2.68E-05	44.2128	cl06973	FerA superfamily	 - 	 - 	FerA (NUC095) domain; This is central domain A in proteins of the Ferlin family.
Q#3153 - 	CGI_10024760	superfamily	246669	1145	1228	0.000259856	41.4077	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3153 - 	CGI_10024760	superfamily	214777	777	832	0.000267067	41.3564	cl02740	DysFN superfamily	 - 	 - 	"Dysferlin domain, N-terminal region; Domain of unknown function present in yeast peroxisomal proteins, dysferlin, myoferlin and hypothetical proteins. Due to an insertion of a dysferlin domain within a second dysferlin domain we have chosen to predict these domains in two parts: the N-terminal region and the C-terminal region."
Q#3154 - 	CGI_10024761	superfamily	206035	103	144	0.00219193	36.7563	cl16440	Enkurin superfamily	N	 - 	"Calmodulin-binding; This is a family of apparent calmodulin-binding proteins found at high levels in the testis and vomeronasal organ and at lower levels in certain other tissues. Enkurin is a scaffold protein that binds PI3 kinase to sperm transient receptor potential (canonical) (TRPC) channels. The mammalian transient receptor potential (canonical) channels are the primary candidates for the Ca(2+) entry pathway activated by the hormones, growth factors, and neurotransmitters that exert their effect through activation of PLC. Calmodulin binds to the C-terminus of all TRPC channels, and dissociation of calmodulin from TRPC4 results in profound activation of the channel."
Q#3156 - 	CGI_10024763	superfamily	222090	5	199	2.48E-16	73.461	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#3157 - 	CGI_10024764	superfamily	222090	5	182	1.19E-14	68.8386	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#3158 - 	CGI_10024765	superfamily	243035	368	478	9.02E-16	74.1933	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3159 - 	CGI_10024766	superfamily	243099	5	124	3.24E-32	113.197	cl02575	Bcl-2_like superfamily	 - 	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#3160 - 	CGI_10024767	superfamily	241629	41	175	2.76E-36	128.587	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#3161 - 	CGI_10024768	superfamily	218493	562	703	1.45E-28	113.221	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#3161 - 	CGI_10024768	superfamily	207716	54	119	2.12E-13	67.2822	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#3162 - 	CGI_10024769	superfamily	243035	96	156	3.92E-18	75.7955	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3163 - 	CGI_10024770	superfamily	199156	60	74	0.00158354	35.1225	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#3164 - 	CGI_10024771	superfamily	243035	53	82	0.00571512	32.3965	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3165 - 	CGI_10024772	superfamily	247794	74	478	0	722.32	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#3169 - 	CGI_10024776	superfamily	247042	35	427	1.87E-34	132.84	cl15693	Sema superfamily	 - 	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#3169 - 	CGI_10024776	superfamily	243104	406	457	4.96E-08	49.8592	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#3170 - 	CGI_10024777	superfamily	245201	754	1017	4.85E-83	271.332	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#3170 - 	CGI_10024777	superfamily	247038	259	349	2.75E-19	85.0598	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3170 - 	CGI_10024777	superfamily	247038	358	434	7.53E-12	63.0121	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3170 - 	CGI_10024777	superfamily	243104	216	257	3.78E-06	45.622	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#3170 - 	CGI_10024777	superfamily	247038	438	544	1.06E-05	45.1005	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3170 - 	CGI_10024777	superfamily	247038	546	635	0.00012365	41.6592	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3171 - 	CGI_10024778	superfamily	223248	235	416	3.03E-12	65.0968	cl18701	SEC59 superfamily	 - 	 - 	Dolichol kinase [Lipid metabolism]
Q#3171 - 	CGI_10024778	superfamily	221533	496	559	2.92E-05	42.2988	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#3171 - 	CGI_10024778	superfamily	241634	430	533	0.000464868	38.8661	cl00143	SynN superfamily	 - 	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#3172 - 	CGI_10024779	superfamily	109875	1	118	1.28E-50	162.26	cl17923	T4_deiodinase superfamily	N	 - 	"Iodothyronine deiodinase; Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3)."
Q#3174 - 	CGI_10024781	superfamily	243092	59	352	5.34E-78	243.781	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3175 - 	CGI_10024782	superfamily	247805	18	217	4.41E-86	264.732	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#3175 - 	CGI_10024782	superfamily	247905	232	362	3.23E-33	122.346	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#3176 - 	CGI_10024783	superfamily	247743	243	322	9.42E-11	59.8523	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3176 - 	CGI_10024783	superfamily	209247	467	551	1.80E-19	84.0323	cl11083	ClpB_D2-small superfamily	 - 	 - 	"C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighboring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724."
Q#3177 - 	CGI_10024784	superfamily	243072	63	174	3.54E-26	100.536	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3177 - 	CGI_10024784	superfamily	243073	251	290	6.69E-05	39.4011	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#3178 - 	CGI_10024785	superfamily	217473	424	635	2.69E-07	51.5969	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#3179 - 	CGI_10024786	superfamily	243263	73	492	3.05E-19	89.7746	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#3181 - 	CGI_10024788	superfamily	241862	17	341	3.14E-16	78.5821	cl00437	COG0428 superfamily	 - 	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#3181 - 	CGI_10024788	superfamily	191382	456	556	2.07E-11	61.1691	cl09387	CENP-H superfamily	 - 	 - 	"Centromere protein H (CENP-H); This family consists of several eukaryotic centromere protein H (CENP-H) sequences. Macromolecular centromere-kinetochore complex plays a critical role in sister chromatid separation, but its complete protein composition as well as its precise dynamic function during mitosis has not yet been clearly determined. CENP-H contains a coiled-coil structure and a nuclear localisation signal. CENP-H is specifically and constitutively localised in kinetochores throughout the cell cycle. CENP-H may play a role in kinetochore organisation and function throughout the cell cycle. This the C-terminus of the region, which is conserved from fungi to humans."
Q#3182 - 	CGI_10024789	superfamily	241862	96	254	2.54E-08	52.3584	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#3183 - 	CGI_10024790	superfamily	218212	1088	1452	3.38E-144	447.132	cl18448	DUF608 superfamily	 - 	 - 	"Protein of unknown function, DUF608; This family represents a conserved region with a pankaryotic distribution in a number of uncharacterized proteins."
Q#3183 - 	CGI_10024790	superfamily	221464	741	1021	1.41E-59	209.118	cl13626	GBA2_N superfamily	 - 	 - 	"beta-Glucocerebrosidase 2 N terminal; This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 320 to 354 amino acids in length. This domain is found associated with pfam04685. This domain is found in the protein beta-Glucocerebrosidase 2. It is found just after the extreme N terminus. This protein is located in the ER. The N terminal is thought to be the luminal domain while the C terminal is the cytosolic domain. The catalytic domain of GBA-2 is unknown."
Q#3184 - 	CGI_10024791	superfamily	245596	14	244	3.88E-120	345.435	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#3185 - 	CGI_10024792	superfamily	218802	4	148	1.70E-54	172.161	cl05462	DUF862 superfamily	 - 	 - 	"PPPDE putative peptidase domain; The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)."
Q#3186 - 	CGI_10024793	superfamily	242611	92	383	7.28E-149	428.067	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#3187 - 	CGI_10024794	superfamily	111929	198	285	1.62E-21	88.2266	cl03885	Str_synth superfamily	 - 	 - 	Strictosidine synthase; Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyzes the condensation of tryptamine with secologanin to form strictosidine.
Q#3188 - 	CGI_10024795	superfamily	247856	173	224	1.48E-09	52.1649	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3189 - 	CGI_10024796	superfamily	248458	81	433	6.78E-12	65.4129	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#3190 - 	CGI_10024797	superfamily	247057	28	81	3.85E-27	95.8497	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#3191 - 	CGI_10024798	superfamily	241566	277	326	2.08E-16	72.1395	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#3191 - 	CGI_10024798	superfamily	241566	126	175	3.45E-13	63.6652	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#3192 - 	CGI_10024799	superfamily	247725	30	115	1.15E-15	67.7655	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3193 - 	CGI_10024800	superfamily	151109	11	136	2.76E-33	115.766	cl11199	UPF0556 superfamily	 - 	 - 	Uncharacterized protein family UPF0556; This family of proteins has no known function.
Q#3194 - 	CGI_10024801	superfamily	245206	5	254	2.06E-165	482.592	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#3194 - 	CGI_10024801	superfamily	241913	481	602	6.50E-65	213.235	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#3194 - 	CGI_10024801	superfamily	241913	321	451	4.21E-16	76.1955	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#3194 - 	CGI_10024801	superfamily	242376	715	817	9.79E-11	59.5462	cl01225	SCP2 superfamily	 - 	 - 	"SCP-2 sterol transfer family; This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145."
Q#3194 - 	CGI_10024801	superfamily	242376	622	690	1.70E-05	43.7531	cl01225	SCP2 superfamily	 - 	 - 	"SCP-2 sterol transfer family; This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145."
Q#3196 - 	CGI_10024803	superfamily	243146	123	165	1.12E-09	53.4342	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#3196 - 	CGI_10024803	superfamily	243146	79	132	8.60E-05	39.5799	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#3196 - 	CGI_10024803	superfamily	243146	12	52	0.00015443	38.7471	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#3196 - 	CGI_10024803	superfamily	243146	173	213	0.00080677	36.4855	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#3197 - 	CGI_10024804	superfamily	247639	1	254	1.20E-33	124.111	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#3198 - 	CGI_10024805	superfamily	241629	27	147	2.45E-13	66.7748	cl00133	SCP superfamily	N	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#3198 - 	CGI_10024805	superfamily	217895	181	263	3.92E-10	57.2679	cl04401	CD20 superfamily	C	 - 	"CD20-like family; This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton."
Q#3199 - 	CGI_10024806	superfamily	215866	8	150	1.93E-32	120.123	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#3199 - 	CGI_10024806	superfamily	243212	179	309	1.49E-21	89.3253	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#3200 - 	CGI_10008582	superfamily	243092	67	413	2.32E-25	103.569	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3201 - 	CGI_10008583	superfamily	246925	69	189	3.23E-05	45.8094	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3201 - 	CGI_10008583	superfamily	214507	615	666	0.000654016	38.9504	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#3201 - 	CGI_10008583	superfamily	246925	190	428	0.0026904	39.6462	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3202 - 	CGI_10008584	superfamily	247805	493	651	1.10E-18	85.4668	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#3202 - 	CGI_10008584	superfamily	247805	1269	1415	2.28E-17	81.6148	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#3202 - 	CGI_10008584	superfamily	247905	783	825	1.37E-06	48.3881	cl17351	HELICc superfamily	NC	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#3202 - 	CGI_10008584	superfamily	214946	903	1212	1.92E-96	314.296	cl15345	Sec63 superfamily	 - 	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#3203 - 	CGI_10008585	superfamily	247905	19	97	1.14E-09	53.7809	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#3204 - 	CGI_10008586	superfamily	241571	171	279	3.42E-18	79.3786	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#3204 - 	CGI_10008586	superfamily	216897	39	114	0.00257542	35.7349	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#3207 - 	CGI_10008589	superfamily	214946	12	176	2.53E-63	211.833	cl15345	Sec63 superfamily	C	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#3207 - 	CGI_10008589	superfamily	214946	396	499	2.28E-13	69.6947	cl15345	Sec63 superfamily	N	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#3210 - 	CGI_10008592	superfamily	110440	96	120	0.00309387	33.1501	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#3211 - 	CGI_10008593	superfamily	219188	98	302	5.33E-45	157.832	cl18498	Lung_7-TM_R superfamily	C	 - 	Lung seven transmembrane receptor; This family represents a conserved region with eukaryotic lung seven transmembrane receptors and related proteins.
Q#3212 - 	CGI_10016414	superfamily	243092	55	212	3.18E-19	87.7756	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3213 - 	CGI_10016415	superfamily	243179	127	254	2.91E-26	100.841	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#3214 - 	CGI_10016416	superfamily	247792	462	505	5.65E-12	61.3076	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3215 - 	CGI_10016417	superfamily	219843	39	251	2.25E-77	242.145	cl18528	ATP-grasp_2 superfamily	 - 	 - 	ATP-grasp domain; ATP-grasp domain.  
Q#3215 - 	CGI_10016417	superfamily	215988	310	430	5.92E-34	123.906	cl18355	Ligase_CoA superfamily	 - 	 - 	"CoA-ligase; This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP."
Q#3216 - 	CGI_10016418	superfamily	241583	301	402	1.62E-20	91.1459	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#3216 - 	CGI_10016418	superfamily	241583	236	351	7.08E-05	42.3092	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#3216 - 	CGI_10016418	superfamily	246968	591	692	0.000444698	40.036	cl15456	ADAM_CR superfamily	 - 	 - 	ADAM cysteine-rich; ADAMs are membrane-anchored proteases that proteolytically modify cell surface and extracellular matrix (ECM) in order to alter cell behaviour. It has been shown that the cysteine-rich domain of ADAM13 regulates the protein's metalloprotease activity.
Q#3222 - 	CGI_10016424	superfamily	248097	69	177	1.36E-18	78.0758	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3223 - 	CGI_10016425	superfamily	245864	11	466	3.53E-64	216.376	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3224 - 	CGI_10016426	superfamily	243061	97	198	2.38E-32	113.976	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#3224 - 	CGI_10016426	superfamily	243061	21	94	9.65E-07	44.255	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#3229 - 	CGI_10016431	superfamily	241754	64	734	0	1157.21	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#3229 - 	CGI_10016431	superfamily	247725	1978	2153	1.78E-108	344.996	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3229 - 	CGI_10016431	superfamily	247725	1448	1584	6.00E-78	256.364	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3229 - 	CGI_10016431	superfamily	243052	1153	1258	2.21E-46	164.814	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#3229 - 	CGI_10016431	superfamily	243052	1733	1843	1.41E-40	149.818	cl02480	MyTH4 superfamily	N	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#3229 - 	CGI_10016431	superfamily	247683	1572	1635	6.83E-33	124.546	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#3229 - 	CGI_10016431	superfamily	243052	1012	1051	6.70E-06	46.97	cl02480	MyTH4 superfamily	C	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#3229 - 	CGI_10016431	superfamily	222636	861	993	0.00304267	38.3915	cl16962	DUF4355 superfamily	 - 	 - 	Domain of unknown function (DUF4355); This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length.
Q#3230 - 	CGI_10016432	superfamily	141815	14	320	1.40E-165	466.456	cl04275	Mtc superfamily	 - 	 - 	Tricarboxylate carrier; Tricarboxylate carrier.  
Q#3232 - 	CGI_10016434	superfamily	241563	18	50	0.000117077	40.0131	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3233 - 	CGI_10016435	superfamily	243141	1	22	8.52E-05	35.755	cl02687	RWD superfamily	C	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#3234 - 	CGI_10016436	superfamily	242406	451	591	3.84E-22	93.4249	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#3234 - 	CGI_10016436	superfamily	245814	339	410	2.01E-10	57.9004	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3234 - 	CGI_10016436	superfamily	245814	48	105	1.68E-09	55.7101	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3234 - 	CGI_10016436	superfamily	245814	419	448	6.65E-05	41.7221	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3234 - 	CGI_10016436	superfamily	245814	227	308	0.000183275	40.1813	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3235 - 	CGI_10016437	superfamily	246669	1307	1444	6.55E-83	269.257	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3235 - 	CGI_10016437	superfamily	246669	737	858	1.05E-50	177.055	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3235 - 	CGI_10016437	superfamily	241622	597	669	2.82E-13	67.5918	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#3236 - 	CGI_10016438	superfamily	243078	10	154	3.38E-61	203.302	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#3236 - 	CGI_10016438	superfamily	247683	216	269	8.40E-32	118.337	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#3237 - 	CGI_10016439	superfamily	217293	1	100	1.76E-12	64.1911	cl03788	Neur_chan_LBD superfamily	NC	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#3237 - 	CGI_10016439	superfamily	202474	151	185	0.00936971	35.7073	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#3239 - 	CGI_10016441	superfamily	222438	378	443	6.97E-16	74.0561	cl16459	zf-C3Hc3H superfamily	 - 	 - 	Potential DNA-binding domain; This domain is likely to be the DNA-binding domain of chromatin re-modelling proteins and helicases.
Q#3240 - 	CGI_10016442	superfamily	222438	41	103	1.47E-12	59.4186	cl16459	zf-C3Hc3H superfamily	 - 	 - 	Potential DNA-binding domain; This domain is likely to be the DNA-binding domain of chromatin re-modelling proteins and helicases.
Q#3242 - 	CGI_10016444	superfamily	241571	4	111	2.39E-29	113.276	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#3242 - 	CGI_10016444	superfamily	241571	115	225	5.22E-22	92.4754	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#3242 - 	CGI_10016444	superfamily	241571	232	346	1.54E-20	88.2382	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#3242 - 	CGI_10016444	superfamily	241571	452	572	1.06E-11	62.4298	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#3242 - 	CGI_10016444	superfamily	241571	351	449	6.96E-11	60.1186	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#3245 - 	CGI_10016447	superfamily	241609	32	98	4.85E-14	62.3955	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#3246 - 	CGI_10017239	superfamily	243092	5	265	4.69E-81	248.404	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3247 - 	CGI_10017240	superfamily	245226	96	262	8.87E-27	104.305	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#3249 - 	CGI_10017243	superfamily	241564	73	142	9.11E-23	86.5507	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#3251 - 	CGI_10017246	superfamily	207794	175	397	1.35E-111	334.181	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#3251 - 	CGI_10017246	superfamily	111707	46	173	1.62E-27	105.575	cl03741	Glyco_hydro_20b superfamily	 - 	 - 	"Glycosyl hydrolase family 20, domain 2; This domain has a zincin-like fold."
Q#3255 - 	CGI_10017250	superfamily	243072	450	548	6.26E-09	54.3118	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3255 - 	CGI_10017250	superfamily	243072	254	379	2.06E-08	52.771	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3255 - 	CGI_10017250	superfamily	243072	33	124	1.68E-05	43.9115	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3256 - 	CGI_10017251	superfamily	208802	751	1042	7.20E-144	441.485	cl07974	DRE_TIM_metallolyase superfamily	 - 	 - 	"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM"."
Q#3256 - 	CGI_10017251	superfamily	245604	1306	1371	4.65E-14	69.3671	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#3256 - 	CGI_10017251	superfamily	247809	336	545	5.68E-89	288.046	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#3256 - 	CGI_10017251	superfamily	201133	222	330	2.53E-49	171.896	cl02837	CPSase_L_chain superfamily	 - 	 - 	"Carbamoyl-phosphate synthase L chain, N-terminal domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117."
Q#3256 - 	CGI_10017251	superfamily	244920	560	667	2.05E-42	152.182	cl08365	Biotin_carb_C superfamily	 - 	 - 	"Biotin carboxylase C-terminal domain; Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyzes the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain."
Q#3257 - 	CGI_10017252	superfamily	247949	22	318	1.87E-79	259.179	cl17395	TAF6 superfamily	 - 	 - 	"TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure.  TAF6 is a shared subunit of histone acetyltransferase complex SAGA and TFIID complexes. TAF6 domain interacts with TAF9 and makes a novel histone-like heterodimer that is structurally related to histones H4 and H3. TAF6 may also interact with the downstream core promoter element (DPE)."
Q#3258 - 	CGI_10017253	superfamily	243092	75	317	1.08E-44	159.808	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3258 - 	CGI_10017253	superfamily	192278	340	488	2.55E-36	131.879	cl15684	UTP15_C superfamily	 - 	 - 	"UTP15 C terminal; U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA. It is a component of the ribosomal small subunit (SSU) processome. UTP15 is needed for optimal pre-ribosomal RNA transcription by RNA polymerase I, together with a subset of U3 proteins required for transcription (t-UTPs). This entry represents the C terminal of UTP15, and is found adjacent to WD40 repeats (pfam00400)."
Q#3259 - 	CGI_10017254	superfamily	243120	186	276	7.65E-35	125.769	cl02633	ARID superfamily	 - 	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#3260 - 	CGI_10017255	superfamily	247684	2	382	0	588.339	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3261 - 	CGI_10017256	superfamily	245201	20	267	9.95E-79	258.219	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#3261 - 	CGI_10017256	superfamily	243239	690	800	5.12E-49	170.171	cl02916	POLO_box superfamily	 - 	 - 	"Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides."
Q#3261 - 	CGI_10017256	superfamily	243239	578	689	2.85E-47	165.131	cl02916	POLO_box superfamily	 - 	 - 	"Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides."
Q#3261 - 	CGI_10017256	superfamily	243239	910	989	1.85E-28	110.758	cl02916	POLO_box superfamily	 - 	 - 	"Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides."
Q#3262 - 	CGI_10017257	superfamily	247725	261	381	1.35E-26	107.405	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3262 - 	CGI_10017257	superfamily	215882	156	282	5.63E-17	79.247	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#3262 - 	CGI_10017257	superfamily	241645	62	142	0.00643375	36.5427	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#3265 - 	CGI_10017260	superfamily	241868	1	216	4.63E-27	102.969	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#3267 - 	CGI_10009381	superfamily	247856	13	42	0.00368811	34.878	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3269 - 	CGI_10009383	superfamily	220692	1	287	3.51E-15	73.3925	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#3270 - 	CGI_10009384	superfamily	244913	985	1423	7.80E-155	484.783	cl08327	Glyco_hydro_47 superfamily	 - 	 - 	"Glycosyl hydrolase family 47; Members of this family are alpha-mannosidases that catalyze the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2)."
Q#3270 - 	CGI_10009384	superfamily	220393	116	315	1.06E-46	171.404	cl10751	Tmem26 superfamily	C	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#3270 - 	CGI_10009384	superfamily	244870	1498	1563	5.56E-23	97.4312	cl08238	PA superfamily	N	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#3270 - 	CGI_10009384	superfamily	193258	484	587	0.000660957	42.3309	cl15087	Innate_immun superfamily	N	 - 	"Invertebrate innate immunity transcript family; The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge."
Q#3272 - 	CGI_10009386	superfamily	247684	7	161	4.88E-22	90.7995	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3273 - 	CGI_10009387	superfamily	243072	658	783	5.17E-20	87.8242	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3273 - 	CGI_10009387	superfamily	243072	731	850	1.54E-18	83.587	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3273 - 	CGI_10009387	superfamily	243072	827	945	3.40E-16	76.6534	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3273 - 	CGI_10009387	superfamily	247724	255	352	6.69E-10	58.5015	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3275 - 	CGI_10009389	superfamily	216939	9	68	1.44E-06	43.0353	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#3275 - 	CGI_10009389	superfamily	216939	93	135	4.99E-05	38.7981	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#3276 - 	CGI_10009390	superfamily	241564	70	139	7.39E-21	81.5431	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#3277 - 	CGI_10009391	superfamily	247724	446	544	1.08E-08	53.4939	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3278 - 	CGI_10009392	superfamily	243034	113	209	7.64E-06	43.5228	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#3278 - 	CGI_10009392	superfamily	243034	180	278	2.35E-05	42.3672	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#3280 - 	CGI_10009394	superfamily	100115	71	424	2.41E-129	381.247	cl18930	StaR_like superfamily	 - 	 - 	"StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure."
Q#3281 - 	CGI_10009395	superfamily	247723	17	96	1.45E-57	186.201	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3281 - 	CGI_10009395	superfamily	247723	102	177	6.30E-53	173.891	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3281 - 	CGI_10009395	superfamily	247723	195	275	8.42E-32	116.519	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3281 - 	CGI_10009395	superfamily	207685	405	446	1.71E-20	85.3034	cl02642	PABP superfamily	N	 - 	"Poly-adenylate binding protein, unique domain; The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family."
Q#3281 - 	CGI_10009395	superfamily	247723	299	324	2.16E-11	59.9404	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3288 - 	CGI_10010664	superfamily	248312	34	158	2.17E-09	54.2904	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#3289 - 	CGI_10010665	superfamily	241832	2	90	1.81E-38	130.551	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#3289 - 	CGI_10010665	superfamily	243175	104	227	2.65E-35	123.585	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#3293 - 	CGI_10024060	superfamily	243066	492	584	6.76E-19	82.7388	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3293 - 	CGI_10024060	superfamily	243066	335	458	1.59E-15	73.4205	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3293 - 	CGI_10024060	superfamily	247724	224	277	6.09E-06	45.5759	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3293 - 	CGI_10024060	superfamily	241622	153	186	0.00920763	35.0472	cl00117	PDZ superfamily	NC	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#3294 - 	CGI_10024061	superfamily	246710	61	197	2.34E-34	127.233	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#3294 - 	CGI_10024061	superfamily	217685	371	528	3.48E-33	124.754	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#3294 - 	CGI_10024061	superfamily	216290	230	355	5.16E-29	111.997	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#3295 - 	CGI_10024062	superfamily	243109	145	282	2.20E-36	129.466	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#3296 - 	CGI_10024063	superfamily	247724	54	215	1.30E-69	225.501	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3296 - 	CGI_10024063	superfamily	243066	441	545	3.28E-17	78.0429	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3296 - 	CGI_10024063	superfamily	243066	281	419	1.31E-06	46.9152	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3297 - 	CGI_10024064	superfamily	243066	192	296	1.50E-17	77.2725	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3297 - 	CGI_10024064	superfamily	243066	32	170	3.36E-07	47.6856	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3298 - 	CGI_10024065	superfamily	241789	12	145	1.25E-80	236.929	cl00328	Ribosomal_L14 superfamily	 - 	 - 	Ribosomal protein L14p/L23e; Ribosomal protein L14p/L23e.  
Q#3299 - 	CGI_10024066	superfamily	243050	5	57	5.91E-34	121.329	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#3299 - 	CGI_10024066	superfamily	247683	379	429	1.13E-27	103.936	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#3299 - 	CGI_10024066	superfamily	159567	67	95	1.02E-05	42.4067	cl11595	Nebulin superfamily	 - 	 - 	Nebulin repeat; Nebulin repeat.  
Q#3299 - 	CGI_10024066	superfamily	159567	172	200	0.000194234	38.9399	cl11595	Nebulin superfamily	 - 	 - 	Nebulin repeat; Nebulin repeat.  
Q#3299 - 	CGI_10024066	superfamily	159567	97	127	0.00124554	36.6748	cl11595	Nebulin superfamily	 - 	 - 	Nebulin repeat; Nebulin repeat.  
Q#3299 - 	CGI_10024066	superfamily	159567	205	228	0.00177666	35.9044	cl11595	Nebulin superfamily	 - 	 - 	Nebulin repeat; Nebulin repeat.  
Q#3301 - 	CGI_10024068	superfamily	247724	192	352	3.68E-06	45.5252	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3301 - 	CGI_10024068	superfamily	242902	25	151	1.43E-14	70.3534	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#3302 - 	CGI_10024069	superfamily	247724	172	378	1.72E-05	43.5992	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3302 - 	CGI_10024069	superfamily	242902	13	129	9.06E-05	41.538	cl02144	TLD superfamily	N	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#3303 - 	CGI_10024070	superfamily	247724	224	384	2.62E-05	43.214	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3303 - 	CGI_10024070	superfamily	242902	25	176	2.95E-16	75.361	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#3304 - 	CGI_10024071	superfamily	247724	225	385	6.26E-05	42.0584	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3304 - 	CGI_10024071	superfamily	242902	26	177	1.97E-15	73.0498	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#3305 - 	CGI_10024072	superfamily	247724	224	384	3.53E-05	42.8288	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3305 - 	CGI_10024072	superfamily	242902	25	176	2.57E-14	69.583	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#3307 - 	CGI_10024074	superfamily	243135	236	539	5.51E-74	243.737	cl02666	KU superfamily	 - 	 - 	"Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by non-homologous end-joining. The bacterial Ku homologs does not contain the conserved N-terminal extension that is present in the eukaryotic Ku protein."
Q#3307 - 	CGI_10024074	superfamily	117355	585	706	2.79E-37	135.946	cl07408	Ku_PK_bind superfamily	 - 	 - 	Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs.
Q#3307 - 	CGI_10024074	superfamily	241578	7	236	2.16E-18	84.7488	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3308 - 	CGI_10024076	superfamily	241575	48	109	2.94E-12	58.8231	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#3309 - 	CGI_10024077	superfamily	241575	80	141	5.84E-16	73.8459	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#3309 - 	CGI_10024077	superfamily	241575	219	280	4.88E-15	71.1495	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#3309 - 	CGI_10024077	superfamily	243132	306	683	3.30E-159	466.855	cl02661	A_deamin superfamily	 - 	 - 	"Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc."
Q#3310 - 	CGI_10024078	superfamily	199166	1649	1825	8.29E-20	90.8496	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#3310 - 	CGI_10024078	superfamily	243074	1491	1537	2.31E-16	76.0061	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#3311 - 	CGI_10024079	superfamily	216381	325	667	1.10E-74	245.578	cl03136	Oxysterol_BP superfamily	 - 	 - 	Oxysterol-binding protein; Oxysterol-binding protein.  
Q#3311 - 	CGI_10024079	superfamily	247725	1	103	1.61E-30	116.204	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3312 - 	CGI_10024080	superfamily	247725	364	410	1.62E-05	43.7861	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3313 - 	CGI_10024081	superfamily	209274	367	412	9.01E-17	74.4906	cl11211	NADH_4Fe-4S superfamily	 - 	 - 	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; NADH-ubiquinone oxidoreductase-F iron-sulfur binding region.  
Q#3313 - 	CGI_10024081	superfamily	220798	278	330	5.56E-05	40.6684	cl14799	SLBB superfamily	 - 	 - 	SLBB domain; SLBB domain.  
Q#3315 - 	CGI_10024083	superfamily	241599	29	83	4.26E-22	83.4468	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#3318 - 	CGI_10024086	superfamily	241599	61	118	9.33E-25	98.0844	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#3319 - 	CGI_10024087	superfamily	241599	145	203	5.51E-24	93.462	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#3323 - 	CGI_10024091	superfamily	241599	158	216	2.26E-23	90.3804	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#3325 - 	CGI_10024093	superfamily	243035	79	190	1.55E-12	64.1781	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3325 - 	CGI_10024093	superfamily	243035	359	454	3.06E-10	57.6297	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3325 - 	CGI_10024093	superfamily	243035	224	276	5.50E-05	41.4514	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3326 - 	CGI_10024094	superfamily	247727	97	193	9.24E-13	64.7586	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#3326 - 	CGI_10024094	superfamily	247727	357	453	1.90E-11	61.2918	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#3327 - 	CGI_10024095	superfamily	247727	162	258	4.76E-14	67.0698	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#3328 - 	CGI_10024096	superfamily	247727	163	259	5.35E-14	67.0698	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#3329 - 	CGI_10024098	superfamily	245213	357	391	1.50E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3329 - 	CGI_10024098	superfamily	245213	280	315	6.83E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3329 - 	CGI_10024098	superfamily	245213	93	131	0.00153399	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3331 - 	CGI_10024100	superfamily	245599	252	472	1.35E-85	264.854	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#3331 - 	CGI_10024100	superfamily	207662	128	209	4.43E-57	185.856	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#3332 - 	CGI_10026403	superfamily	245226	54	205	1.86E-88	261.681	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#3333 - 	CGI_10026404	superfamily	247692	49	548	1.17E-57	200.521	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#3336 - 	CGI_10026408	superfamily	245226	5	94	7.01E-52	164.226	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#3337 - 	CGI_10026409	superfamily	247692	42	149	1.07E-12	64.1071	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#3338 - 	CGI_10026410	superfamily	247692	53	323	1.00E-45	159.994	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#3339 - 	CGI_10026411	superfamily	242787	97	163	0.00523644	36.7251	cl01935	DUF2391 superfamily	C	 - 	"Putative integral membrane protein (DUF2391); This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighborhood. Proteins containing this entry appear to span the membrane seven times."
Q#3340 - 	CGI_10026412	superfamily	242212	69	153	2.18E-17	73.1751	cl00945	Ribosomal_L18ae superfamily	 - 	 - 	Ribosomal L18ae/LX protein domain; This family includes eukaryotic L18ae as well as archaebacterial specific LX. Ribosomal protein L18ae forms part of the 60S ribosomal subunit.
Q#3341 - 	CGI_10026413	superfamily	241578	265	526	4.21E-111	334.34	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3341 - 	CGI_10026413	superfamily	246669	149	258	3.26E-61	199.329	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3341 - 	CGI_10026413	superfamily	246669	16	129	2.57E-59	194.325	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3350 - 	CGI_10026422	superfamily	241563	104	139	0.000746421	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3350 - 	CGI_10026422	superfamily	188588	1164	1215	0.000884133	39.1091	cl14866	exo_TIGR04073 superfamily	 - 	 - 	"putative exosortase-associated protein, TIGR04073 family; Members of this protein family are found in beta, gamma, and delta proteobacteria, and in the verrucomicrobia. Twenty-two of twenty-four species encountered contain the PEP-CTERM/exosortase system for modulating extracellular polysaccharide biosynthesis production, suggesting a role in protein sorting. The N-terminal signal sequence is divergent and not included in the model. PSI-BLAST and HMM searches suggest a distant sequence relationship between a region of this protein of about 100 amino acids and a corresponding region of the very large eukaryotic protein vps13, associated with vacuolar protein sorting in yeast."
Q#3350 - 	CGI_10026422	superfamily	243092	362	473	0.00283104	40.0108	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3351 - 	CGI_10026423	superfamily	241591	25	100	2.04E-26	97.6919	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#3352 - 	CGI_10026424	superfamily	241594	456	808	4.01E-162	477.828	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#3352 - 	CGI_10026424	superfamily	241647	389	419	2.82E-10	56.7674	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#3352 - 	CGI_10026424	superfamily	241647	178	207	2.69E-09	54.071	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#3352 - 	CGI_10026424	superfamily	241647	324	353	2.92E-08	50.9894	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#3352 - 	CGI_10026424	superfamily	241647	219	249	6.94E-08	49.8338	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#3352 - 	CGI_10026424	superfamily	246669	18	115	1.68E-39	143.262	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3354 - 	CGI_10026426	superfamily	243034	57	154	0.000823467	38.5152	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#3355 - 	CGI_10026427	superfamily	242372	50	162	1.33E-19	82.8047	cl01221	DTW superfamily	N	 - 	DTW domain; This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after.
Q#3356 - 	CGI_10026428	superfamily	207637	6	82	2.40E-31	110.705	cl02541	CIDE_N superfamily	 - 	 - 	"CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein."
Q#3356 - 	CGI_10026428	superfamily	220094	77	181	7.05E-08	48.7289	cl07593	DFF-C superfamily	C	 - 	"DNA Fragmentation factor 45kDa, C terminal domain; The C terminal domain of DNA Fragmentation factor 45kDa (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFF40 by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFF40, the C-terminal region of DFF45 is also important for the DFF40-specific folding chaperone activity, as demonstrated by the ability of DFF45 to refold DFF40."
Q#3357 - 	CGI_10026429	superfamily	246669	498	630	3.18E-77	244.18	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3357 - 	CGI_10026429	superfamily	246669	357	479	3.87E-72	230.247	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3357 - 	CGI_10026429	superfamily	145459	7	93	6.46E-36	130.298	cl12264	RPH3A_effect_N superfamily	 - 	 - 	"Rabphilin-3A effector domain N-terminal; This is a the N-terminus of a family of proteins involved in protein transport in synaptic vesicles. Rabphilin-3A has been shown to contact Rab3A, a small G protein important in neurotransmitter release, in two distinct areas. Most member proteins carry an FVHE-PHD type zinc-finger domain at the C-terminus."
Q#3357 - 	CGI_10026429	superfamily	203315	92	145	0.00384463	35.9415	cl05335	zf-piccolo superfamily	 - 	 - 	"Piccolo Zn-finger; This (predicted) Zinc finger is found in the bassoon and piccolo proteins. There are eight conserved cysteines, suggesting that it coordinates two zinc ligands."
Q#3358 - 	CGI_10026430	superfamily	201778	7	133	8.56E-28	105.369	cl18219	GFO_IDH_MocA superfamily	 - 	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#3358 - 	CGI_10026430	superfamily	217272	149	239	1.60E-07	48.2996	cl18400	GFO_IDH_MocA_C superfamily	 - 	 - 	"Oxidoreductase family, C-terminal alpha/beta domain; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#3362 - 	CGI_10026434	superfamily	201778	24	150	4.41E-28	106.524	cl18219	GFO_IDH_MocA superfamily	 - 	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#3362 - 	CGI_10026434	superfamily	217272	166	253	5.81E-11	58.7	cl18400	GFO_IDH_MocA_C superfamily	 - 	 - 	"Oxidoreductase family, C-terminal alpha/beta domain; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#3364 - 	CGI_10026436	superfamily	243033	60	165	2.08E-06	43.8461	cl02428	Ependymin superfamily	N	 - 	Ependymin; Ependymin.  
Q#3366 - 	CGI_10026438	superfamily	238076	44	153	3.02E-75	234.236	cl18938	PAX superfamily	 - 	 - 	Paired Box domain
Q#3366 - 	CGI_10026438	superfamily	241599	234	292	7.43E-25	96.9288	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#3369 - 	CGI_10026441	superfamily	243072	529	666	2.97E-27	108.24	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3369 - 	CGI_10026441	superfamily	243072	463	588	2.33E-26	105.929	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3369 - 	CGI_10026441	superfamily	115363	4	65	1.14E-15	73.1749	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#3369 - 	CGI_10026441	superfamily	241760	76	118	2.00E-14	69.4095	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#3369 - 	CGI_10026441	superfamily	115363	145	214	1.24E-12	64.3153	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#3369 - 	CGI_10026441	superfamily	247792	707	740	3.21E-06	45.4484	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3373 - 	CGI_10026445	superfamily	245201	483	529	9.25E-05	42.9294	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#3374 - 	CGI_10026446	superfamily	247069	111	233	1.66E-19	84.359	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#3374 - 	CGI_10026446	superfamily	243095	252	409	1.08E-67	215.279	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#3375 - 	CGI_10026447	superfamily	243100	331	369	3.38E-05	41.9067	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#3376 - 	CGI_10026448	superfamily	247743	2518	2666	0.00259985	40.2071	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3376 - 	CGI_10026448	superfamily	193256	2837	3107	3.16E-78	264.117	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#3376 - 	CGI_10026448	superfamily	193257	3486	3715	2.50E-57	202.138	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#3376 - 	CGI_10026448	superfamily	193253	3120	3466	8.30E-51	187.166	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#3376 - 	CGI_10026448	superfamily	203878	128	156	1.09E-13	69.5428	cl07007	Sgf11 superfamily	 - 	 - 	"Sgf11 (transcriptional regulation protein); The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae. The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation."
Q#3376 - 	CGI_10026448	superfamily	247743	2158	2304	3.47E-06	48.8308	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3377 - 	CGI_10026449	superfamily	241750	84	574	9.51E-113	349.3	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#3377 - 	CGI_10026449	superfamily	241750	562	604	0.00767062	37.654	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#3378 - 	CGI_10026450	superfamily	221377	205	342	3.82E-10	58.6342	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#3379 - 	CGI_10026451	superfamily	247724	10	210	1.08E-58	188.898	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3380 - 	CGI_10026452	superfamily	243066	31	87	6.50E-05	36.9001	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3382 - 	CGI_10026454	superfamily	243066	35	100	9.43E-11	53.4636	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3383 - 	CGI_10026455	superfamily	222150	345	367	0.00343385	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3385 - 	CGI_10026457	superfamily	216347	483	907	2.18E-82	273.643	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#3386 - 	CGI_10026458	superfamily	202715	59	156	6.66E-27	98.4192	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#3387 - 	CGI_10026459	superfamily	217617	118	341	2.69E-30	116.747	cl15988	Sulfotransfer_2 superfamily	 - 	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#3390 - 	CGI_10026463	superfamily	241546	4	127	1.16E-47	151.554	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#3392 - 	CGI_10026465	superfamily	245213	27	57	0.000281592	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3392 - 	CGI_10026465	superfamily	241546	495	589	1.68E-19	85.02	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#3393 - 	CGI_10026466	superfamily	189857	1	72	2.83E-14	63.0378	cl07832	Caveolin superfamily	N	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#3397 - 	CGI_10021632	superfamily	248281	181	264	2.89E-07	47.2651	cl17727	GT1 superfamily	 - 	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#3398 - 	CGI_10021633	superfamily	247727	245	343	1.76E-07	48.5803	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#3399 - 	CGI_10021634	superfamily	247692	81	616	0	556.239	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#3400 - 	CGI_10021635	superfamily	247723	42	121	1.27E-39	139.177	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3400 - 	CGI_10021635	superfamily	247723	155	223	5.51E-34	123.63	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3404 - 	CGI_10021639	superfamily	152683	8	100	2.11E-08	48.4381	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#3404 - 	CGI_10021639	superfamily	241568	106	161	0.000950747	35.2436	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#3405 - 	CGI_10021640	superfamily	241750	255	598	0	524.239	cl00281	metallo-dependent_hydrolases superfamily	C	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#3408 - 	CGI_10021643	superfamily	243092	1	223	1.67E-55	180.609	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3409 - 	CGI_10021644	superfamily	241584	633	720	6.93E-07	48.2615	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3409 - 	CGI_10021644	superfamily	245814	41	114	7.21E-05	42.0911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3409 - 	CGI_10021644	superfamily	245814	431	510	0.000166785	40.9355	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3409 - 	CGI_10021644	superfamily	245814	226	308	6.84E-14	68.686	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3409 - 	CGI_10021644	superfamily	245814	312	388	1.34E-06	47.5206	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3409 - 	CGI_10021644	superfamily	245814	129	214	0.000590189	39.0257	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3409 - 	CGI_10021644	superfamily	241584	516	605	0.00521885	36.2479	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3410 - 	CGI_10021645	superfamily	243129	122	195	1.13E-10	55.3374	cl02653	MA3 superfamily	C	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#3412 - 	CGI_10021647	superfamily	247723	17	96	2.54E-58	191.979	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3412 - 	CGI_10021647	superfamily	247723	102	177	2.42E-53	178.129	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3412 - 	CGI_10021647	superfamily	247723	299	376	3.82E-53	177.426	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3412 - 	CGI_10021647	superfamily	247723	195	275	4.58E-32	119.216	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3412 - 	CGI_10021647	superfamily	207685	560	630	6.30E-39	137.691	cl02642	PABP superfamily	 - 	 - 	"Poly-adenylate binding protein, unique domain; The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family."
Q#3413 - 	CGI_10021648	superfamily	100115	59	177	1.09E-23	94.6582	cl18930	StaR_like superfamily	C	 - 	"StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure."
Q#3416 - 	CGI_10021652	superfamily	241574	9	237	2.20E-84	263.678	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#3416 - 	CGI_10021652	superfamily	241574	305	502	8.00E-17	79.1669	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#3417 - 	CGI_10021653	superfamily	247947	450	484	0.000199179	39.2901	cl17393	HTH_Hin_like superfamily	 - 	 - 	"Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a DNA-binding domain (HTH_Hin) and a catalytic domain."
Q#3418 - 	CGI_10003256	superfamily	243035	52	166	2.37E-13	63.0225	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3419 - 	CGI_10003257	superfamily	243035	17	63	1.70E-05	38.126	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3420 - 	CGI_10003258	superfamily	241609	160	233	1.30E-18	77.8035	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#3420 - 	CGI_10003258	superfamily	241629	104	163	4.94E-10	55.0878	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#3421 - 	CGI_10014485	superfamily	248022	13	108	7.64E-12	62.6803	cl17468	Aa_trans superfamily	N	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#3424 - 	CGI_10014488	superfamily	248458	22	404	1.95E-18	85.4433	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#3425 - 	CGI_10014489	superfamily	215776	34	92	1.35E-20	81.101	cl18343	OTCace superfamily	N	 - 	"Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain.  "
Q#3426 - 	CGI_10014490	superfamily	241600	51	241	7.46E-76	231.36	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3427 - 	CGI_10014491	superfamily	243507	143	235	4.80E-15	72.7307	cl03728	Alpha_kinase superfamily	N	 - 	"Alpha-kinase family; This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains."
Q#3430 - 	CGI_10014494	superfamily	247725	128	208	2.17E-11	57.9732	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3431 - 	CGI_10014495	superfamily	217247	286	576	1.82E-85	271.189	cl18397	Glyco_hydro_2_C superfamily	 - 	 - 	"Glycosyl hydrolases family 2, TIM barrel domain; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities."
Q#3431 - 	CGI_10014495	superfamily	217248	1	174	1.66E-33	125.461	cl18398	Glyco_hydro_2_N superfamily	 - 	 - 	"Glycosyl hydrolases family 2, sugar binding domain; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold."
Q#3431 - 	CGI_10014495	superfamily	216070	176	278	9.16E-12	62.5372	cl12242	Glyco_hydro_2 superfamily	 - 	 - 	"Glycosyl hydrolases family 2; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities."
Q#3433 - 	CGI_10014497	superfamily	243035	663	784	3.50E-31	118.876	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3433 - 	CGI_10014497	superfamily	241578	14	165	3.18E-30	117.778	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3433 - 	CGI_10014497	superfamily	243119	241	286	1.44E-05	43.5865	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3434 - 	CGI_10014498	superfamily	241578	10	161	3.16E-30	115.081	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3434 - 	CGI_10014498	superfamily	241611	402	479	0.00265628	37.368	cl00102	PTX superfamily	N	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#3435 - 	CGI_10014499	superfamily	241600	69	279	1.29E-82	250.235	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3436 - 	CGI_10014500	superfamily	241600	69	267	8.48E-77	235.212	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3437 - 	CGI_10014502	superfamily	241578	33	183	9.85E-30	114.311	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3438 - 	CGI_10014503	superfamily	217903	47	198	1.38E-47	167.136	cl09317	Mak10 superfamily	 - 	 - 	"Mak10 subunit, NatC N(alpha)-terminal acetyltransferase; NatC N(alpha)-terminal acetyltransferases contains Mak10p, Mak31p and Mak3p subunits. All three subunits are associated with each other to form the active complex."
Q#3440 - 	CGI_10014505	superfamily	245306	37	135	5.63E-21	83.0187	cl10465	Peptidase_S24_S26 superfamily	 - 	 - 	"The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases."
Q#3441 - 	CGI_10005215	superfamily	248020	206	285	0.00454955	38.9848	cl17466	Sulfatase superfamily	N	 - 	Sulfatase; Sulfatase.  
Q#3442 - 	CGI_10005216	superfamily	241705	258	507	1.66E-118	354.687	cl00228	HIT_like superfamily	N	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#3442 - 	CGI_10005216	superfamily	241705	55	212	6.16E-65	215.63	cl00228	HIT_like superfamily	C	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#3444 - 	CGI_10005218	superfamily	243082	517	642	6.67E-42	154.723	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#3446 - 	CGI_10005220	superfamily	248097	32	160	3.46E-13	62.2826	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3447 - 	CGI_10005221	superfamily	248097	62	184	7.95E-17	73.0682	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3448 - 	CGI_10005222	superfamily	238076	13	138	1.40E-82	246.947	cl18938	PAX superfamily	 - 	 - 	Paired Box domain
Q#3451 - 	CGI_10004348	superfamily	247684	312	726	4.45E-85	279.933	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3454 - 	CGI_10004986	superfamily	247684	1	263	7.26E-51	173.232	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3456 - 	CGI_10004988	superfamily	247069	1321	1467	4.74E-14	71.6474	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#3456 - 	CGI_10004988	superfamily	221603	1279	1337	1.03E-16	78.9756	cl13877	BNIP2 superfamily	N	 - 	"Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2; This domain family is found in eukaryotes, and is typically between 119 and 133 amino acids in length. There is a conserved HGGY sequence motif. This family is Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2. It interacts with pro- and anti- apoptotic molecules in the cell."
Q#3456 - 	CGI_10004988	superfamily	202421	7	139	3.99E-06	47.1226	cl03740	DHHA2 superfamily	 - 	 - 	DHHA2 domain; This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA2 for DHH associated domain. This domain is diagnostic of DHH subfamily 2 members. The domain is about 120 residues long and contains a conserved DXK motif at its amino terminus.
Q#3458 - 	CGI_10006649	superfamily	241563	62	96	6.74E-05	41.9391	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3459 - 	CGI_10006650	superfamily	110440	390	417	0.00828724	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#3462 - 	CGI_10006653	superfamily	241645	193	267	7.86E-11	59.6243	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#3462 - 	CGI_10006653	superfamily	199166	453	581	1.82E-09	57.3372	cl15308	AMN1 superfamily	N	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#3462 - 	CGI_10006653	superfamily	246925	684	784	0.000761089	41.187	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3463 - 	CGI_10006654	superfamily	215647	1008	1230	7.96E-06	47.2181	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#3466 - 	CGI_10003894	superfamily	241563	38	73	6.68E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3466 - 	CGI_10003894	superfamily	110440	462	488	0.00822535	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#3469 - 	CGI_10019885	superfamily	243090	344	464	1.36E-65	209.51	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3469 - 	CGI_10019885	superfamily	243090	185	328	7.50E-25	100.605	cl02565	RGS superfamily	N	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3469 - 	CGI_10019885	superfamily	243090	51	110	1.60E-15	74.026	cl02565	RGS superfamily	C	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3470 - 	CGI_10019887	superfamily	216050	3	73	9.11E-06	40.7503	cl18357	rve superfamily	C	 - 	Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.
Q#3471 - 	CGI_10019888	superfamily	241578	420	476	0.000209925	41.0122	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3473 - 	CGI_10019891	superfamily	241888	85	332	4.43E-116	339.357	cl00473	BI-1-like superfamily	 - 	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#3474 - 	CGI_10019892	superfamily	218440	42	234	0.004874	38.3641	cl14936	AF-4 superfamily	NC	 - 	"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila."
Q#3474 - 	CGI_10019892	superfamily	208802	240	299	0.00729625	37.0255	cl07974	DRE_TIM_metallolyase superfamily	NC	 - 	"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM"."
Q#3475 - 	CGI_10019893	superfamily	245202	14	56	9.03E-21	78.0607	cl09927	S1_like superfamily	C	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#3476 - 	CGI_10019894	superfamily	241866	27	357	0	523.482	cl00445	Iso_dh superfamily	 - 	 - 	Isocitrate/isopropylmalate dehydrogenase; Isocitrate/isopropylmalate dehydrogenase.  
Q#3477 - 	CGI_10019895	superfamily	242122	1546	1676	0.000323333	41.0785	cl00824	HEPN superfamily	 - 	 - 	HEPN domain; HEPN domain.  
Q#3478 - 	CGI_10019897	superfamily	242122	279	409	4.07E-06	44.5453	cl00824	HEPN superfamily	 - 	 - 	HEPN domain; HEPN domain.  
Q#3480 - 	CGI_10019899	superfamily	241733	1077	1144	5.11E-42	149.209	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#3480 - 	CGI_10019899	superfamily	217744	164	1064	0	588.878	cl09313	Nrap superfamily	 - 	 - 	"Nrap protein; Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript."
Q#3481 - 	CGI_10019900	superfamily	243077	107	166	1.59E-07	46.7697	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#3481 - 	CGI_10019900	superfamily	219548	191	262	1.54E-15	69.1811	cl06670	HSCB_C superfamily	 - 	 - 	HSCB C-terminal oligomerisation domain; This domain is the HSCB C-terminal oligomerisation domain and is found on co-chaperone proteins.
Q#3482 - 	CGI_10019901	superfamily	243100	331	383	4.74E-10	55.7739	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#3483 - 	CGI_10019902	superfamily	247757	59	276	4.31E-73	225.422	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#3485 - 	CGI_10019904	superfamily	247757	1	51	3.76E-15	67.875	cl17203	Fer4_NifH superfamily	N	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#3486 - 	CGI_10019905	superfamily	241563	60	100	0.000701713	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3487 - 	CGI_10019906	superfamily	243072	684	810	1.43E-28	113.247	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3487 - 	CGI_10019906	superfamily	220879	252	312	0.00571181	37.0281	cl12395	DUF2730 superfamily	N	 - 	Protein of unknown function (DUF2730); This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Q#3487 - 	CGI_10019906	superfamily	247746	110	208	0.00755828	36.8526	cl17192	ATP-synt_B superfamily	N	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#3488 - 	CGI_10019907	superfamily	245864	48	273	3.92E-24	99.6602	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3489 - 	CGI_10019908	superfamily	245864	54	518	6.11E-86	275.311	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3493 - 	CGI_10005140	superfamily	217403	351	451	1.31E-20	86.7078	cl18408	2OG-FeII_Oxy superfamily	 - 	 - 	"2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalyzing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB."
Q#3493 - 	CGI_10005140	superfamily	222608	248	312	2.01E-15	72.287	cl18680	DIOX_N superfamily	C	 - 	non-haem dioxygenase in morphine synthesis N-terminal; This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.
Q#3493 - 	CGI_10005140	superfamily	248281	95	176	3.14E-07	48.0355	cl17727	GT1 superfamily	 - 	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#3494 - 	CGI_10005141	superfamily	243035	5	127	6.54E-23	87.6753	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3495 - 	CGI_10005142	superfamily	241572	53	138	6.12E-14	65.3376	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#3495 - 	CGI_10005142	superfamily	241572	146	233	2.14E-08	49.9297	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#3496 - 	CGI_10005143	superfamily	241563	172	206	4.49E-05	40.3983	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3497 - 	CGI_10005144	superfamily	241563	96	135	1.17E-06	47.474	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3497 - 	CGI_10005144	superfamily	128778	146	253	0.00916432	36.4739	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#3498 - 	CGI_10005145	superfamily	246669	1008	1131	2.03E-55	189.766	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#3498 - 	CGI_10005145	superfamily	241622	678	772	1.76E-16	76.8366	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#3499 - 	CGI_10005847	superfamily	247723	215	293	8.71E-44	146.581	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3499 - 	CGI_10005847	superfamily	247723	1	73	5.81E-40	136.741	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3502 - 	CGI_10024562	superfamily	241755	9	339	1.66E-133	387.345	cl00288	EPT_RTPC-like superfamily	 - 	 - 	"This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while  RTPC has 3 similar repeats with a 4th slightly different domain inserted between the 2nd and 3rd repeat. They evidently share the same active site location, although the catalytic residues differ."
Q#3504 - 	CGI_10024564	superfamily	241619	569	627	9.73E-06	45.1533	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#3504 - 	CGI_10024564	superfamily	241619	633	706	0.000119236	41.7956	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#3504 - 	CGI_10024564	superfamily	241619	42	98	0.0019411	38.2197	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#3506 - 	CGI_10024566	superfamily	245213	1163	1199	1.85E-10	58.8022	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3506 - 	CGI_10024566	superfamily	245213	1377	1410	2.00E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3506 - 	CGI_10024566	superfamily	245213	1126	1160	0.000359978	40.3126	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3506 - 	CGI_10024566	superfamily	245213	1347	1372	0.0069789	36.4606	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3506 - 	CGI_10024566	superfamily	150843	238	430	3.26E-38	144.66	cl10917	Med8 superfamily	 - 	 - 	"Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20."
Q#3506 - 	CGI_10024566	superfamily	150843	24	177	3.29E-24	103.829	cl10917	Med8 superfamily	 - 	 - 	"Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20."
Q#3506 - 	CGI_10024566	superfamily	246680	517	598	2.18E-08	53.5836	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#3506 - 	CGI_10024566	superfamily	219501	934	971	0.000289397	40.7766	cl06622	MNNL superfamily	C	 - 	N terminus of Notch ligand; This entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins.
Q#3507 - 	CGI_10024567	superfamily	241592	49	66	0.000187188	35.6654	cl00074	H2A superfamily	C	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#3508 - 	CGI_10024568	superfamily	219632	14	92	1.14E-24	91.1804	cl06786	Eaf7 superfamily	 - 	 - 	"Chromatin modification-related protein EAF7; The S. cerevisiae member of this family is part of NuA4, the only essential histone acetyltransferase complex in Saccharomyces cerevisiae involved in global histone acetylation."
Q#3509 - 	CGI_10024569	superfamily	247805	244	442	7.10E-88	275.132	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#3509 - 	CGI_10024569	superfamily	247905	470	584	1.39E-32	122.732	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#3509 - 	CGI_10024569	superfamily	247799	82	128	3.05E-10	57.1847	cl17245	KH-I superfamily	N	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#3511 - 	CGI_10024571	superfamily	241554	82	214	3.25E-18	81.5379	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#3511 - 	CGI_10024571	superfamily	241752	457	590	1.98E-15	74.6743	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#3512 - 	CGI_10024572	superfamily	247684	9	182	1.54E-20	87.2591	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3513 - 	CGI_10024573	superfamily	241832	501	601	7.62E-05	41.8274	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#3514 - 	CGI_10024574	superfamily	222150	379	404	0.000164019	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3515 - 	CGI_10024575	superfamily	202715	117	213	2.64E-29	106.508	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#3516 - 	CGI_10024576	superfamily	202715	114	212	3.02E-31	111.516	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#3517 - 	CGI_10024577	superfamily	202715	117	213	1.88E-36	124.998	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#3518 - 	CGI_10024578	superfamily	202715	11	114	2.07E-29	103.427	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#3519 - 	CGI_10024579	superfamily	247684	9	182	1.09E-20	87.6443	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3520 - 	CGI_10024580	superfamily	248028	150	304	8.27E-30	111.343	cl17474	Steroid_dh superfamily	 - 	 - 	"3-oxo-5-alpha-steroid 4-dehydrogenase; This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development."
Q#3520 - 	CGI_10024580	superfamily	241645	2	78	4.38E-09	52.0769	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#3521 - 	CGI_10024581	superfamily	247723	469	538	0.000446714	39.5957	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3521 - 	CGI_10024581	superfamily	192930	153	266	1.78E-32	122.89	cl13496	DUF3546 superfamily	 - 	 - 	Domain of unknown function (DUF3546); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 93 to 114 amino acids in length. This domain has two completely conserved Y residues that may be functionally important.
Q#3523 - 	CGI_10024583	superfamily	214560	38	237	9.08E-22	94.3464	cl18311	TSPN superfamily	 - 	 - 	Thrombospondin N-terminal -like domains; Heparin-binding and cell adhesion domain of thrombospondin
Q#3524 - 	CGI_10024584	superfamily	241793	16	129	4.81E-34	118.376	cl00333	Ribosomal_L13 superfamily	 - 	 - 	"Ribosomal protein L13.  Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site.  It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer.  L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies."
Q#3525 - 	CGI_10024585	superfamily	243058	128	238	0.00011654	40.3756	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#3526 - 	CGI_10024586	superfamily	218708	38	276	4.71E-54	177.927	cl05328	DUF829 superfamily	 - 	 - 	Eukaryotic protein of unknown function (DUF829); This family consists of several uncharacterized eukaryotic proteins.
Q#3527 - 	CGI_10024587	superfamily	248469	62	184	0.00205729	36.9643	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#3529 - 	CGI_10024589	superfamily	241838	11	77	6.75E-13	63.6163	cl00395	FMT_core superfamily	N	 - 	"Formyltransferase, catalytic core domain; Formyltransferase, catalytic core domain. The proteins of this superfamily contain a formyltransferase domain that hydrolyzes the removal of a formyl group from its substrate as part of a multistep transfer mechanism, and this alignment model represents the catalytic core of the formyltransferase domain.  This family includes the following known members; Glycinamide Ribonucleotide Transformylase (GART), Formyl-FH4 Hydrolase, Methionyl-tRNA Formyltransferase, ArnA, and 10-Formyltetrahydrofolate Dehydrogenase (FDH).  Glycinamide Ribonucleotide Transformylase  (GART) catalyzes the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Methionyl-tRNA Formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA, which plays important role in translation initiation. ArnA is required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. 10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. Members of this family are multidomain proteins. The formyltransferase domain is located at the N-terminus of FDH, Methionyl-tRNA Formyltransferase and ArnA, and at the C-terminus of Formyl-FH4 Hydrolase.  Prokaryotic Glycinamide Ribonucleotide Transformylase (GART) is a single domain protein while eukaryotic GART is a trifunctional protein that catalyzes the second, third and fifth steps in de novo purine biosynthesis."
Q#3534 - 	CGI_10024594	superfamily	241832	12	105	7.74E-35	122.667	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#3534 - 	CGI_10024594	superfamily	218936	125	268	1.02E-56	181.634	cl05619	PITH superfamily	 - 	 - 	"PITH domain; This family was formerly known as DUF1000. The full-length, Txnl1, protein which is a probable component of the 26S proteasome, uses its C-terminal, PITH, domain to associate specifically with the 26S proteasome. PITH derives from proteasome-interacting thioredoxin domain."
Q#3535 - 	CGI_10024595	superfamily	248097	92	217	2.06E-14	66.5198	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3536 - 	CGI_10024596	superfamily	248097	14	139	2.54E-10	53.423	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3537 - 	CGI_10024597	superfamily	248097	24	148	1.30E-17	74.2238	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3538 - 	CGI_10024598	superfamily	216686	10	190	8.10E-39	140.921	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#3538 - 	CGI_10024598	superfamily	216686	335	517	2.38E-38	139.766	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#3541 - 	CGI_10024601	superfamily	241874	22	320	3.42E-151	444.041	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#3542 - 	CGI_10024602	superfamily	241600	223	438	2.41E-100	301.467	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3543 - 	CGI_10024603	superfamily	247736	95	161	2.23E-09	50.7373	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#3545 - 	CGI_10024605	superfamily	247723	8	73	4.56E-24	91.9044	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3545 - 	CGI_10024605	superfamily	199156	91	104	0.0015423	35.1116	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#3546 - 	CGI_10024606	superfamily	248097	48	170	9.81E-17	72.2978	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3547 - 	CGI_10024607	superfamily	245202	79	157	4.57E-34	126.585	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#3547 - 	CGI_10024607	superfamily	247805	398	536	1.56E-28	113.201	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#3547 - 	CGI_10024607	superfamily	219532	896	996	5.88E-37	135.905	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#3547 - 	CGI_10024607	superfamily	243778	772	862	6.70E-35	129.651	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#3547 - 	CGI_10024607	superfamily	247905	607	675	2.92E-08	52.5993	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#3548 - 	CGI_10024608	superfamily	247740	306	522	1.10E-89	277.068	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#3549 - 	CGI_10024609	superfamily	216901	202	393	3.58E-61	205.897	cl03466	Rap_GAP superfamily	 - 	 - 	Rap/ran-GAP; Rap/ran-GAP.  
Q#3549 - 	CGI_10024609	superfamily	243036	450	737	1.32E-43	159.711	cl02434	CNH superfamily	 - 	 - 	"CNH domain; Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations."
Q#3552 - 	CGI_10024612	superfamily	248012	108	212	8.55E-20	81.47	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#3553 - 	CGI_10024613	superfamily	217473	24	293	5.70E-24	102.058	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#3556 - 	CGI_10022585	superfamily	247684	1	337	1.16E-61	208.285	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3557 - 	CGI_10022586	superfamily	247684	32	458	4.40E-98	307.667	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3559 - 	CGI_10022588	superfamily	241758	55	80	0.00143091	33.7699	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#3560 - 	CGI_10022589	superfamily	243119	14	59	1.18E-05	37.7985	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3561 - 	CGI_10022590	superfamily	248097	73	170	1.41E-15	73.4534	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3561 - 	CGI_10022590	superfamily	243119	448	502	4.82E-05	41.2653	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3562 - 	CGI_10022591	superfamily	248097	71	201	1.75E-22	88.8614	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3563 - 	CGI_10022592	superfamily	248097	45	147	5.90E-17	74.609	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3564 - 	CGI_10022593	superfamily	245595	430	729	3.19E-143	424.241	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#3564 - 	CGI_10022593	superfamily	243119	340	384	1.53E-06	46.2728	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3564 - 	CGI_10022593	superfamily	243119	45	92	6.80E-06	44.3569	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3564 - 	CGI_10022593	superfamily	243119	185	226	0.000223738	39.7245	cl02629	CBM_14 superfamily	C	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3565 - 	CGI_10022594	superfamily	245847	4	144	5.08E-17	72.9745	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#3579 - 	CGI_10022610	superfamily	241563	93	135	0.000348101	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3580 - 	CGI_10022611	superfamily	247723	32	132	2.02E-52	177.1	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3580 - 	CGI_10022611	superfamily	241563	486	528	4.80E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3581 - 	CGI_10022612	superfamily	247744	3	184	6.47E-74	224.706	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#3583 - 	CGI_10022614	superfamily	247856	52	111	1.04E-05	40.6089	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3583 - 	CGI_10022614	superfamily	247856	85	155	8.49E-05	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3584 - 	CGI_10022615	superfamily	247736	259	314	0.00123163	37.2553	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#3584 - 	CGI_10022615	superfamily	202401	348	536	6.39E-110	328.748	cl03719	NMT_C superfamily	 - 	 - 	"Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain; The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold."
Q#3585 - 	CGI_10022616	superfamily	243090	377	509	4.48E-39	142.552	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3585 - 	CGI_10022616	superfamily	243089	97	281	2.29E-37	139.316	cl02564	PXA superfamily	 - 	 - 	PXA domain; This domain is associated with PX domains pfam00787.
Q#3585 - 	CGI_10022616	superfamily	243088	540	643	3.97E-36	133.548	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#3585 - 	CGI_10022616	superfamily	149621	734	845	2.75E-27	108.141	cl07303	Nexin_C superfamily	 - 	 - 	Sorting nexin C terminal; This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787.
Q#3587 - 	CGI_10022618	superfamily	248262	7	280	5.57E-108	321.1	cl17708	HMBS superfamily	 - 	 - 	"Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12.  HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB).  HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II.  HMBS is found in all organisms except viruses."
Q#3588 - 	CGI_10022619	superfamily	243065	225	380	4.88E-17	78.2125	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#3589 - 	CGI_10022620	superfamily	243065	583	729	2.73E-30	118.658	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#3589 - 	CGI_10022620	superfamily	243065	94	265	8.31E-19	85.1461	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#3589 - 	CGI_10022620	superfamily	244710	774	851	3.27E-12	63.5633	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#3590 - 	CGI_10022621	superfamily	241613	65	101	4.80E-10	58.3722	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#3590 - 	CGI_10022621	superfamily	241613	185	219	2.19E-09	56.4462	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#3590 - 	CGI_10022621	superfamily	241613	148	183	2.25E-09	56.4462	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#3590 - 	CGI_10022621	superfamily	241613	112	144	3.99E-07	49.8978	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#3590 - 	CGI_10022621	superfamily	241613	24	61	5.79E-06	46.431	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#3590 - 	CGI_10022621	superfamily	241613	1	20	0.00373277	37.9566	cl00104	LDLa superfamily	N	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#3590 - 	CGI_10022621	superfamily	246918	2617	2667	1.58E-12	66.0711	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3590 - 	CGI_10022621	superfamily	246918	2673	2722	5.68E-07	49.5075	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3590 - 	CGI_10022621	superfamily	246918	2368	2415	5.46E-06	46.8111	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3590 - 	CGI_10022621	superfamily	246918	2729	2774	2.88E-05	44.4999	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3590 - 	CGI_10022621	superfamily	246918	2574	2612	0.000112614	42.7778	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3591 - 	CGI_10022622	superfamily	217293	28	227	2.41E-44	154.328	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#3591 - 	CGI_10022622	superfamily	202474	234	322	5.31E-08	51.8857	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#3592 - 	CGI_10006983	superfamily	245201	1	201	5.62E-61	202.467	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#3595 - 	CGI_10006986	superfamily	247694	37	118	2.96E-11	55.3079	cl17070	AMPKA_C_like superfamily	 - 	 - 	"C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha subunit and similar domains; This family is composed of AMPKs, microtubule-associated protein/microtubule affinity regulating kinases (MARKs), yeast Kcc4p-like proteins, plant calcineurin B-Like (CBL)-interacting protein kinases (CIPKs), and similar proteins. They are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. AMPKs act as sensors for the energy status of the cell and are activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. MARKs phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Kcc4p and related proteins are septin-associated proteins that are involved in septin organization and in the yeast morphogenesis checkpoint coordinating the cell cycle with bud formation. CIPKs interact with the calcineurin B-like (CBL) calcium sensors to form a signaling network that decode specific calcium signals triggered by a variety of environmental stimuli including salinity, drought, cold, light, and mechanical perturbation, among others. All members of this family contain an N-terminal catalytic kinase domain and a C-terminal regulatory domain which is also called kinase associated domain 1 (KA1) in some cases. The C-terminal regulatory domain serves as a protein interaction domain in AMPKs and CIPKs. In MARKs and Kcc4p-like proteins, this domain binds phospholipids and may be involved in membrane localization."
Q#3598 - 	CGI_10006989	superfamily	209898	90	112	0.00330323	34.6866	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#3598 - 	CGI_10006989	superfamily	209898	42	63	0.003796	34.6235	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#3598 - 	CGI_10006989	superfamily	209898	65	86	0.0088717	33.4679	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#3604 - 	CGI_10000715	superfamily	241779	8	185	6.74E-50	163.893	cl00318	YjeF_N superfamily	N	 - 	"YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions."
Q#3605 - 	CGI_10001102	superfamily	241563	75	110	3.24E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3607 - 	CGI_10011661	superfamily	248192	46	426	6.78E-89	277.613	cl17638	PLN02808 superfamily	 - 	 - 	alpha-galactosidase
Q#3609 - 	CGI_10011663	superfamily	217645	75	338	8.69E-79	248.028	cl04187	DUF303 superfamily	 - 	 - 	Domain of unknown function (DUF303); Distribution of this domain seems limited to prokaryotes and viruses.
Q#3610 - 	CGI_10011664	superfamily	241600	105	260	1.12E-47	159.328	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3610 - 	CGI_10011664	superfamily	241600	26	98	1.80E-15	71.5027	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3611 - 	CGI_10011665	superfamily	241600	16	141	1.23E-41	139.683	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3612 - 	CGI_10011666	superfamily	217007	89	396	2.94E-102	319.931	cl11995	Syja_N superfamily	 - 	 - 	SacI homology domain; This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
Q#3613 - 	CGI_10011667	superfamily	202715	175	263	2.62E-25	96.8784	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#3614 - 	CGI_10011668	superfamily	215648	189	424	1.00E-66	223.241	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#3614 - 	CGI_10011668	superfamily	245225	1	93	2.70E-26	111.951	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#3614 - 	CGI_10011668	superfamily	219467	109	158	7.93E-14	67.7435	cl08456	NCD3G superfamily	 - 	 - 	"Nine Cysteines Domain of family 3 GPCR; This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins."
Q#3615 - 	CGI_10011669	superfamily	243035	30	147	2.31E-29	105.78	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3616 - 	CGI_10011670	superfamily	243035	29	90	6.13E-13	61.0965	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3616 - 	CGI_10011670	superfamily	243035	105	130	0.0030449	34.5878	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3617 - 	CGI_10011671	superfamily	243035	23	82	6.47E-13	60.3062	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3618 - 	CGI_10011672	superfamily	243035	62	129	8.13E-18	74.1933	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3619 - 	CGI_10011673	superfamily	243035	130	256	2.97E-26	100.002	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3619 - 	CGI_10011673	superfamily	243035	24	110	1.32E-15	70.3413	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3620 - 	CGI_10011674	superfamily	215731	52	332	4.53E-35	129.64	cl08245	Gln-synt_C superfamily	 - 	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#3621 - 	CGI_10000223	superfamily	246597	2	88	1.51E-59	185.892	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#3622 - 	CGI_10009100	superfamily	241578	1454	1617	3.66E-11	63.5206	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3622 - 	CGI_10009100	superfamily	241578	263	461	4.70E-06	47.7274	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3623 - 	CGI_10009101	superfamily	241578	265	463	1.19E-06	48.4978	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3624 - 	CGI_10009102	superfamily	241888	161	324	1.15E-59	192.756	cl00473	BI-1-like superfamily	 - 	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#3625 - 	CGI_10009103	superfamily	144608	308	395	0.000274082	41.3465	cl18013	Mg_chelatase superfamily	N	 - 	"Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa."
Q#3626 - 	CGI_10009104	superfamily	202500	162	192	0.00396033	37.1121	cl03819	HEAT superfamily	 - 	 - 	HEAT repeat; The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514).
Q#3627 - 	CGI_10009105	superfamily	214560	170	347	5.46E-22	94.3464	cl18311	TSPN superfamily	 - 	 - 	Thrombospondin N-terminal -like domains; Heparin-binding and cell adhesion domain of thrombospondin
Q#3627 - 	CGI_10009105	superfamily	246918	119	165	6.16E-10	56.0559	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3627 - 	CGI_10009105	superfamily	246918	419	468	1.08E-07	49.5075	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3630 - 	CGI_10006280	superfamily	243077	66	102	1.97E-15	69.4965	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#3633 - 	CGI_10006283	superfamily	219184	143	320	6.29E-47	158.999	cl12337	Clp1 superfamily	 - 	 - 	"Pre-mRNA cleavage complex II protein Clp1; This family consists of several pre-mRNA cleavage complex II Clp1 (or HeaB) proteins. Six different protein factors are required in vitro for 3' end formation of mammalian pre-mRNAs by endonucleolytic cleavage and polyadenylation. Clp1 is a subunit of cleavage complex IIA, which is required for cleavage, but not for polyadenylation of pre-mRNA."
Q#3633 - 	CGI_10006283	superfamily	247757	26	141	5.19E-30	111.718	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#3634 - 	CGI_10012165	superfamily	177822	11	189	8.64E-19	81.5049	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#3637 - 	CGI_10012168	superfamily	241702	644	878	2.75E-104	326.845	cl00224	PLPDE_IV superfamily	 - 	 - 	"PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate lyases (ADCL). BCAT catalyzes the reversible transamination reaction between the L-branched-chain amino and alpha-keto acids. DAAT catalyzes the synthesis of D-glutamic acid and D-alanine, and ADCL converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate. Except for a few enzymes, i. e.,  Escherichia coli and Salmonella BCATs, which are homohexamers arranged as a double trimer, the class IV PLPDEs are homodimers. Homodimer formation is required for catalytic activity."
Q#3637 - 	CGI_10012168	superfamily	241597	381	452	1.18E-37	136.274	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#3637 - 	CGI_10012168	superfamily	241721	322	382	0.00289723	39.1362	cl00246	MTHFR superfamily	N	 - 	"Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease."
Q#3638 - 	CGI_10012169	superfamily	241872	13	368	1.58E-39	145.691	cl00453	CDP-OH_P_transf superfamily	 - 	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#3640 - 	CGI_10012171	superfamily	247725	19	123	4.26E-67	210.207	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3640 - 	CGI_10012171	superfamily	222294	275	370	3.77E-09	53.3831	cl16338	UCH37_bd superfamily	 - 	 - 	"Ubiquitin C-terminal hydrolase 37 receptor binding site; This domain appears frequently at the C-terminus of Proteasom_Rpn13, pfam04683. It is a proteasome subunit that binds the de-ubiquitinating enzyme, UCH37."
Q#3641 - 	CGI_10012172	superfamily	245213	38	68	0.00131118	34.5346	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3641 - 	CGI_10012172	superfamily	245213	74	103	0.00162719	34.5346	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3641 - 	CGI_10012172	superfamily	245213	2	31	0.00738061	32.6086	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3642 - 	CGI_10012173	superfamily	241596	195	231	0.0038064	34.4971	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#3643 - 	CGI_10012174	superfamily	243035	98	205	2.04E-10	58.0149	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3648 - 	CGI_10004250	superfamily	148650	29	112	5.46E-10	56.5547	cl06269	Pex26 superfamily	C	 - 	Pex26 protein; This family consists of Pex26 and related mammalian proteins. Pex26 is a type II peroxisomal membrane protein which recruits Pex6-Pex1 complexes to peroxisomes. Mutations in Pex26 can lead to human disorders.
Q#3649 - 	CGI_10004251	superfamily	241758	62	111	1.93E-17	72.7878	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#3650 - 	CGI_10004252	superfamily	243072	39	155	8.14E-30	109.01	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3653 - 	CGI_10007661	superfamily	243125	5	41	0.000723419	36.6134	cl02649	LEM superfamily	 - 	 - 	"LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins; The family corresponds to a group of inner nuclear membrane proteins containing LEM domain. Emerin occurs in four phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy. Emerin interacts with A-type and B-type lamins. Man1, also termed LEM domain-containing protein 3 (LEMD3) is an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and post-mitotic reassembly. Some LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are non-membrane nuclear polypeptides. This family also contains LEM domain-containing protein LEMP-1 and LEM2. LEMP-1, also termed cancer/testis antigen 50 (CT50), is encoded by LEMD1, a novel testis-specific gene expressed in colorectal cancers. LEMP-1 may function as a cancer-testis antigen for immunotherapy of colorectal carcinoma (CRC). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization while its binding to lamin C plays an important role in the organization of lamin A/C complexes. Some uncharacterized LEM domain-containing proteins are also included in this family. Unlike other family members, these harbor an ankyrin repeat region that may mediate protein-protein interactions."
Q#3654 - 	CGI_10007662	superfamily	245201	32	274	4.98E-54	177.429	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#3656 - 	CGI_10007664	superfamily	241675	62	295	1.24E-92	281.442	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#3657 - 	CGI_10007665	superfamily	222150	719	744	0.00589298	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3657 - 	CGI_10007665	superfamily	222150	747	772	0.0075341	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3657 - 	CGI_10007665	superfamily	222150	578	603	0.00862079	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3657 - 	CGI_10007665	superfamily	205629	617	654	0.00994712	35.2574	cl16278	zf-trcl superfamily	C	 - 	Probable zinc-binding domain; This is a probably zinc-binding domain with two CxxC sequence motifs found in various families of bacteria.
Q#3660 - 	CGI_10007668	superfamily	219542	38	148	5.89E-39	139.299	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#3660 - 	CGI_10007668	superfamily	219541	469	608	9.39E-27	106.013	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#3660 - 	CGI_10007668	superfamily	215896	159	322	1.17E-11	62.6976	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#3662 - 	CGI_10014323	superfamily	241882	542	761	0.00314669	39.1569	cl00465	yhhT superfamily	C	 - 	"Predicted permease, member of the PurR regulon [General function prediction only]"
Q#3671 - 	CGI_10014332	superfamily	241610	151	199	1.03E-14	70.3566	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#3671 - 	CGI_10014332	superfamily	241610	300	347	7.55E-12	62.2674	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#3673 - 	CGI_10014334	superfamily	218570	128	159	0.00754401	33.9153	cl05109	Pacifastin_I superfamily	 - 	 - 	"Pacifastin inhibitor (LCMII); Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors."
Q#3676 - 	CGI_10022206	superfamily	246925	147	334	2.76E-07	51.9726	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3676 - 	CGI_10022206	superfamily	246925	302	498	7.23E-06	47.7354	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3677 - 	CGI_10022207	superfamily	248012	275	409	1.01E-13	68.1188	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#3678 - 	CGI_10022208	superfamily	246925	366	612	3.90E-06	48.1206	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3678 - 	CGI_10022208	superfamily	246925	154	338	0.0082507	37.335	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3679 - 	CGI_10022209	superfamily	242899	18	167	3.07E-63	194.316	cl02135	TRAPP superfamily	 - 	 - 	"Transport protein particle (TRAPP) component; TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterized TRAPP proteins and has a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi."
Q#3681 - 	CGI_10022211	superfamily	219635	147	356	1.74E-61	198.639	cl06790	Peptidase_C78 superfamily	 - 	 - 	Peptidase family C78; This family formerly known as DUF1671 has been shown to be a cysteine peptidase called (Ufm1)-specific protease.
Q#3682 - 	CGI_10022212	superfamily	241600	2	35	0.000999621	37.2199	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3683 - 	CGI_10022213	superfamily	243360	6	302	6.74E-119	347.751	cl03253	SAM_decarbox superfamily	 - 	 - 	"Adenosylmethionine decarboxylase; This is a family of S-adenosylmethionine decarboxylase (SAMDC) proenzymes. In the biosynthesis of polyamines SAMDC produces decarboxylated S-adenosylmethionine, which serves as the aminopropyl moiety necessary for spermidine and spermine biosynthesis from putrescine. The Pfam alignment contains both the alpha and beta chains that are cleaved to form the active enzyme."
Q#3684 - 	CGI_10022214	superfamily	241647	99	126	3.77E-10	55.997	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#3684 - 	CGI_10022214	superfamily	241647	137	167	1.61E-07	48.6782	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#3684 - 	CGI_10022214	superfamily	207669	272	321	2.14E-13	65.9286	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#3684 - 	CGI_10022214	superfamily	207669	405	463	0.000108026	40.6349	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#3684 - 	CGI_10022214	superfamily	207669	491	541	0.00323039	36.2682	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#3688 - 	CGI_10022218	superfamily	243061	1	42	3.20E-19	80.4638	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#3690 - 	CGI_10022220	superfamily	247684	9	327	6.74E-74	241.027	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3692 - 	CGI_10022222	superfamily	247941	480	656	0.000108544	42.1145	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#3693 - 	CGI_10022223	superfamily	243193	54	86	0.000557954	34.6766	cl02797	Cyt_c_Oxidase_VIIc superfamily	N	 - 	"Cytochrome c oxidase subunit VIIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIc subunit is found only in eukaryotes and its specific function remains unclear. Peroxide inactivation of bovine CcO coincides with the direct oxidation of tryptophan (W19) within subunit VIIc, along with other structural changes in other subunits."
Q#3695 - 	CGI_10022225	superfamily	243061	209	306	2.12E-37	130.54	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#3697 - 	CGI_10022227	superfamily	245596	78	154	0.000552764	38.9825	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#3698 - 	CGI_10022228	superfamily	241584	140	223	1.28E-09	53.2691	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3699 - 	CGI_10022229	superfamily	241584	635	708	2.15E-10	59.0471	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3699 - 	CGI_10022229	superfamily	241584	245	335	3.17E-09	55.5803	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3699 - 	CGI_10022229	superfamily	241584	748	818	1.12E-08	54.0395	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3699 - 	CGI_10022229	superfamily	241584	537	624	5.54E-05	42.4835	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3699 - 	CGI_10022229	superfamily	241584	438	519	0.00414924	36.7055	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#3699 - 	CGI_10022229	superfamily	245814	158	227	2.39E-05	43.6593	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3700 - 	CGI_10022230	superfamily	247727	110	213	3.22E-08	50.5063	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#3701 - 	CGI_10004009	superfamily	241574	294	427	3.62E-12	65.2997	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#3705 - 	CGI_10001832	superfamily	248312	79	117	0.00314614	35.4069	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#3707 - 	CGI_10004425	superfamily	241600	1	176	4.74E-84	249.465	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3713 - 	CGI_10007306	superfamily	227554	52	481	4.16E-25	109.522	cl18816	LOC7 superfamily	C	 - 	"Chromosome condensation complex Condensin, subunit H [Chromatin structure and dynamics / Cell division and chromosome partitioning]"
Q#3713 - 	CGI_10007306	superfamily	227554	665	737	3.79E-05	45.5788	cl18816	LOC7 superfamily	N	 - 	"Chromosome condensation complex Condensin, subunit H [Chromatin structure and dynamics / Cell division and chromosome partitioning]"
Q#3714 - 	CGI_10007307	superfamily	245818	101	479	1.74E-75	241.716	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#3714 - 	CGI_10007307	superfamily	241565	6	82	0.00387126	35.3751	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#3715 - 	CGI_10007308	superfamily	241563	218	254	1.42E-05	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3716 - 	CGI_10007309	superfamily	247723	33	101	1.84E-17	76.1869	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3716 - 	CGI_10007309	superfamily	247723	195	263	2.19E-10	56.1216	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3718 - 	CGI_10007311	superfamily	241554	154	242	9.44E-19	80.3923	cl00019	Macro superfamily	NC	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#3718 - 	CGI_10007311	superfamily	241554	3	68	1.60E-13	65.3696	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#3725 - 	CGI_10008765	superfamily	248264	2	67	1.12E-10	57.6322	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#3726 - 	CGI_10008766	superfamily	246723	12	209	1.74E-33	122.013	cl14813	GluZincin superfamily	C	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#3727 - 	CGI_10008767	superfamily	246723	250	508	9.80E-59	199.824	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#3733 - 	CGI_10002567	superfamily	219561	61	284	1.91E-71	226.224	cl06682	FEZ superfamily	 - 	 - 	"FEZ-like protein; This is a family of eukaryotic proteins thought to be involved in axonal outgrowth and fasciculation. The N-terminal regions of these sequences are less conserved than the C-terminal regions, and are highly acidic. The C. elegans homolog, UNC-76, may play structural and signalling roles in the control of axonal extension and adhesion (particularly in the presence of adjacent neuronal cells) and these roles have also been postulated for other FEZ family proteins. Certain homologs have been definitively found to interact with the N-terminal variable region (V1) of PKC-zeta, and this interaction causes cytoplasmic translocation of the FEZ family protein in mammalian neuronal cells. The C-terminal region probably participates in the association with the regulatory domain of PKC-zeta. The members of this family are predicted to form coiled-coil structures, which may interact with members of the RhoA family of signalling proteins, but are not thought to contain other characteristic protein motifs. Certain members of this family are expressed almost exclusively in the brain, whereas others (such as FEZ2) are expressed in other tissues, and are thought to perform similar but unknown functions in these tissues."
Q#3734 - 	CGI_10002568	superfamily	247723	243	312	1.33E-39	138.614	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3734 - 	CGI_10002568	superfamily	247723	349	451	1.07E-37	133.647	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#3734 - 	CGI_10002568	superfamily	247065	25	134	1.54E-05	43.4874	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#3736 - 	CGI_10002570	superfamily	247065	25	135	2.75E-07	46.569	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#3737 - 	CGI_10007682	superfamily	203720	67	109	8.17E-11	56.0174	cl08457	A2M_recep superfamily	N	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#3741 - 	CGI_10007686	superfamily	243092	35	214	4.33E-09	55.804	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3747 - 	CGI_10003818	superfamily	241758	3	96	6.63E-21	81.2622	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#3749 - 	CGI_10003820	superfamily	245814	28	93	5.63E-07	42.8615	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3750 - 	CGI_10003821	superfamily	245814	147	221	7.55E-05	39.7799	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3750 - 	CGI_10003821	superfamily	245814	37	109	0.000401818	37.8539	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3756 - 	CGI_10000983	superfamily	248097	253	375	7.53E-21	86.5502	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3756 - 	CGI_10000983	superfamily	248097	57	156	5.72E-14	67.6754	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3761 - 	CGI_10001109	superfamily	218284	43	211	8.35E-46	151.638	cl04786	SOUL superfamily	 - 	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#3762 - 	CGI_10001175	superfamily	217617	52	285	4.68E-48	162.586	cl15988	Sulfotransfer_2 superfamily	 - 	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#3765 - 	CGI_10006498	superfamily	247725	216	363	8.30E-54	184.851	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3765 - 	CGI_10006498	superfamily	152255	446	533	8.66E-23	96.7644	cl13287	DUF3338 superfamily	N	 - 	Domain of unknown function (DUF3338); This family of proteins are functionally uncharacterized. This family is found in eukaryotes. This presumed domain is about 130 amino acids in length.
Q#3765 - 	CGI_10006498	superfamily	215882	111	223	3.08E-21	91.5734	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#3765 - 	CGI_10006498	superfamily	220215	26	105	5.13E-20	86.8954	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#3765 - 	CGI_10006498	superfamily	245835	507	610	0.00389514	38.8862	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#3768 - 	CGI_10006501	superfamily	241868	106	212	2.53E-39	136.24	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#3769 - 	CGI_10006502	superfamily	222269	171	403	6.07E-46	161.337	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#3773 - 	CGI_10006506	superfamily	241832	82	195	3.36E-40	138.123	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#3773 - 	CGI_10006506	superfamily	241645	257	308	3.70E-20	82.7534	cl00155	UBQ superfamily	N	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#3774 - 	CGI_10006507	superfamily	215647	373	616	6.92E-56	191.668	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#3774 - 	CGI_10006507	superfamily	243086	317	356	1.61E-10	57.7702	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#3774 - 	CGI_10006507	superfamily	243029	58	108	0.000712556	38.4857	cl02422	HRM superfamily	N	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#3775 - 	CGI_10007987	superfamily	241600	2	65	1.18E-13	61.4875	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3777 - 	CGI_10007989	superfamily	245847	218	361	1.75E-17	77.9821	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#3777 - 	CGI_10007989	superfamily	241619	53	120	0.00748535	34.0949	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#3778 - 	CGI_10007990	superfamily	245847	185	319	3.06E-19	82.2193	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#3778 - 	CGI_10007990	superfamily	241619	84	128	0.00520056	34.4801	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#3779 - 	CGI_10007991	superfamily	241600	598	818	4.15E-78	252.932	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3779 - 	CGI_10007991	superfamily	241600	289	526	4.25E-71	234.057	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3780 - 	CGI_10007992	superfamily	241600	346	389	2.14E-12	64.5691	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3781 - 	CGI_10007993	superfamily	241600	859	1078	2.97E-77	253.317	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3781 - 	CGI_10007993	superfamily	241600	3	135	3.45E-49	174.736	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3782 - 	CGI_10007994	superfamily	248097	34	163	1.53E-13	63.4382	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3783 - 	CGI_10007995	superfamily	248097	34	163	1.53E-13	63.4382	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3784 - 	CGI_10004623	superfamily	147609	47	121	5.06E-19	77.7819	cl05205	p25-alpha superfamily	N	 - 	"p25-alpha; This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila."
Q#3785 - 	CGI_10004624	superfamily	241642	149	190	6.26E-05	40.1714	cl00152	t_SNARE superfamily	C	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#3785 - 	CGI_10004624	superfamily	216143	95	147	8.06E-08	48.3124	cl02979	SNAP-25 superfamily	 - 	 - 	SNAP-25 family; SNAP-25 (synaptosome-associated protein 25 kDa) proteins are components of SNARE complexes. Members of this family contain a cluster of cysteine residues that can be palmitoylated for membrane attachment.
Q#3786 - 	CGI_10004625	superfamily	248097	443	570	1.98E-17	78.8462	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3786 - 	CGI_10004625	superfamily	248097	101	207	6.86E-13	65.7494	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3786 - 	CGI_10004625	superfamily	248097	222	290	0.000115528	40.7114	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3787 - 	CGI_10004626	superfamily	245213	107	153	0.00016362	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3787 - 	CGI_10004626	superfamily	243051	157	239	4.96E-05	41.5673	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#3787 - 	CGI_10004626	superfamily	245213	36	69	0.00523739	33.7642	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3788 - 	CGI_10004627	superfamily	245213	55	90	1.46E-11	54.9502	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3789 - 	CGI_10004628	superfamily	241592	49	113	5.32E-21	84.5857	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#3790 - 	CGI_10004629	superfamily	246940	82	328	1.68E-11	62.7361	cl15377	Radical_SAM superfamily	 - 	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#3795 - 	CGI_10010289	superfamily	241750	91	260	1.64E-26	105.733	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#3798 - 	CGI_10010292	superfamily	245205	129	205	4.97E-07	47.6177	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#3798 - 	CGI_10010292	superfamily	245205	424	500	6.44E-07	47.6177	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#3800 - 	CGI_10010294	superfamily	216363	9	82	3.50E-09	49.0058	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#3801 - 	CGI_10001408	superfamily	243051	148	222	7.56E-08	49.6838	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#3803 - 	CGI_10001556	superfamily	245847	48	131	9.93E-05	40.1784	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#3805 - 	CGI_10002246	superfamily	243035	565	691	2.15E-24	99.2313	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#3805 - 	CGI_10002246	superfamily	207794	1	428	0	540.727	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#3805 - 	CGI_10002246	superfamily	245008	450	485	7.67E-09	52.9608	cl09101	E_set superfamily	C	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#3806 - 	CGI_10002383	superfamily	220695	36	142	0.00825464	36.4027	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#3807 - 	CGI_10001794	superfamily	241563	61	100	8.35E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3813 - 	CGI_10021997	superfamily	241570	464	573	1.95E-26	105.486	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#3813 - 	CGI_10021997	superfamily	149466	88	163	4.26E-22	92.0853	cl07147	Ion_trans_N superfamily	 - 	 - 	Ion transport protein N-terminal; This metazoan domain is found to the N-terminus of pfam00520 in voltage- and cyclic nucleotide-gated K/Na ion channels.
Q#3814 - 	CGI_10021998	superfamily	241754	10	681	0	777.984	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#3814 - 	CGI_10021998	superfamily	246908	858	954	1.29E-29	114.988	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#3814 - 	CGI_10021998	superfamily	210118	688	707	0.00306785	36.9304	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#3815 - 	CGI_10021999	superfamily	245814	218	290	4.84E-07	46.7135	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3815 - 	CGI_10021999	superfamily	245814	6	98	2.88E-12	62.0597	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3815 - 	CGI_10021999	superfamily	245814	116	196	1.03E-08	51.7373	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3816 - 	CGI_10022000	superfamily	247805	225	364	1.42E-22	96.6375	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#3816 - 	CGI_10022000	superfamily	241762	60	119	1.64E-20	88.1391	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#3816 - 	CGI_10022000	superfamily	247905	610	756	8.78E-09	55.3217	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#3816 - 	CGI_10022000	superfamily	243072	487	566	1.27E-07	51.6154	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3816 - 	CGI_10022000	superfamily	217926	1269	1399	2.72E-38	141.929	cl04418	YTH superfamily	 - 	 - 	"YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily."
Q#3816 - 	CGI_10022000	superfamily	243778	813	906	6.29E-27	107.695	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#3816 - 	CGI_10022000	superfamily	219532	943	1065	1.62E-16	78.125	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#3817 - 	CGI_10022001	superfamily	241868	170	322	7.71E-50	166.116	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#3817 - 	CGI_10022001	superfamily	247999	55	92	0.00194454	36.0358	cl17445	PHD superfamily	C	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#3818 - 	CGI_10022002	superfamily	241578	2	164	1.93E-40	148.594	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3818 - 	CGI_10022002	superfamily	241578	1256	1417	9.65E-38	140.89	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3818 - 	CGI_10022002	superfamily	241581	276	389	1.34E-05	45.0698	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#3818 - 	CGI_10022002	superfamily	247792	540	569	3.50E-05	43.2032	cl17238	RING superfamily	N	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3818 - 	CGI_10022002	superfamily	241578	1102	1218	5.53E-20	89.5946	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3819 - 	CGI_10022003	superfamily	241578	85	250	1.63E-38	133.951	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3819 - 	CGI_10022003	superfamily	241578	6	67	0.00350439	36.594	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3820 - 	CGI_10022004	superfamily	241578	108	269	1.30E-36	135.112	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3820 - 	CGI_10022004	superfamily	241578	315	482	3.30E-36	134.278	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3820 - 	CGI_10022004	superfamily	241578	530	694	3.14E-31	120.084	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3821 - 	CGI_10022005	superfamily	241578	92	253	3.03E-27	104.296	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3821 - 	CGI_10022005	superfamily	241578	14	72	2.03E-08	51.4599	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3822 - 	CGI_10022006	superfamily	241578	128	287	7.20E-35	125.867	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3823 - 	CGI_10022007	superfamily	246679	1668	1862	1.27E-91	297.158	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#3823 - 	CGI_10022007	superfamily	246679	1508	1652	6.42E-58	198.523	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#3823 - 	CGI_10022007	superfamily	241581	34	75	9.19E-06	46.2254	cl00062	FHA superfamily	N	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#3823 - 	CGI_10022007	superfamily	242046	1123	1200	2.19E-05	44.5686	cl00718	TOPRIM superfamily	 - 	 - 	"Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function."
Q#3823 - 	CGI_10022007	superfamily	241565	84	149	0.000618146	39.9975	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#3823 - 	CGI_10022007	superfamily	247787	1258	1448	3.39E-40	152.166	cl17233	RecA-like_NTPases superfamily	 - 	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#3825 - 	CGI_10022009	superfamily	245835	15	256	1.79E-41	149.549	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#3825 - 	CGI_10022009	superfamily	242067	340	518	1.19E-27	112.446	cl00751	DUF155 superfamily	N	 - 	"Uncharacterized ACR, YagE family COG1723; Uncharacterized ACR, YagE family COG1723.  "
Q#3826 - 	CGI_10022010	superfamily	241739	178	319	3.45E-79	254.422	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#3826 - 	CGI_10022010	superfamily	245205	45	174	3.17E-46	159.994	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#3826 - 	CGI_10022010	superfamily	241739	458	588	1.26E-66	220.91	cl00268	class_II_aaRS-like_core superfamily	N	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#3826 - 	CGI_10022010	superfamily	145868	359	426	0.00304191	36.4622	cl08382	GAD superfamily	 - 	 - 	GAD domain; This domain is found in some members of the GatB and aspartyl tRNA synthetases.
Q#3827 - 	CGI_10022011	superfamily	247792	27	76	2.27E-08	51.6776	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3827 - 	CGI_10022011	superfamily	241563	175	205	0.000382216	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3828 - 	CGI_10022012	superfamily	151744	126	203	6.42E-19	79.6878	cl12843	DUF3105 superfamily	N	 - 	Protein of unknown function (DUF3105); Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Q#3829 - 	CGI_10022013	superfamily	247775	14	572	3.75E-34	134.776	cl17221	ArsB_NhaD_permease superfamily	 - 	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#3830 - 	CGI_10022014	superfamily	247775	247	595	4.69E-28	117.442	cl17221	ArsB_NhaD_permease superfamily	N	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#3830 - 	CGI_10022014	superfamily	247775	686	838	3.03E-27	114.219	cl17221	ArsB_NhaD_permease superfamily	N	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#3830 - 	CGI_10022014	superfamily	247775	49	162	1.71E-24	105.745	cl17221	ArsB_NhaD_permease superfamily	C	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#3831 - 	CGI_10022015	superfamily	241860	42	286	4.43E-92	277.062	cl00435	ICL_KPHMT superfamily	 - 	 - 	"Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), 2-methylisocitrate lyase (MICL), and ketopantoate hydroxymethyltransferase (KPHMT)."
Q#3832 - 	CGI_10022016	superfamily	248469	584	701	0.000237135	40.8163	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#3832 - 	CGI_10022016	superfamily	215733	93	323	5.99E-49	173.905	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#3832 - 	CGI_10022016	superfamily	216063	765	968	4.74E-48	169.721	cl02929	Cation_ATPase_C superfamily	 - 	 - 	"Cation transporting ATPase, C-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices."
Q#3832 - 	CGI_10022016	superfamily	222006	400	508	7.75E-27	106.538	cl16182	Hydrolase_like2 superfamily	 - 	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#3832 - 	CGI_10022016	superfamily	243244	4	62	1.85E-17	78.7314	cl02930	Cation_ATPase_N superfamily	 - 	 - 	"Cation transporter/ATPase, N-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport."
Q#3839 - 	CGI_10002812	superfamily	241550	91	375	8.80E-102	306.433	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#3840 - 	CGI_10002813	superfamily	243072	13	127	7.14E-27	99.7654	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3841 - 	CGI_10002814	superfamily	243072	3	124	1.91E-24	92.0614	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3844 - 	CGI_10003726	superfamily	241580	81	156	8.50E-42	144.234	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#3846 - 	CGI_10010480	superfamily	241763	465	680	8.32E-130	385.999	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#3846 - 	CGI_10010480	superfamily	241613	155	185	0.00166382	36.801	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#3847 - 	CGI_10010481	superfamily	246925	458	568	4.06E-05	44.6538	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3848 - 	CGI_10010482	superfamily	198867	102	202	3.34E-30	114.178	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#3848 - 	CGI_10010482	superfamily	243066	1	94	3.18E-28	108.859	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3848 - 	CGI_10010482	superfamily	243146	336	383	1.77E-05	42.8205	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#3849 - 	CGI_10010483	superfamily	216411	26	146	0.000701782	36.8711	cl15974	MARVEL superfamily	 - 	 - 	"Membrane-associating domain; MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis."
Q#3851 - 	CGI_10010485	superfamily	243066	371	467	1.29E-20	86.976	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#3851 - 	CGI_10010485	superfamily	201217	93	143	1.10E-11	60.6172	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#3851 - 	CGI_10010485	superfamily	201217	146	196	3.00E-09	53.2984	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#3851 - 	CGI_10010485	superfamily	201217	251	287	8.31E-08	49.4464	cl08266	RCC1 superfamily	C	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#3851 - 	CGI_10010485	superfamily	205718	235	264	3.38E-07	47.0998	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#3851 - 	CGI_10010485	superfamily	201217	40	90	4.71E-07	47.1352	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#3851 - 	CGI_10010485	superfamily	198867	475	521	0.00345656	36.1653	cl06652	BACK superfamily	C	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#3852 - 	CGI_10010486	superfamily	247725	85	141	3.57E-25	100.429	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3852 - 	CGI_10010486	superfamily	211425	472	559	3.54E-20	86.1927	cl16935	Orc6_mid superfamily	 - 	 - 	"Middle domain of the origin recognition complex subunit 6; Orc6 is a subunit of the origin recognition complex in eukaryotes, and it may be involved in binding to DNA. This model describes the central or middle domain of Orc6, whose structure resembles that of TFIIB, a DNA-binding transcription factor. Orc6 appears to form distinct complexes with DNA, and a putative DNA-binding site has been identified."
Q#3852 - 	CGI_10010486	superfamily	241622	2	47	4.51E-09	54.1099	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#3852 - 	CGI_10010486	superfamily	247725	164	275	0.000210844	40.143	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3852 - 	CGI_10010486	superfamily	218595	422	493	0.0010243	40.3261	cl18465	ORC6 superfamily	C	 - 	"Origin recognition complex subunit 6 (ORC6); This family consists of several eukaryotic origin recognition complex subunit 6 (ORC6) proteins. Despite differences in their structure and sequences among eukaryotic replicators, ORC is a conserved feature of replication initiation in all eukaryotes. ORC-related genes have been identified in organisms ranging from S. pombe to plants to humans. All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. The function of ORC is reviewed in."
Q#3853 - 	CGI_10010487	superfamily	247065	8	112	6.26E-22	85.8594	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#3854 - 	CGI_10010488	superfamily	221130	37	153	1.07E-19	81.1679	cl13043	ARL2_Bind_BART superfamily	 - 	 - 	The ARF-like 2 binding protein BART; BART binds specifically to ARL2.GTP with a high affinity however it does not bind to ARL2.GDP. It is thought that this specific interaction is due to BART being the first identified ARL2-specific effector. The function is not completely characterized. BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1.
Q#3855 - 	CGI_10010489	superfamily	243092	479	608	7.59E-12	66.5896	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3855 - 	CGI_10010489	superfamily	243092	42	223	2.55E-11	65.0488	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3856 - 	CGI_10010490	superfamily	247724	3	170	1.07E-129	365.207	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3857 - 	CGI_10010491	superfamily	247724	148	216	1.12E-10	57.5171	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3858 - 	CGI_10014165	superfamily	248012	51	153	3.14E-24	92.2556	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#3858 - 	CGI_10014165	superfamily	248012	4	34	0.00148714	35.2461	cl17458	TIR_2 superfamily	NC	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#3859 - 	CGI_10014166	superfamily	222150	315	339	5.73E-05	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3859 - 	CGI_10014166	superfamily	222150	398	422	0.000153547	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3859 - 	CGI_10014166	superfamily	222150	342	367	0.000361149	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3859 - 	CGI_10014166	superfamily	222150	374	395	0.00138326	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#3860 - 	CGI_10014167	superfamily	241578	187	376	1.65E-24	102.472	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#3863 - 	CGI_10014170	superfamily	241547	53	360	2.65E-34	128.543	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#3863 - 	CGI_10014170	superfamily	241749	391	531	1.46E-26	105.16	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#3864 - 	CGI_10014171	superfamily	245864	48	469	4.07E-114	348.114	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3865 - 	CGI_10014172	superfamily	245864	91	531	3.88E-109	336.558	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3865 - 	CGI_10014172	superfamily	245864	18	50	0.000903944	40.3394	cl12078	p450 superfamily	NC	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3866 - 	CGI_10014173	superfamily	245864	37	501	1.15E-109	336.943	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3867 - 	CGI_10014174	superfamily	245864	5	434	3.02E-113	343.877	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3868 - 	CGI_10014175	superfamily	245864	42	478	2.42E-116	353.507	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#3869 - 	CGI_10014176	superfamily	247792	115	150	4.55E-05	40.1216	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3869 - 	CGI_10014176	superfamily	190233	198	253	0.000524953	37.4338	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#3870 - 	CGI_10014177	superfamily	248024	156	323	9.71E-16	75.0121	cl17470	SBF superfamily	 - 	 - 	"Sodium Bile acid symporter family; This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae, this is a putative transmembrane protein involved in resistance to arsenic compounds."
Q#3871 - 	CGI_10014178	superfamily	241600	22	157	1.90E-53	170.499	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#3872 - 	CGI_10014179	superfamily	241583	215	349	1.35E-14	71.6138	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#3873 - 	CGI_10014180	superfamily	217473	572	782	6.96E-15	75.0941	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#3873 - 	CGI_10014180	superfamily	216981	314	431	2.55E-06	47.1422	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#3874 - 	CGI_10014181	superfamily	246925	47	231	0.000341944	41.187	cl15309	LRR_RI superfamily	C	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#3875 - 	CGI_10014182	superfamily	242900	9	151	5.93E-33	116.216	cl02137	PRA1 superfamily	 - 	 - 	PRA1 family protein; This family includes the PRA1 (Prenylated rab acceptor) protein which is a Rab guanine dissociation inhibitor (GDI) displacement factor. This family also includes the glutamate transporter EAAC1 interacting protein GTRAP3-18.
Q#3876 - 	CGI_10014183	superfamily	247809	138	302	3.97E-28	108.132	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#3878 - 	CGI_10014185	superfamily	248312	21	191	2.17E-07	47.7333	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#3884 - 	CGI_10014191	superfamily	220695	74	309	0.000587881	39.8695	cl18571	7TM_GPCR_Srx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#3892 - 	CGI_10002286	superfamily	216572	4	82	3.11E-05	40.3359	cl03265	Pep_M12B_propep superfamily	N	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#3893 - 	CGI_10002287	superfamily	247684	200	409	5.32E-30	120.46	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3893 - 	CGI_10002287	superfamily	247684	73	163	2.52E-14	73.8507	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#3894 - 	CGI_10007199	superfamily	248097	7	130	1.65E-20	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3895 - 	CGI_10007200	superfamily	243119	519	565	1.17E-09	55.1425	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3895 - 	CGI_10007200	superfamily	243119	581	633	5.00E-05	41.6505	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3895 - 	CGI_10007200	superfamily	243119	241	286	0.00146647	37.0382	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3895 - 	CGI_10007200	superfamily	245814	428	498	0.00409841	36.1603	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3896 - 	CGI_10007201	superfamily	243060	193	258	3.71E-09	53.922	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#3898 - 	CGI_10007203	superfamily	219849	336	427	5.15E-19	82.2323	cl09597	RIH_assoc superfamily	 - 	 - 	"RyR and IP3R Homology associated; This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815."
Q#3901 - 	CGI_10005299	superfamily	248264	5	125	6.11E-06	41.4538	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#3903 - 	CGI_10005301	superfamily	243072	558	683	9.88E-38	138.671	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3903 - 	CGI_10005301	superfamily	243072	855	980	2.42E-37	137.515	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3903 - 	CGI_10005301	superfamily	243072	624	749	2.94E-34	129.041	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3903 - 	CGI_10005301	superfamily	243072	791	914	7.55E-33	124.803	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3903 - 	CGI_10005301	superfamily	243072	479	617	3.43E-13	67.7938	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3903 - 	CGI_10005301	superfamily	243072	761	793	0.000555795	39.0744	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3903 - 	CGI_10005301	superfamily	247743	12	47	0.00258871	38.3348	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3904 - 	CGI_10005337	superfamily	243090	1092	1214	1.60E-27	110.174	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3904 - 	CGI_10005337	superfamily	243090	392	504	3.51E-16	78.1561	cl02565	RGS superfamily	C	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3904 - 	CGI_10005337	superfamily	243090	605	703	0.000146963	41.8273	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3904 - 	CGI_10005337	superfamily	243090	848	949	0.000625659	39.6818	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#3905 - 	CGI_10005338	superfamily	247743	1857	1942	0.00499124	39.4367	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#3905 - 	CGI_10005338	superfamily	193256	3056	3320	4.41E-62	217.508	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#3905 - 	CGI_10005338	superfamily	193257	3686	3862	2.36E-48	176.329	cl15086	AAA_9 superfamily	C	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#3905 - 	CGI_10005338	superfamily	193253	3333	3664	3.59E-40	155.965	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#3905 - 	CGI_10005338	superfamily	193251	2757	2965	3.63E-36	142.382	cl18188	AAA_7 superfamily	N	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#3906 - 	CGI_10005339	superfamily	190637	102	178	1.08E-32	121.739	cl04081	HELP superfamily	 - 	 - 	"HELP motif; The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family. The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain. In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation. The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons."
Q#3906 - 	CGI_10005339	superfamily	243092	286	619	3.87E-25	105.88	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3906 - 	CGI_10005339	superfamily	243092	172	362	8.28E-14	71.212	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3906 - 	CGI_10005339	superfamily	243092	589	733	6.78E-09	56.5744	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#3907 - 	CGI_10005340	superfamily	241597	490	546	1.73E-13	66.1031	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#3910 - 	CGI_10026706	superfamily	215847	158	622	4.10E-64	224.633	cl09510	Lipoxygenase superfamily	 - 	 - 	Lipoxygenase; Lipoxygenase.  
Q#3910 - 	CGI_10026706	superfamily	241546	2	106	1.42E-22	93.7736	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#3911 - 	CGI_10026707	superfamily	215847	213	654	6.47E-74	252.367	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#3911 - 	CGI_10026707	superfamily	241546	4	106	5.47E-15	72.2024	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#3912 - 	CGI_10026708	superfamily	241546	4	111	2.10E-24	98.9504	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#3912 - 	CGI_10026708	superfamily	215847	214	654	1.95E-86	286.265	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#3913 - 	CGI_10026709	superfamily	245213	587	621	0.000935784	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#3913 - 	CGI_10026709	superfamily	246918	743	794	1.54E-13	66.8415	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3913 - 	CGI_10026709	superfamily	246918	686	737	1.08E-10	58.7523	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3913 - 	CGI_10026709	superfamily	246918	636	656	0.00490886	36.0255	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#3915 - 	CGI_10026711	superfamily	241599	89	138	9.08E-18	74.5872	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#3916 - 	CGI_10026712	superfamily	245206	26	262	4.21E-56	188.641	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#3916 - 	CGI_10026712	superfamily	245206	268	365	1.03E-17	81.5553	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#3916 - 	CGI_10026712	superfamily	245206	376	428	1.27E-05	45.3466	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#3917 - 	CGI_10026713	superfamily	206084	573	594	1.54E-06	45.6696	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#3917 - 	CGI_10026713	superfamily	206084	466	488	9.39E-06	43.3584	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#3918 - 	CGI_10026714	superfamily	241593	30	82	9.09E-05	42.6338	cl00075	HATPase_c superfamily	C	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#3918 - 	CGI_10026714	superfamily	243181	212	351	6.62E-33	126.662	cl02783	TopoII_MutL_Trans superfamily	 - 	 - 	"MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2.  MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families."
Q#3918 - 	CGI_10026714	superfamily	244692	1522	1658	5.11E-21	92.0322	cl07336	MutL_C superfamily	 - 	 - 	"MutL C terminal dimerisation domain; MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation."
Q#3920 - 	CGI_10026716	superfamily	248097	90	194	1.75E-22	89.2466	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#3925 - 	CGI_10026721	superfamily	245814	39	123	3.69E-11	59.247	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3925 - 	CGI_10026721	superfamily	245814	240	315	2.67E-15	70.612	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3925 - 	CGI_10026721	superfamily	204025	325	358	9.72E-07	45.3201	cl07344	PLAC superfamily	 - 	 - 	PLAC (protease and lacunin) domain; The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins. It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin.
Q#3925 - 	CGI_10026721	superfamily	245814	182	223	4.08E-05	41.0679	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3927 - 	CGI_10026723	superfamily	222070	326	470	9.65E-14	68.4732	cl18634	DDE_3 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#3927 - 	CGI_10026723	superfamily	238076	230	283	4.91E-10	57.0438	cl18938	PAX superfamily	N	 - 	Paired Box domain
Q#3927 - 	CGI_10026723	superfamily	245814	12	71	5.54E-08	50.0979	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3927 - 	CGI_10026723	superfamily	248005	180	218	2.63E-05	41.8319	cl17451	HTH_23 superfamily	C	 - 	Homeodomain-like domain; Homeodomain-like domain.  
Q#3927 - 	CGI_10026723	superfamily	245814	89	159	0.00443614	35.4298	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#3930 - 	CGI_10026726	superfamily	247725	487	619	1.00E-58	196.017	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3930 - 	CGI_10026726	superfamily	247725	254	376	6.05E-48	165.221	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3930 - 	CGI_10026726	superfamily	245835	19	234	4.45E-80	256.759	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#3936 - 	CGI_10026732	superfamily	193607	2332	2462	1.90E-72	240.552	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#3936 - 	CGI_10026732	superfamily	247792	2283	2323	3.37E-08	52.8332	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#3936 - 	CGI_10026732	superfamily	241554	1800	1969	1.02E-53	188.633	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#3936 - 	CGI_10026732	superfamily	241554	1206	1346	4.36E-34	130.458	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#3941 - 	CGI_10026738	superfamily	241563	79	119	3.17E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3941 - 	CGI_10026738	superfamily	241563	25	70	0.00223319	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3942 - 	CGI_10026739	superfamily	144673	56	104	1.49E-19	76.6594	cl18014	TSC22 superfamily	 - 	 - 	TSC-22/dip/bun family; TSC-22/dip/bun family.  
Q#3952 - 	CGI_10026750	superfamily	248022	37	284	2.55E-06	48.4279	cl17468	Aa_trans superfamily	C	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#3953 - 	CGI_10026751	superfamily	242534	543	740	2.73E-42	156.24	cl01495	Glyco_hydro_10 superfamily	 - 	 - 	Glycosyl hydrolase family 10; Glycosyl hydrolase family 10.  
Q#3953 - 	CGI_10026751	superfamily	216848	288	423	2.97E-11	62.0688	cl03406	CBM_4_9 superfamily	 - 	 - 	Carbohydrate binding domain; This family includes diverse carbohydrate binding domains.
Q#3955 - 	CGI_10006847	superfamily	245610	2	262	1.09E-164	460.356	cl11424	nitrilase superfamily	 - 	 - 	"Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy."
Q#3956 - 	CGI_10006848	superfamily	241692	121	373	9.75E-94	295.219	cl00214	Aldolase_II superfamily	 - 	 - 	"Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and  include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations."
Q#3957 - 	CGI_10006849	superfamily	247739	241	333	4.25E-36	136.934	cl17185	LPLAT superfamily	C	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#3957 - 	CGI_10006849	superfamily	247739	665	956	6.86E-08	55.2373	cl17185	LPLAT superfamily	N	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#3957 - 	CGI_10006849	superfamily	247739	335	375	1.29E-07	51.8052	cl17185	LPLAT superfamily	N	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#3958 - 	CGI_10006850	superfamily	243038	1290	1365	0.000890649	39.6313	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#3959 - 	CGI_10006851	superfamily	198898	1307	1337	0.000781802	39.6586	cl07406	c-SKI_SMAD_bind superfamily	C	 - 	c-SKI Smad4 binding domain; c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins. This domain binds to Smad4
Q#3962 - 	CGI_10006854	superfamily	248054	6	62	7.63E-10	55.1708	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#3963 - 	CGI_10006855	superfamily	216686	39	228	2.04E-41	142.847	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#3964 - 	CGI_10006856	superfamily	241646	132	167	2.11E-05	40.1259	cl00156	WAP superfamily	N	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#3965 - 	CGI_10004003	superfamily	243179	153	268	3.04E-08	50.6091	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#3966 - 	CGI_10004004	superfamily	243179	94	200	2.30E-05	41.3643	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#3968 - 	CGI_10004006	superfamily	245201	161	481	8.24E-55	190.388	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#3970 - 	CGI_10004008	superfamily	243119	413	462	0.00363861	37.0281	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#3971 - 	CGI_10016932	superfamily	241563	38	75	1.58E-06	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#3971 - 	CGI_10016932	superfamily	110440	463	489	0.00232346	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#3972 - 	CGI_10016933	superfamily	243267	20	384	3.76E-110	329.96	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#3973 - 	CGI_10016934	superfamily	243267	25	389	1.38E-136	398.14	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#3975 - 	CGI_10016936	superfamily	243267	36	401	8.10E-123	362.702	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#3976 - 	CGI_10016937	superfamily	243267	48	417	1.11E-97	298.373	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#3978 - 	CGI_10016939	superfamily	241624	449	598	2.20E-26	108.953	cl00120	PP2Cc superfamily	N	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#3978 - 	CGI_10016939	superfamily	241624	199	261	2.97E-05	45.0099	cl00120	PP2Cc superfamily	C	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#3979 - 	CGI_10016940	superfamily	247856	333	394	0.0032917	35.9865	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3980 - 	CGI_10016941	superfamily	247724	20	182	4.20E-115	327.972	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#3981 - 	CGI_10016942	superfamily	247725	88	206	1.01E-53	182.92	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#3981 - 	CGI_10016942	superfamily	216381	575	902	1.84E-154	460.519	cl03136	Oxysterol_BP superfamily	 - 	 - 	Oxysterol-binding protein; Oxysterol-binding protein.  
Q#3982 - 	CGI_10016943	superfamily	241647	147	174	5.87E-07	45.9818	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#3985 - 	CGI_10016946	superfamily	243054	1790	1995	1.27E-21	96.7459	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	243054	2544	2743	5.11E-16	79.7971	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	243054	1895	2110	6.22E-14	73.2487	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	243054	2114	2324	3.05E-12	67.8559	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	243054	2224	2430	2.06E-11	65.1596	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	243054	2360	2537	1.48E-09	59.3816	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	243054	1233	1426	1.27E-08	56.3	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	243054	1342	1582	2.27E-07	52.8332	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3985 - 	CGI_10016946	superfamily	207632	535	563	0.000464104	40.5433	cl02531	Plectin superfamily	 - 	 - 	"Plectin repeat; This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen."
Q#3985 - 	CGI_10016946	superfamily	207632	611	647	0.00135195	39.3561	cl02531	Plectin superfamily	C	 - 	"Plectin repeat; This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen."
Q#3985 - 	CGI_10016946	superfamily	243054	1584	1781	0.00189609	40.892	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3986 - 	CGI_10016947	superfamily	243054	18	218	2.83E-28	113.309	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3986 - 	CGI_10016947	superfamily	247856	368	430	2.23E-05	42.9201	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3986 - 	CGI_10016947	superfamily	141488	450	522	1.64E-29	112.542	cl02524	GAS2 superfamily	 - 	 - 	Growth-Arrest-Specific Protein 2 Domain; Growth-Arrest-Specific Protein 2 Domain.  
Q#3986 - 	CGI_10016947	superfamily	243054	228	334	1.51E-06	46.9393	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#3987 - 	CGI_10016948	superfamily	247038	1041	1121	1.23E-12	67.8649	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	259	318	1.10E-11	64.7833	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	1125	1203	5.58E-11	62.8573	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	1802	1852	1.94E-08	55.1533	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	1622	1689	3.63E-07	51.3013	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	1898	1964	9.12E-06	47.0641	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	1734	1772	1.21E-05	46.6789	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	24	114	0.000193994	43.2188	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	220608	2147	2261	1.44E-30	120.874	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#3987 - 	CGI_10016948	superfamily	220608	3021	3141	1.33E-24	103.54	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#3987 - 	CGI_10016948	superfamily	247038	1298	1376	0.000757344	41.274	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	247038	1982	2048	0.000829415	40.8888	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3987 - 	CGI_10016948	superfamily	244965	357	467	0.000845209	41.2335	cl08459	PA14 superfamily	 - 	 - 	"PA14 domain; This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding."
Q#3987 - 	CGI_10016948	superfamily	247038	1531	1616	0.00306907	39.3602	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#3988 - 	CGI_10016949	superfamily	243072	771	921	7.03E-23	96.2986	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3988 - 	CGI_10016949	superfamily	243072	734	797	3.71E-08	52.771	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#3989 - 	CGI_10016950	superfamily	247856	69	124	2.12E-17	72.1953	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3989 - 	CGI_10016950	superfamily	247856	1	56	0.000341473	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#3990 - 	CGI_10005653	superfamily	246902	142	262	6.97E-41	140.832	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#3990 - 	CGI_10005653	superfamily	246902	19	119	5.52E-20	83.8827	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#3994 - 	CGI_10014616	superfamily	128937	4	69	4.13E-12	57.6576	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#3994 - 	CGI_10014616	superfamily	128937	79	142	3.11E-08	46.872	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#3997 - 	CGI_10014619	superfamily	128937	30	91	6.37E-11	53.4204	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#3998 - 	CGI_10014620	superfamily	128937	3	69	1.20E-16	69.984	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#3998 - 	CGI_10014620	superfamily	128937	79	140	4.75E-12	57.6576	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#3999 - 	CGI_10014621	superfamily	128937	4	69	3.07E-09	49.5684	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#3999 - 	CGI_10014621	superfamily	128937	79	142	8.73E-09	48.4128	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#4000 - 	CGI_10014622	superfamily	241805	42	90	1.33E-08	46.9218	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#4001 - 	CGI_10014623	superfamily	245839	2	113	1.43E-29	110.272	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#4001 - 	CGI_10014623	superfamily	241805	267	310	1.68E-08	50.1634	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#4002 - 	CGI_10014624	superfamily	241550	283	645	1.58E-150	441.971	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#4002 - 	CGI_10014624	superfamily	243175	75	177	1.50E-13	67.5238	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#4003 - 	CGI_10014625	superfamily	248226	624	719	0.00228178	41.17	cl17672	PRK13629 superfamily	N	 - 	threonine/serine transporter TdcC; Provisional
Q#4003 - 	CGI_10014625	superfamily	218825	1804	1900	0.00717482	39.3383	cl05490	APC_basic superfamily	C	 - 	APC basic domain; This region of the APC family of proteins is known as the basic domain. It contains a high proportion of positively charged amino acids and interacts with microtubules.
Q#4004 - 	CGI_10014626	superfamily	241571	905	1016	3.61E-40	147.944	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1140	1249	1.27E-38	143.707	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2549	2660	1.22E-37	140.625	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1021	1133	4.67E-37	139.085	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1256	1366	1.50E-36	137.544	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	673	785	4.97E-35	133.307	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	3130	3241	5.03E-35	133.307	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1370	1479	5.52E-35	132.921	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1714	1826	6.20E-35	132.921	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1599	1712	1.90E-34	131.381	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	792	903	1.05E-32	126.373	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2784	2895	1.07E-32	126.373	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1482	1594	1.10E-32	126.373	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1944	2054	1.25E-32	126.373	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2314	2426	3.51E-32	124.832	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	1832	1941	9.59E-32	123.677	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	3483	3594	1.34E-31	123.291	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2087	2188	1.51E-30	120.21	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	3249	3360	1.82E-30	119.825	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	3015	3127	2.13E-30	119.825	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	3601	3712	4.00E-30	119.054	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	556	668	9.61E-30	117.899	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2191	2308	2.66E-27	110.965	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2433	2544	8.98E-26	106.343	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2666	2779	1.26E-25	105.957	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	2900	3013	3.25E-23	99.0238	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	241571	3366	3480	2.59E-20	90.5494	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4004 - 	CGI_10014626	superfamily	245213	514	550	2.13E-09	56.8762	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4004 - 	CGI_10014626	superfamily	245213	244	284	1.00E-08	54.9502	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4004 - 	CGI_10014626	superfamily	245213	208	241	1.60E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4004 - 	CGI_10014626	superfamily	245213	480	512	3.46E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4004 - 	CGI_10014626	superfamily	245213	338	375	0.000484637	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4004 - 	CGI_10014626	superfamily	205157	386	424	3.14E-07	50.2287	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4004 - 	CGI_10014626	superfamily	205157	430	464	4.13E-06	47.1471	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4004 - 	CGI_10014626	superfamily	216053	122	214	0.00337287	39.199	cl02922	Flagellin_N superfamily	C	 - 	Bacterial flagellin N-terminal helical region; Flagellins polymerise to form bacterial flagella. This family includes flagellins and hook associated protein 3. Structurally this family forms an extended helix that interacts with pfam00700.
Q#4005 - 	CGI_10014627	superfamily	243093	62	146	1.02E-06	47.0797	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#4006 - 	CGI_10014628	superfamily	247727	79	181	4.87E-10	55.899	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#4007 - 	CGI_10014629	superfamily	241596	3	68	0.0049692	35.2675	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#4008 - 	CGI_10014630	superfamily	241570	902	1032	2.53E-17	80.4478	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#4008 - 	CGI_10014630	superfamily	245312	111	363	3.07E-07	53.0123	cl10482	KefB superfamily	C	 - 	"Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]"
Q#4009 - 	CGI_10014631	superfamily	216300	140	351	5.36E-26	106.341	cl18362	Bac_surface_Ag superfamily	 - 	 - 	"Surface antigen; This entry includes the following surface antigens; D15 antigen from H.influenzae, OMA87 from P.multocida, OMP85 from N.meningitidis and N.gonorrhoeae. The family also includes a number of eukaryotic proteins that are members of the UPF0140 family. There also appears to be a relationship to pfam03865 (personal obs: C Yeats). In eukaryotes, it appears that these proteins are not surface antigens; S. cerevisiae YNL026W (SAM50) is an essential component of the Sorting and Assembly Machinery (SAM) of the mitochondrial outer membrane. The protein was localised to the mitochondria."
Q#4009 - 	CGI_10014631	superfamily	219346	13	92	0.00645354	34.6071	cl18507	Surf_Ag_VNR superfamily	 - 	 - 	"Surface antigen variable number repeat; This family is found primarily in bacterial surface antigens, normally as variable number repeats at the N-terminus. The C-terminus of these proteins is normally represented by pfam01103. The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure."
Q#4011 - 	CGI_10014633	superfamily	241580	208	287	3.67E-39	136.53	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#4012 - 	CGI_10014634	superfamily	247683	226	276	7.89E-18	76.1009	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#4013 - 	CGI_10001670	superfamily	241563	85	121	2.55E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4015 - 	CGI_10001672	superfamily	241563	68	108	1.68E-05	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4016 - 	CGI_10001673	superfamily	241563	130	170	3.62E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4017 - 	CGI_10004701	superfamily	150884	206	317	1.13E-46	159.222	cl10958	Med19 superfamily	C	 - 	Mediator of RNA pol II transcription subunit 19; Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators.
Q#4019 - 	CGI_10004703	superfamily	245201	11	282	3.60E-155	444.752	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4020 - 	CGI_10015543	superfamily	149701	209	253	3.75E-23	89.1977	cl07373	Integrin_b_cyt superfamily	 - 	 - 	"Integrin beta cytoplasmic domain; Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion. Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit. Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity. This domain corresponds to the cytoplasmic domain of the beta subunit."
Q#4020 - 	CGI_10015543	superfamily	219669	106	185	6.00E-17	73.1959	cl06832	Integrin_B_tail superfamily	 - 	 - 	Integrin beta tail domain; This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
Q#4021 - 	CGI_10015544	superfamily	248097	74	197	2.79E-21	85.3946	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4022 - 	CGI_10015545	superfamily	215647	57	149	7.31E-05	42.2105	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#4023 - 	CGI_10015546	superfamily	241599	289	347	2.42E-23	95.388	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4023 - 	CGI_10015546	superfamily	245876	19	117	8.60E-12	63.289	cl12113	HSF_DNA-bind superfamily	 - 	 - 	HSF-type DNA-binding; HSF-type DNA-binding.  
Q#4025 - 	CGI_10015548	superfamily	241599	160	217	3.39E-22	87.2988	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4026 - 	CGI_10015549	superfamily	247986	298	419	1.66E-05	45.4418	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#4026 - 	CGI_10015549	superfamily	197504	523	654	6.81E-37	135.495	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#4026 - 	CGI_10015549	superfamily	245225	1	205	3.07E-22	97.7348	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#4027 - 	CGI_10015550	superfamily	245225	55	332	3.71E-10	60.9853	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#4027 - 	CGI_10015550	superfamily	247986	377	466	5.13E-10	58.9238	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#4027 - 	CGI_10015550	superfamily	197504	578	712	1.68E-43	153.984	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#4028 - 	CGI_10015551	superfamily	247986	369	470	4.74E-09	55.457	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#4028 - 	CGI_10015551	superfamily	245225	67	332	6.15E-07	49.97	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#4029 - 	CGI_10015552	superfamily	243058	106	221	1.69E-12	65.4135	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#4029 - 	CGI_10015552	superfamily	243058	443	556	1.17E-09	56.9391	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#4029 - 	CGI_10015552	superfamily	243058	30	139	4.95E-09	55.0131	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#4029 - 	CGI_10015552	superfamily	243058	370	478	5.62E-08	51.9315	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#4029 - 	CGI_10015552	superfamily	243058	186	290	1.51E-07	50.3907	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#4029 - 	CGI_10015552	superfamily	222722	747	885	2.50E-21	93.427	cl18686	EDR1 superfamily	N	 - 	"Ethylene-responsive protein kinase Le-CTR1; EDR1 regulates disease resistance and ethylene-induced senescence, and is also involved in stress response signalling and cell death regulation."
Q#4031 - 	CGI_10015554	superfamily	246681	1046	1241	3.65E-97	309.624	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#4031 - 	CGI_10015554	superfamily	247057	154	213	1.01E-31	119.83	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#4031 - 	CGI_10015554	superfamily	243095	793	1011	7.32E-105	332.075	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#4033 - 	CGI_10015556	superfamily	241578	105	278	5.95E-47	161.402	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4033 - 	CGI_10015556	superfamily	247097	290	324	0.00821797	34.349	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#4034 - 	CGI_10015557	superfamily	243064	268	304	4.94E-05	42.4026	cl02512	NTR_like superfamily	NC	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#4039 - 	CGI_10015562	superfamily	217294	180	433	3.05E-122	361.381	cl08381	GatB_N superfamily	 - 	 - 	GatB/GatE catalytic domain; This domain is found in the GatB and GatE proteins.
Q#4040 - 	CGI_10015563	superfamily	220656	33	138	5.48E-22	85.7669	cl10939	Erf4 superfamily	 - 	 - 	Golgin subfamily A member 7/ERF4 family; This family of proteins includes Golgin subfamily A member 7 proteins as well as Ras modification protein ERF4.
Q#4041 - 	CGI_10015564	superfamily	241682	63	120	5.97E-08	47.4159	cl00203	Ribosomal_L30_like superfamily	 - 	 - 	"Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome.  The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs.  L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea."
Q#4042 - 	CGI_10015565	superfamily	248012	436	572	1.37E-23	97.394	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#4043 - 	CGI_10015566	superfamily	243263	3	388	2.29E-72	236.921	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#4044 - 	CGI_10015567	superfamily	241610	48	99	6.53E-20	77.2902	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#4050 - 	CGI_10014670	superfamily	219542	38	147	1.43E-38	137.758	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#4050 - 	CGI_10014670	superfamily	219541	420	561	1.64E-22	94.0723	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#4050 - 	CGI_10014670	superfamily	215896	154	314	3.78E-12	64.2384	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#4051 - 	CGI_10014671	superfamily	219542	44	148	1.51E-41	146.233	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#4051 - 	CGI_10014671	superfamily	219541	419	565	9.17E-25	100.235	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#4051 - 	CGI_10014671	superfamily	215896	177	311	2.06E-18	82.3428	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#4052 - 	CGI_10014672	superfamily	248097	3	121	5.87E-14	63.4382	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4053 - 	CGI_10014673	superfamily	248097	5	117	6.76E-11	54.9638	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4054 - 	CGI_10014674	superfamily	246925	97	181	0.00255732	40.0314	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#4056 - 	CGI_10014677	superfamily	217380	711	946	1.81E-72	244.542	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#4057 - 	CGI_10014678	superfamily	246680	367	443	3.85E-16	73.3899	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4058 - 	CGI_10014679	superfamily	246680	12	94	1.08E-16	69.3262	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4059 - 	CGI_10014680	superfamily	214773	137	375	3.05E-79	247.335	cl18315	CAP10 superfamily	 - 	 - 	Putative lipopolysaccharide-modifying enzyme; Putative lipopolysaccharide-modifying enzyme.  
Q#4060 - 	CGI_10014681	superfamily	204791	7	286	1.53E-89	275.919	cl13393	WASH_WAHD superfamily	 - 	 - 	"WAHD domain of WASH complex; This domain forms part of the WASH-complex of domains and proteins that activates the Arp2/3 complex, see pfam04062. The Arp2/3 complex regulates endocytosis, sorting, and trafficking within the cell. The WAHD domain attaches to the FAM21 proteins via its N-terminal residues and to the microtubules via its C-terminal residues."
Q#4061 - 	CGI_10014682	superfamily	241758	7	150	2.92E-14	65.469	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#4062 - 	CGI_10014683	superfamily	241758	7	147	1.13E-19	80.1066	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#4063 - 	CGI_10014684	superfamily	247856	100	173	8.21E-11	54.4761	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4063 - 	CGI_10014684	superfamily	247856	65	126	2.42E-09	50.2389	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4063 - 	CGI_10014684	superfamily	244899	40	85	0.00457968	33.6174	cl08302	S-100 superfamily	N	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#4064 - 	CGI_10014685	superfamily	241758	16	96	7.71E-19	76.2546	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#4065 - 	CGI_10014686	superfamily	247724	2	29	0.00318347	36.2316	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4067 - 	CGI_10014688	superfamily	221676	167	242	1.43E-05	45.8658	cl14995	Vezatin superfamily	NC	 - 	Mysoin-binding motif of peroxisomes; Vezatin is a peroxisome transmembrane receptor that is involved in membrane-membrane and cell-cell adhesions. In the movement of peroxisomes it binds to class V and class VIIa myosins to guide the organelle through the microtubules and allow pathogens to internalise themselves into host cells. Vezatin is crucial for spermatozoan production. In mouse cells it interacts with the cadherin-catenin complex bridging it to the C-terminal FERM domain of myosin VIIA.
Q#4068 - 	CGI_10014689	superfamily	241567	66	234	9.43E-15	71.4775	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#4069 - 	CGI_10014690	superfamily	241567	44	215	4.22E-19	81.901	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#4074 - 	CGI_10009148	superfamily	241571	346	452	2.76E-23	99.409	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4074 - 	CGI_10009148	superfamily	241571	232	339	1.62E-14	73.9858	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4074 - 	CGI_10009148	superfamily	241568	552	598	4.97E-09	56.3172	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#4074 - 	CGI_10009148	superfamily	241613	193	228	6.73E-09	55.2906	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#4074 - 	CGI_10009148	superfamily	241568	660	714	7.54E-09	55.932	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#4074 - 	CGI_10009148	superfamily	241568	1002	1056	1.07E-08	55.1616	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#4074 - 	CGI_10009148	superfamily	245213	3396	3430	5.16E-08	53.0242	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	3282	3318	5.55E-08	53.0242	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	3170	3207	1.28E-07	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	3433	3469	2.10E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	241568	1060	1102	1.82E-06	48.6132	cl00043	CCP superfamily	C	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#4074 - 	CGI_10009148	superfamily	241568	936	988	3.75E-06	47.8428	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#4074 - 	CGI_10009148	superfamily	241571	454	541	4.44E-06	48.1775	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4074 - 	CGI_10009148	superfamily	241568	602	656	5.64E-06	47.4576	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#4074 - 	CGI_10009148	superfamily	245213	3245	3279	5.64E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	241568	719	772	1.72E-05	45.9168	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#4074 - 	CGI_10009148	superfamily	245213	3514	3545	4.34E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	815	846	4.87E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	773	804	0.000324286	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	3106	3134	0.00146673	39.9274	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	3057	3096	0.00195847	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	3475	3507	0.00417034	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	245213	4301	4342	0.00870653	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4074 - 	CGI_10009148	superfamily	111397	3792	3870	1.74E-11	63.8994	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#4074 - 	CGI_10009148	superfamily	219525	4090	4137	2.98E-10	59.7401	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#4074 - 	CGI_10009148	superfamily	219525	4252	4297	3.86E-08	53.5769	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#4074 - 	CGI_10009148	superfamily	241611	3593	3733	2.17E-07	52.776	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#4074 - 	CGI_10009148	superfamily	219525	4144	4191	3.09E-07	50.8805	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#4074 - 	CGI_10009148	superfamily	219525	4204	4244	7.55E-06	46.6433	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#4074 - 	CGI_10009148	superfamily	243035	104	190	1.31E-05	46.9142	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4074 - 	CGI_10009148	superfamily	219525	2953	3000	1.96E-05	45.4877	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#4074 - 	CGI_10009148	superfamily	219525	3007	3054	3.56E-05	44.7174	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#4075 - 	CGI_10009149	superfamily	241591	21	85	1.02E-12	60.7127	cl00073	H15 superfamily	C	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#4077 - 	CGI_10009151	superfamily	246680	134	203	1.39E-09	54.5152	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4078 - 	CGI_10009152	superfamily	246680	134	203	2.82E-09	53.3596	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4080 - 	CGI_10009154	superfamily	150458	114	158	2.10E-11	55.7807	cl10765	Oxidored-like superfamily	 - 	 - 	"Oxidoreductase-like protein, N-terminal; Members of this family are found in the N terminal region of various oxidoreductase like proteins. Their exact function is, as yet, unknown."
Q#4081 - 	CGI_10009156	superfamily	246925	126	275	1.46E-12	66.9953	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#4085 - 	CGI_10007449	superfamily	241754	52	385	0	636.737	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#4086 - 	CGI_10007450	superfamily	192483	78	132	4.29E-13	63.0394	cl10893	Pet191_N superfamily	 - 	 - 	Cytochrome c oxidase assembly protein PET191; Pet191_N is the conserved N-terminal of a family of conserved proteins found from nematodes to humans. It carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex.
Q#4089 - 	CGI_10007453	superfamily	218223	51	550	7.64E-135	404.058	cl04698	Radial_spoke superfamily	 - 	 - 	"Radial spokehead-like protein; This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene."
Q#4091 - 	CGI_10007455	superfamily	241822	186	234	0.00123658	35.9133	cl00373	Ribosomal_S18 superfamily	 - 	 - 	Ribosomal protein S18; Ribosomal protein S18.  
Q#4092 - 	CGI_10007456	superfamily	241637	83	148	4.55E-06	45.377	cl00146	TFIIS_I superfamily	 - 	 - 	N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Q#4092 - 	CGI_10007456	superfamily	245716	849	870	1.04E-05	43.7721	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#4094 - 	CGI_10007458	superfamily	241547	68	316	4.08E-71	239.623	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#4095 - 	CGI_10007459	superfamily	218601	6	148	4.72E-39	138.514	cl05181	SURF2 superfamily	C	 - 	"Surfeit locus protein 2 (SURF2); Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown."
Q#4096 - 	CGI_10007460	superfamily	217293	51	263	1.71E-47	163.573	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#4096 - 	CGI_10007460	superfamily	202474	272	363	3.08E-29	113.518	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#4096 - 	CGI_10007460	superfamily	202474	396	424	0.00044246	40.3297	cl08379	Neur_chan_memb superfamily	N	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#4097 - 	CGI_10007461	superfamily	217293	80	297	8.64E-37	135.068	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#4097 - 	CGI_10007461	superfamily	202474	305	386	1.46E-29	114.673	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#4097 - 	CGI_10007461	superfamily	202474	419	448	0.00936713	36.0925	cl08379	Neur_chan_memb superfamily	N	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#4098 - 	CGI_10007462	superfamily	202474	6	87	8.28E-21	84.6277	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#4098 - 	CGI_10007462	superfamily	202474	103	140	1.04E-05	42.2557	cl08379	Neur_chan_memb superfamily	N	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#4099 - 	CGI_10007463	superfamily	241563	93	132	0.00035173	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4101 - 	CGI_10000714	superfamily	245225	16	136	7.01E-17	75.4256	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	NC	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#4102 - 	CGI_10027552	superfamily	245205	96	175	3.84E-10	55.3217	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#4105 - 	CGI_10027555	superfamily	243035	249	379	4.17E-25	100.387	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4107 - 	CGI_10027557	superfamily	243035	268	395	4.80E-25	98.4609	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4107 - 	CGI_10027557	superfamily	243035	60	186	5.83E-25	98.4609	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4111 - 	CGI_10027561	superfamily	243035	107	219	2.20E-21	86.5197	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4111 - 	CGI_10027561	superfamily	245814	52	86	0.00609633	33.882	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4112 - 	CGI_10027562	superfamily	245814	282	348	1.80E-09	54.9136	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4112 - 	CGI_10027562	superfamily	221377	19	132	3.41E-09	55.1674	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#4112 - 	CGI_10027562	superfamily	245814	121	181	9.24E-05	40.8532	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4114 - 	CGI_10027564	superfamily	245596	252	470	3.24E-62	206.775	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#4116 - 	CGI_10027566	superfamily	247724	10	175	4.18E-128	360.876	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4117 - 	CGI_10027567	superfamily	246722	256	390	8.97E-106	311.095	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#4117 - 	CGI_10027567	superfamily	207684	84	118	7.04E-07	45.8327	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#4118 - 	CGI_10027568	superfamily	241607	451	499	7.62E-20	84.6633	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#4118 - 	CGI_10027568	superfamily	248458	45	274	1.47E-10	61.9461	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4119 - 	CGI_10027569	superfamily	241752	647	989	1.74E-164	489.089	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#4119 - 	CGI_10027569	superfamily	242589	520	623	1.36E-49	171.624	cl01581	WGR superfamily	 - 	 - 	"WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain."
Q#4119 - 	CGI_10027569	superfamily	241565	374	447	0.00415293	36.5307	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#4119 - 	CGI_10027569	superfamily	189650	12	86	4.94E-28	109.679	cl02913	zf-PARP superfamily	 - 	 - 	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
Q#4119 - 	CGI_10027569	superfamily	191934	270	324	6.41E-21	88.5062	cl06892	PADR1 superfamily	 - 	 - 	PADR1 (NUC008) domain; This domain is found in poly(ADP-ribose)-synthetases. The function of this domain is unknown.
Q#4119 - 	CGI_10027569	superfamily	189650	112	192	3.86E-20	86.9522	cl02913	zf-PARP superfamily	 - 	 - 	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
Q#4120 - 	CGI_10027570	superfamily	241599	130	184	2.04E-13	63.0312	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4121 - 	CGI_10027571	superfamily	187395	46	80	0.0050963	36.2778	cl14622	flgI superfamily	NC	 - 	flagellar basal body P-ring protein; Reviewed
Q#4125 - 	CGI_10027576	superfamily	219677	69	95	0.0018631	37.4172	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#4127 - 	CGI_10027579	superfamily	241619	889	931	1.93E-06	50.1609	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#4127 - 	CGI_10027579	superfamily	243065	3078	3238	2.28E-12	69.3529	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	243065	5081	5244	1.76E-11	66.6565	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	243065	8300	8453	4.25E-11	65.5409	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	243065	6093	6253	5.53E-11	65.1157	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	243065	1309	1472	6.28E-10	61.6889	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	243065	2282	2442	2.02E-09	60.1081	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	243065	308	465	5.47E-09	58.9925	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	243065	7101	7261	1.07E-08	57.7969	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4127 - 	CGI_10027579	superfamily	241611	5682	5828	1.82E-05	47.7684	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#4127 - 	CGI_10027579	superfamily	241619	1953	2028	0.000289089	43.3397	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#4127 - 	CGI_10027579	superfamily	243065	4085	4226	0.0057881	40.0777	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#4128 - 	CGI_10027580	superfamily	247799	64	122	3.29E-11	58.2921	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#4128 - 	CGI_10027580	superfamily	177724	131	357	1.56E-28	111.699	cl15624	PLN00108 superfamily	 - 	 - 	unknown protein; Provisional
Q#4129 - 	CGI_10027581	superfamily	219849	1829	1920	6.42E-17	79.9211	cl09597	RIH_assoc superfamily	 - 	 - 	"RyR and IP3R Homology associated; This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815."
Q#4129 - 	CGI_10027581	superfamily	216456	520	672	1.46E-16	81.2158	cl03182	RYDR_ITPR superfamily	 - 	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#4129 - 	CGI_10027581	superfamily	216456	1182	1347	2.62E-06	49.2442	cl03182	RYDR_ITPR superfamily	 - 	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#4132 - 	CGI_10027584	superfamily	247724	50	243	2.43E-05	42.8288	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4134 - 	CGI_10027586	superfamily	247683	1378	1439	1.65E-37	137.038	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#4134 - 	CGI_10027586	superfamily	247683	584	645	7.34E-36	132.477	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#4134 - 	CGI_10027586	superfamily	247683	1495	1555	3.82E-24	98.6055	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#4134 - 	CGI_10027586	superfamily	151039	243	330	0.000170549	42.0927	cl11115	Cenp-F_leu_zip superfamily	C	 - 	"Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance."
Q#4134 - 	CGI_10027586	superfamily	241584	757	832	0.00574345	36.8237	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#4138 - 	CGI_10027590	superfamily	247856	365	419	1.87E-12	64.9335	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4139 - 	CGI_10027591	superfamily	241737	11	167	9.53E-91	264.406	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#4140 - 	CGI_10027592	superfamily	219502	306	358	5.93E-11	60.1507	cl06625	Nucleos_tra2_C superfamily	C	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#4140 - 	CGI_10027592	superfamily	201962	124	194	1.11E-10	57.0004	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#4140 - 	CGI_10027592	superfamily	219507	203	287	2.39E-09	53.7823	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#4141 - 	CGI_10027593	superfamily	219502	1	104	4.62E-42	139.887	cl06625	Nucleos_tra2_C superfamily	N	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#4142 - 	CGI_10027594	superfamily	245227	22	188	4.13E-25	109.013	cl10013	Glycosyltransferase_GTB_type superfamily	N	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#4142 - 	CGI_10027594	superfamily	241559	245	375	1.58E-15	75.4251	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#4142 - 	CGI_10027594	superfamily	141488	412	480	3.37E-35	131.104	cl02524	GAS2 superfamily	 - 	 - 	Growth-Arrest-Specific Protein 2 Domain; Growth-Arrest-Specific Protein 2 Domain.  
Q#4143 - 	CGI_10027595	superfamily	243081	242	479	9.50E-75	237.893	cl02549	OLF superfamily	 - 	 - 	Olfactomedin-like domain; Olfactomedin-like domain.  
Q#4144 - 	CGI_10027596	superfamily	241758	41	162	7.97E-18	75.8694	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#4146 - 	CGI_10027598	superfamily	241547	369	455	1.48E-23	99.6647	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#4146 - 	CGI_10027598	superfamily	241547	545	647	5.97E-17	80.0195	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#4147 - 	CGI_10027599	superfamily	241547	75	192	7.82E-29	112.376	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#4147 - 	CGI_10027599	superfamily	241547	311	381	5.09E-16	75.8133	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#4153 - 	CGI_10027605	superfamily	247856	50	111	2.21E-11	55.6317	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4156 - 	CGI_10027608	superfamily	243066	41	84	0.000313599	36.0561	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#4157 - 	CGI_10027609	superfamily	243066	82	195	6.35E-09	51.0789	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#4158 - 	CGI_10027610	superfamily	243091	548	649	3.10E-10	58.8851	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#4158 - 	CGI_10027610	superfamily	222150	731	756	0.000249464	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4158 - 	CGI_10027610	superfamily	222150	816	841	0.00236118	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4158 - 	CGI_10027610	superfamily	246975	803	824	0.00808643	35.4005	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#4159 - 	CGI_10027611	superfamily	241770	48	150	2.40E-11	57.0204	cl00309	PRTases_typeI superfamily	 - 	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#4160 - 	CGI_10027612	superfamily	247755	414	653	5.19E-111	336.895	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#4160 - 	CGI_10027612	superfamily	216049	89	366	9.62E-15	73.8594	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#4161 - 	CGI_10027613	superfamily	247755	169	403	9.74E-117	343.058	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#4161 - 	CGI_10027613	superfamily	216049	5	121	7.57E-09	54.9846	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#4162 - 	CGI_10027614	superfamily	220695	87	225	1.38E-05	44.4919	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#4163 - 	CGI_10027615	superfamily	243064	33	83	4.68E-05	39.6494	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#4164 - 	CGI_10027616	superfamily	243064	21	118	1.13E-10	55.0574	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#4166 - 	CGI_10027618	superfamily	145834	13	44	4.98E-07	42.4996	cl03761	Glycos_trans_3N superfamily	N	 - 	"Glycosyl transferase family, helical bundle domain; This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate."
Q#4166 - 	CGI_10027618	superfamily	216013	57	85	1.03E-05	40.7037	cl02901	Glycos_transf_3 superfamily	C	 - 	"Glycosyl transferase family, a/b domain; This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate."
Q#4167 - 	CGI_10027619	superfamily	216013	84	327	2.26E-42	151.256	cl02901	Glycos_transf_3 superfamily	 - 	 - 	"Glycosyl transferase family, a/b domain; This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate."
Q#4167 - 	CGI_10027619	superfamily	145834	7	71	8.25E-16	72.16	cl03761	Glycos_trans_3N superfamily	 - 	 - 	"Glycosyl transferase family, helical bundle domain; This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate."
Q#4167 - 	CGI_10027619	superfamily	244483	359	432	6.71E-13	64.0955	cl06734	PYNP_C superfamily	 - 	 - 	"Pyrimidine nucleoside phosphorylase C-terminal domain; This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer."
Q#4168 - 	CGI_10027620	superfamily	241578	274	471	1.08E-08	55.3291	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4170 - 	CGI_10027622	superfamily	246908	87	171	6.57E-16	69.7918	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#4173 - 	CGI_10027625	superfamily	243035	63	159	6.72E-15	66.8745	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4174 - 	CGI_10027626	superfamily	247941	144	275	3.16E-10	58.5013	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#4174 - 	CGI_10027626	superfamily	247941	407	541	4.89E-10	57.7309	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#4175 - 	CGI_10027627	superfamily	128937	3	69	2.10E-14	64.206	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#4175 - 	CGI_10027627	superfamily	128937	78	143	2.76E-11	55.3464	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#4176 - 	CGI_10027628	superfamily	128937	3	69	2.10E-14	64.206	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#4176 - 	CGI_10027628	superfamily	128937	78	143	2.76E-11	55.3464	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#4177 - 	CGI_10002387	superfamily	247684	73	483	5.24E-81	263.754	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4179 - 	CGI_10026933	superfamily	246664	224	595	4.75E-157	459.348	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#4179 - 	CGI_10026933	superfamily	246664	75	165	2.63E-06	48.82	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#4180 - 	CGI_10026934	superfamily	246664	124	523	4.16E-146	428.917	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#4180 - 	CGI_10026934	superfamily	246664	22	65	7.32E-08	53.4682	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#4181 - 	CGI_10026935	superfamily	247057	961	1026	1.01E-33	125.466	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#4181 - 	CGI_10026935	superfamily	248259	538	635	1.77E-35	131.218	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#4181 - 	CGI_10026935	superfamily	248259	646	733	2.37E-32	122.358	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#4181 - 	CGI_10026935	superfamily	248259	449	527	4.44E-32	121.588	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#4181 - 	CGI_10026935	superfamily	201844	828	857	5.23E-12	62.313	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#4181 - 	CGI_10026935	superfamily	201844	750	779	7.14E-09	53.4534	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#4183 - 	CGI_10026937	superfamily	243062	289	386	5.30E-35	125.466	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#4183 - 	CGI_10026937	superfamily	216062	36	217	4.06E-16	75.9374	cl02928	TGFb_propeptide superfamily	 - 	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#4184 - 	CGI_10026938	superfamily	241705	33	114	8.66E-26	97.071	cl00228	HIT_like superfamily	N	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#4185 - 	CGI_10026939	superfamily	241889	95	241	1.71E-63	199.008	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#4188 - 	CGI_10026942	superfamily	241581	3	83	1.34E-14	67.7966	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#4189 - 	CGI_10026943	superfamily	241596	38	87	1.28E-10	53.7571	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#4190 - 	CGI_10026944	superfamily	241596	42	85	1.28E-06	42.2011	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#4192 - 	CGI_10026946	superfamily	220756	1262	1463	2.43E-14	73.4858	cl11092	Urb2 superfamily	 - 	 - 	Urb2/Npa2 family; This family includes the Urb2 protein from yeast that are involved in ribosome biogenesis.
Q#4198 - 	CGI_10026952	superfamily	243263	97	586	7.89E-72	240.773	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#4199 - 	CGI_10026953	superfamily	243263	128	346	3.00E-33	129.078	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#4201 - 	CGI_10026955	superfamily	247725	300	413	6.03E-57	185.517	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4202 - 	CGI_10026956	superfamily	247723	65	146	3.78E-44	148.225	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4202 - 	CGI_10026956	superfamily	247723	149	230	3.78E-44	148.225	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4202 - 	CGI_10026956	superfamily	247723	12	57	1.31E-18	78.9174	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4205 - 	CGI_10026959	superfamily	199908	148	208	0.000107429	39.5463	cl16908	DnaJ_zf superfamily	 - 	 - 	"Zinc finger domain of DnaJ and HSP40; Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. Hsp40 proteins are characterized by the presence of an N-terminal J domain, which mediates the interaction with Hsp70. This central domain contains four repeats of a CxxCxGxG motif and binds to two Zinc ions. It has been implicated in substrate binding."
Q#4206 - 	CGI_10026960	superfamily	199908	417	468	1.04E-06	46.4799	cl16908	DnaJ_zf superfamily	 - 	 - 	"Zinc finger domain of DnaJ and HSP40; Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. Hsp40 proteins are characterized by the presence of an N-terminal J domain, which mediates the interaction with Hsp70. This central domain contains four repeats of a CxxCxGxG motif and binds to two Zinc ions. It has been implicated in substrate binding."
Q#4207 - 	CGI_10026961	superfamily	247739	1	217	2.51E-34	123.552	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#4210 - 	CGI_10026964	superfamily	247725	560	733	1.48E-77	251.036	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4210 - 	CGI_10026964	superfamily	243096	382	568	8.70E-45	160.156	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#4210 - 	CGI_10026964	superfamily	241565	116	178	7.49E-11	59.6426	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#4210 - 	CGI_10026964	superfamily	241565	209	274	4.85E-05	42.3087	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#4212 - 	CGI_10026966	superfamily	241559	27	131	1.24E-21	92.3739	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#4212 - 	CGI_10026966	superfamily	241559	140	239	1.90E-10	59.6319	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#4212 - 	CGI_10026966	superfamily	241559	249	335	1.38E-07	50.7723	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#4212 - 	CGI_10026966	superfamily	216033	1003	1093	4.39E-19	84.3076	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4212 - 	CGI_10026966	superfamily	216033	913	997	8.76E-16	75.0628	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4212 - 	CGI_10026966	superfamily	216033	616	702	9.88E-14	68.8996	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4212 - 	CGI_10026966	superfamily	216033	815	903	2.33E-11	61.966	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4212 - 	CGI_10026966	superfamily	216033	526	611	1.12E-09	56.9584	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4212 - 	CGI_10026966	superfamily	216033	363	431	3.34E-05	43.4764	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4212 - 	CGI_10026966	superfamily	216033	490	521	0.00313315	37.3132	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4213 - 	CGI_10026967	superfamily	215847	217	355	9.21E-28	113.695	cl09510	Lipoxygenase superfamily	NC	 - 	Lipoxygenase; Lipoxygenase.  
Q#4213 - 	CGI_10026967	superfamily	241546	2	106	5.03E-24	94.9292	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#4215 - 	CGI_10026970	superfamily	247905	834	942	2.04E-26	107.709	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#4215 - 	CGI_10026970	superfamily	247805	536	681	2.69E-23	98.9487	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#4215 - 	CGI_10026970	superfamily	248013	420	474	7.97E-08	51.4959	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#4215 - 	CGI_10026970	superfamily	248013	342	385	5.86E-06	46.1031	cl17459	CHROMO superfamily	N	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#4215 - 	CGI_10026970	superfamily	206078	1422	1514	2.66E-34	129.308	cl16467	DUF4208 superfamily	 - 	 - 	Domain of unknown function (DUF4208); This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins. The exact function of the domain is undetermined.
Q#4215 - 	CGI_10026970	superfamily	247804	1231	1265	0.000222532	41.0135	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#4216 - 	CGI_10026971	superfamily	241739	43	287	1.07E-96	305.438	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#4216 - 	CGI_10026971	superfamily	244970	684	724	3.91E-07	48.1474	cl08469	tRNA_SAD superfamily	 - 	 - 	"Threonyl and Alanyl tRNA synthetase second additional domain; The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain."
Q#4218 - 	CGI_10026973	superfamily	243066	1	61	2.92E-06	43.3105	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#4220 - 	CGI_10026975	superfamily	241645	10	72	6.80E-10	55.351	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#4220 - 	CGI_10026975	superfamily	241578	185	350	2.13E-09	55.2646	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4222 - 	CGI_10026977	superfamily	243035	115	236	5.19E-12	60.0109	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4223 - 	CGI_10026978	superfamily	247792	359	401	9.74E-08	49.7516	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4223 - 	CGI_10026978	superfamily	241644	194	291	1.33E-13	68.7681	cl00154	UBCc superfamily	N	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#4223 - 	CGI_10026978	superfamily	241563	689	716	0.006056	35.3907	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4225 - 	CGI_10026980	superfamily	247038	197	285	2.16E-13	65.5537	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#4225 - 	CGI_10026980	superfamily	246669	18	89	4.70E-07	47.4467	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#4226 - 	CGI_10026981	superfamily	241758	1	114	5.93E-21	82.4178	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#4227 - 	CGI_10026982	superfamily	241758	8	108	4.49E-14	63.543	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#4230 - 	CGI_10026985	superfamily	243061	11	113	1.33E-35	134.007	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	2738	2841	3.71E-33	127.073	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	979	1081	2.64E-32	124.377	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1296	1412	8.86E-24	99.7238	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	2296	2397	2.54E-22	95.4866	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	342	442	6.88E-21	91.6346	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1953	2056	4.48E-20	88.9382	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1191	1289	2.07E-19	87.0122	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1850	1945	9.55E-19	85.0862	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	660	760	1.20E-18	85.0862	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	2523	2612	2.40E-17	80.9738	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1415	1515	6.35E-17	80.0786	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	763	864	9.75E-17	79.3082	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	2401	2498	1.02E-16	79.3082	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	553	653	2.95E-16	78.1526	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1646	1733	2.24E-15	75.4562	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	128	219	1.77E-14	72.8846	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	894	972	2.22E-14	72.3746	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1106	1181	3.13E-14	72.1142	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1737	1834	3.50E-14	71.9894	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	249	334	3.61E-13	68.9078	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	1533	1630	1.42E-12	67.367	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	2621	2728	3.81E-12	65.8262	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	445	543	5.40E-12	65.441	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	2072	2157	3.20E-10	60.0482	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4230 - 	CGI_10026985	superfamily	243061	2206	2285	3.07E-07	51.3134	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4231 - 	CGI_10026986	superfamily	247692	269	765	4.06E-168	498.844	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#4231 - 	CGI_10026986	superfamily	241567	1	256	1.61E-12	66.8551	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#4232 - 	CGI_10026987	superfamily	204502	26	77	1.31E-26	101.422	cl11146	GalKase_gal_bdg superfamily	 - 	 - 	"Galactokinase galactose-binding signature; This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry. The function of this domain appears to be to bind galactose, and the domain is normally at the N-terminus of the enzymes, EC:2.7.1.6. This domain is associated with the families GHMP_kinases_C, pfam08544 and GHMP_kinases_N, pfam00288."
Q#4232 - 	CGI_10026987	superfamily	219894	355	435	1.51E-08	51.7316	cl08484	GHMP_kinases_C superfamily	 - 	 - 	"GHMP kinases C terminal; This family includes homoserine kinases, galactokinases and mevalonate kinases."
Q#4233 - 	CGI_10026988	superfamily	219309	1	496	5.50E-36	138.392	cl06259	PDCD9 superfamily	 - 	 - 	Mitochondrial 28S ribosomal protein S30 (PDCD9); This family consists of several eukaryotic mitochondrial 28S ribosomal protein S30 (or programmed cell death protein 9 PDCD9) sequences. The exact function of this family is unknown although it is known to be a component of the mitochondrial ribosome and a component in cellular apoptotic signaling pathways.
Q#4236 - 	CGI_10026991	superfamily	221137	228	284	4.39E-14	66.2404	cl13084	Med27 superfamily	C	 - 	"Mediator complex subunit 27; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells."
Q#4238 - 	CGI_10026993	superfamily	247755	1	57	1.54E-27	99.5362	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#4239 - 	CGI_10026994	superfamily	243077	132	159	2.27E-08	47.1549	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#4239 - 	CGI_10026994	superfamily	243077	10	37	5.80E-07	43.3029	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#4240 - 	CGI_10005755	superfamily	248458	2	327	2.49E-06	47.3085	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4241 - 	CGI_10005756	superfamily	248458	44	220	5.37E-13	66.1833	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4242 - 	CGI_10005757	superfamily	241600	7	187	1.05E-89	264.488	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#4243 - 	CGI_10005758	superfamily	216033	334	369	4.85E-05	41.5504	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#4244 - 	CGI_10005759	superfamily	241613	76	106	3.16E-09	50.283	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#4244 - 	CGI_10005759	superfamily	241571	17	70	7.16E-07	45.0959	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4245 - 	CGI_10005760	superfamily	245175	5	31	1.54E-08	48.0992	cl09847	Sen15 superfamily	N	 - 	"Sen15 protein; The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly."
Q#4245 - 	CGI_10005760	superfamily	245175	59	84	1.20E-07	45.4028	cl09847	Sen15 superfamily	N	 - 	"Sen15 protein; The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly."
Q#4246 - 	CGI_10005761	superfamily	247792	367	407	2.85E-09	52.8332	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4248 - 	CGI_10005763	superfamily	241732	896	1010	1.48E-37	139.285	cl00258	RIBOc superfamily	 - 	 - 	"RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing."
Q#4248 - 	CGI_10005763	superfamily	241732	1057	1189	8.94E-34	128.499	cl00258	RIBOc superfamily	 - 	 - 	"RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing."
Q#4248 - 	CGI_10005763	superfamily	241575	1195	1267	5.80E-13	66.1419	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#4249 - 	CGI_10005764	superfamily	247639	42	384	0	539.125	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#4250 - 	CGI_10005765	superfamily	247856	80	138	3.42E-14	64.1061	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4250 - 	CGI_10005765	superfamily	247856	113	185	2.36E-13	61.7949	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4250 - 	CGI_10005765	superfamily	247856	53	103	0.00389266	33.6753	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4251 - 	CGI_10005766	superfamily	247792	285	332	2.21E-06	43.9736	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4252 - 	CGI_10005767	superfamily	247792	141	180	6.48E-05	38.5808	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4253 - 	CGI_10005768	superfamily	247905	416	536	4.47E-25	101.546	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#4253 - 	CGI_10005768	superfamily	247805	146	356	1.69E-63	211.574	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#4253 - 	CGI_10005768	superfamily	222474	595	655	1.09E-20	87.0933	cl16500	DUF4217 superfamily	 - 	 - 	Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many helicase proteins.
Q#4254 - 	CGI_10005769	superfamily	241600	77	291	1.79E-104	306.089	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#4255 - 	CGI_10005770	superfamily	241782	86	470	1.81E-90	281.923	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#4256 - 	CGI_10005771	superfamily	247792	419	458	4.63E-06	43.9736	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4256 - 	CGI_10005771	superfamily	247057	348	391	2.72E-12	62.3054	cl15755	SAM_superfamily superfamily	C	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#4258 - 	CGI_10015523	superfamily	245815	25	499	0	896.181	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#4259 - 	CGI_10015524	superfamily	245814	13	106	1.27E-11	61.2491	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4259 - 	CGI_10015524	superfamily	245814	313	391	1.62E-10	57.4542	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4259 - 	CGI_10015524	superfamily	245814	187	282	2.51E-10	57.1301	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4259 - 	CGI_10015524	superfamily	245814	112	176	8.04E-07	46.9967	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4262 - 	CGI_10015527	superfamily	245205	2019	2129	1.86E-39	144.677	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#4262 - 	CGI_10015527	superfamily	245205	2139	2386	1.52E-60	211.154	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#4262 - 	CGI_10015527	superfamily	245205	2397	2503	1.49E-07	52.5363	cl09930	RPA_2b-aaRSs_OBF_like superfamily	C	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#4262 - 	CGI_10015527	superfamily	201361	1162	1184	0.00422306	37.8427	cl02912	BRCA2 superfamily	 - 	 - 	BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
Q#4262 - 	CGI_10015527	superfamily	201361	1284	1311	0.00460424	37.4575	cl02912	BRCA2 superfamily	 - 	 - 	BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
Q#4262 - 	CGI_10015527	superfamily	201361	731	761	0.00601951	37.0723	cl02912	BRCA2 superfamily	 - 	 - 	BRCA2 repeat; The alignment covers only the most conserved region of the repeat.
Q#4263 - 	CGI_10015528	superfamily	247792	19	62	2.28E-07	48.2108	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4263 - 	CGI_10015528	superfamily	241563	150	181	0.000413612	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4265 - 	CGI_10015530	superfamily	244906	9	75	3.96E-28	99.9071	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#4268 - 	CGI_10015534	superfamily	247724	18	132	1.57E-46	155.427	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4268 - 	CGI_10015534	superfamily	243035	142	256	2.29E-26	100.772	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4269 - 	CGI_10015535	superfamily	241596	65	121	5.54E-14	68.0095	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#4269 - 	CGI_10015535	superfamily	241563	234	270	5.24E-06	44.5855	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4269 - 	CGI_10015535	superfamily	110440	661	687	0.000585923	38.5429	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#4270 - 	CGI_10015536	superfamily	247792	18	69	2.35E-08	51.2924	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4271 - 	CGI_10015537	superfamily	247792	18	69	2.43E-07	48.2108	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4271 - 	CGI_10015537	superfamily	241563	101	147	0.00659347	35.0055	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4272 - 	CGI_10015538	superfamily	247792	35	86	1.48E-07	48.596	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4273 - 	CGI_10015539	superfamily	220386	43	223	4.09E-83	261.099	cl10743	KOG2701 superfamily	 - 	 - 	"Coiled-coil domain-containing protein (DUF2037); This entry represents the conserved N-terminal 200 residues of a family of proteins conserved from plants to vertebrates. In Drosophila it comes from the Fidipidine gene, and is of unknown function."
Q#4274 - 	CGI_10015540	superfamily	148723	3	191	4.82E-62	195.77	cl06350	INSIG superfamily	 - 	 - 	"Insulin-induced protein (INSIG); This family contains a number of eukaryotic Insulin-induced proteins (INSIG-1 and INSIG-2) approximately 200 residues long. INSIG-1 and INSIG-2 are found in the endoplasmic reticulum and bind the sterol-sensing domain of SREBP cleavage-activating protein (SCAP), preventing it from escorting SREBPs to the Golgi. Their combined action permits feedback regulation of cholesterol synthesis over a wide range of sterol concentrations."
Q#4275 - 	CGI_10015541	superfamily	241600	23	193	4.69E-63	196.693	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#4276 - 	CGI_10015542	superfamily	241600	70	114	2.93E-08	49.1611	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#4279 - 	CGI_10001766	superfamily	242146	1	63	2.45E-11	56.052	cl00859	Cytochrome_b_N superfamily	N	 - 	"Cytochrome b (N-terminus)/b6/petB:  Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms.  Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites.  The C-terminal portion of cytochrome b is described in a separate CD."
Q#4279 - 	CGI_10001766	superfamily	241673	42	106	1.94E-06	42.2477	cl00193	cytochrome_b_C superfamily	C	 - 	"Cytochrome b(C-terminus)/b6/petD:  Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms.  Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites.  The C-terminal domain is involved in forming the ubiquinol/ubiquinone binding sites, but not the heme binding sites.  The N-terminal portion of cytochrome b, which contains both heme binding sites,  is described in a separate CD."
Q#4281 - 	CGI_10007884	superfamily	241563	65	100	0.00875052	31.874	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4283 - 	CGI_10007886	superfamily	241563	72	112	0.000117322	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4289 - 	CGI_10007892	superfamily	243092	444	716	1.60E-15	76.6048	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4290 - 	CGI_10007893	superfamily	212559	282	326	5.96E-24	94.9886	cl18297	SANT_MTA3_like superfamily	 - 	 - 	"Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle.  MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis."
Q#4290 - 	CGI_10007893	superfamily	216509	175	226	2.75E-07	48.0038	cl03218	ELM2 superfamily	 - 	 - 	"ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a member from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain."
Q#4291 - 	CGI_10007894	superfamily	245815	39	98	0.000524406	39.107	cl11961	ALDH-SF superfamily	NC	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#4292 - 	CGI_10013049	superfamily	243035	25	91	8.65E-12	56.6156	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4293 - 	CGI_10013050	superfamily	245201	12	299	0	514.497	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4294 - 	CGI_10013051	superfamily	187408	362	700	2.09E-179	524.919	cl14654	V_Alix_like superfamily	 - 	 - 	"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain."
Q#4294 - 	CGI_10013051	superfamily	187403	2	346	2.80E-177	519.545	cl14649	BRO1_Alix_like superfamily	 - 	 - 	"Protein-interacting Bro1-like domain of mammalian Alix and related domains; This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, HD-PTP, and Brox) and Snf7 (in the case of yeast Bro1, and Rim20). The single domain protein human Brox, and the isolated Bro1-like domains of Alix, HD-PTP and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V) domain, which in the case of Alix, has been shown to be a dimerization domain and to contain a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in this superfamily. Alix, HD-PTP and Bro1 also have a proline-rich region (PRR); the Alix PRR binds multiple partners. Rhophilin-1, and -2, in addition to this Bro1-like domain, have an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This protein has a C-terminal, catalytically inactive tyrosine phosphatase domain."
Q#4296 - 	CGI_10013053	superfamily	245213	28	65	8.11E-05	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4299 - 	CGI_10013056	superfamily	241599	77	135	5.80E-24	92.6916	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4301 - 	CGI_10013058	superfamily	241599	66	124	5.60E-22	86.9136	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4302 - 	CGI_10013059	superfamily	149667	81	171	3.48E-08	50.0615	cl07343	GON superfamily	C	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#4303 - 	CGI_10013060	superfamily	149667	1	111	5.30E-07	47.7503	cl07343	GON superfamily	N	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#4308 - 	CGI_10013065	superfamily	243051	94	248	5.03E-26	100.53	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#4308 - 	CGI_10013065	superfamily	245213	53	90	2.64E-07	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4308 - 	CGI_10013065	superfamily	245213	14	48	1.25E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4310 - 	CGI_10012186	superfamily	241584	2622	2713	1.56E-10	60.9731	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#4310 - 	CGI_10012186	superfamily	241584	2552	2616	1.98E-06	48.6467	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#4310 - 	CGI_10012186	superfamily	243092	2085	2412	4.29E-25	108.576	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4310 - 	CGI_10012186	superfamily	243092	1816	2160	2.99E-23	103.184	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4310 - 	CGI_10012186	superfamily	204895	149	220	1.48E-21	92.4033	cl13764	DUF3651 superfamily	 - 	 - 	"Protein of unknown function (DUF3651); This domain family is found in eukaryotes, and is approximately 70 amino acids in length. This family is frequently annotated as a membrane protein but there is little associated literature to back this up."
Q#4311 - 	CGI_10012187	superfamily	218231	96	163	3.84E-07	46.5026	cl04708	ELMO_CED12 superfamily	N	 - 	"ELMO/CED-12 family; This family represents a conserved domain which is found in a number of eukaryotic proteins including CED-12, ELMO I and ELMO II. ELMO1 is a component of signalling pathways that regulate phagocytosis and cell migration and is the mammalian orthologue of the C. elegans gene, ced-12. CED-12 is required for the engulfment of dying cells and cell migration. In mammalian cells, ELMO1 interacts with Dock180 as part of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. ELMO1 is ubiquitously expressed, although its expression is highest in the spleen, an organ rich in immune cells. ELMO1 has a PH domain and a polyproline sequence motif at its C terminus which are not present in this alignment."
Q#4312 - 	CGI_10012188	superfamily	241645	59	145	5.87E-07	44.0717	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#4313 - 	CGI_10012189	superfamily	241622	41	83	4.42E-08	52.5691	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#4313 - 	CGI_10012189	superfamily	241647	420	438	0.00642267	36.4247	cl00157	WW superfamily	C	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#4318 - 	CGI_10012194	superfamily	219000	31	178	2.11E-25	101.184	cl05717	Drf_FH3 superfamily	 - 	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#4319 - 	CGI_10012195	superfamily	219001	1	45	5.64E-05	37.6735	cl05720	Drf_GBD superfamily	N	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#4320 - 	CGI_10012196	superfamily	242914	21	60	1.93E-17	69.1796	cl02163	zf-CSL superfamily	N	 - 	CSL zinc finger; This is a zinc binding motif which contains four cysteine residues which chelate zinc. This domain is often found associated with a pfam00226 domain. This domain is named after the conserved motif of the final cysteine.
Q#4322 - 	CGI_10012198	superfamily	247792	80	125	0.000950668	38.1956	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4322 - 	CGI_10012198	superfamily	128778	263	383	1.48E-10	59.9711	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#4322 - 	CGI_10012198	superfamily	110440	683	710	4.55E-06	45.0913	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#4322 - 	CGI_10012198	superfamily	241563	213	256	9.12E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4323 - 	CGI_10012199	superfamily	220421	11	482	6.00E-47	172.305	cl10789	DUF2352 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2352); Members of this family of uncharacterized proteins have no known function.
Q#4324 - 	CGI_10012200	superfamily	243306	33	291	1.85E-126	364.186	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#4325 - 	CGI_10012201	superfamily	247724	2333	2495	4.50E-47	169.439	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4325 - 	CGI_10012201	superfamily	243109	1443	1572	4.99E-32	126.255	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#4325 - 	CGI_10012201	superfamily	248012	2989	3096	1.32E-14	73.3808	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#4325 - 	CGI_10012201	superfamily	243109	553	693	1.42E-08	56.1483	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#4325 - 	CGI_10012201	superfamily	246925	2020	2131	0.00309471	41.187	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#4325 - 	CGI_10012201	superfamily	199166	60	109	0.00703288	39.618	cl15308	AMN1 superfamily	NC	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#4327 - 	CGI_10003583	superfamily	218118	64	101	3.79E-09	51.0757	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#4328 - 	CGI_10003584	superfamily	218118	38	103	1.12E-06	42.2161	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#4329 - 	CGI_10003585	superfamily	218118	122	187	1.77E-15	68.4096	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#4331 - 	CGI_10003587	superfamily	199156	236	251	0.00156408	35.8929	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#4332 - 	CGI_10004785	superfamily	247743	1773	1916	9.32E-08	52.6828	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#4333 - 	CGI_10004786	superfamily	193256	551	814	1.33E-69	237.923	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#4333 - 	CGI_10004786	superfamily	193251	180	453	2.64E-51	185.139	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#4333 - 	CGI_10004786	superfamily	193257	1192	1403	3.58E-40	151.291	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#4333 - 	CGI_10004786	superfamily	193253	831	1172	8.11E-39	150.958	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#4334 - 	CGI_10004787	superfamily	247792	746	787	0.000387706	39.3512	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4335 - 	CGI_10004788	superfamily	243109	67	194	4.30E-82	249.523	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#4339 - 	CGI_10014720	superfamily	217293	40	173	3.68E-25	99.6295	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#4341 - 	CGI_10014722	superfamily	217293	177	383	1.27E-24	101.555	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#4341 - 	CGI_10014722	superfamily	217293	29	168	4.76E-24	100.015	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#4341 - 	CGI_10014722	superfamily	202474	391	457	3.98E-06	46.8781	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#4342 - 	CGI_10014723	superfamily	243092	50	342	2.49E-77	241.47	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4345 - 	CGI_10014726	superfamily	241814	25	226	6.42E-26	104.292	cl00360	COG0212 superfamily	 - 	 - 	5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]
Q#4345 - 	CGI_10014726	superfamily	247723	430	498	2.08E-15	71.6018	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4346 - 	CGI_10014727	superfamily	208802	10	283	0	510.012	cl07974	DRE_TIM_metallolyase superfamily	 - 	 - 	"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM"."
Q#4348 - 	CGI_10014729	superfamily	241583	118	205	3.59E-09	56.0403	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#4348 - 	CGI_10014729	superfamily	241571	321	417	3.78E-07	48.9256	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#4348 - 	CGI_10014729	superfamily	241583	219	251	0.000389179	40.6323	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#4352 - 	CGI_10014734	superfamily	226447	746	842	0.00103297	38.6074	cl18758	COG3937 superfamily	 - 	 - 	Uncharacterized conserved protein [Function unknown]
Q#4356 - 	CGI_10009615	superfamily	241640	1	225	8.66E-43	145.882	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#4357 - 	CGI_10009616	superfamily	241802	384	869	3.77E-176	520.643	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#4357 - 	CGI_10009616	superfamily	247744	212	365	3.51E-29	114.96	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#4358 - 	CGI_10009617	superfamily	220651	178	358	3.18E-46	158.46	cl10932	Mlf1IP superfamily	 - 	 - 	"Myelodysplasia-myeloid leukemia factor 1-interacting protein; This entry is the conserved central region of a group of proteins that are putative transcriptional repressors. The structure contains a putative 14-3-3 binding motif involved in the subcellular localisation of various regulatory molecules, and it may be that interaction with the transcription factor DREF could be regulated through this motif. DREF regulates proliferation-related genes in Drosophila. Mlf1IP is expressed in both the nuclei and the cytoplasm and thus may have multi-functions."
Q#4358 - 	CGI_10009617	superfamily	216981	24	42	0.0087079	34.8158	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#4360 - 	CGI_10003702	superfamily	216112	47	162	1.34E-38	135.117	cl02964	RNB superfamily	C	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#4361 - 	CGI_10003703	superfamily	241563	68	109	9.05E-07	46.3184	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4361 - 	CGI_10003703	superfamily	241563	28	59	0.00338096	35.918	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4364 - 	CGI_10006073	superfamily	241691	403	523	0.000332083	40.5732	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#4366 - 	CGI_10001021	superfamily	247916	126	216	3.88E-20	85.127	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#4367 - 	CGI_10001022	superfamily	242274	3	71	6.13E-21	84.0034	cl01053	SGNH_hydrolase superfamily	N	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#4370 - 	CGI_10005773	superfamily	245022	2	35	0.00278323	33.1859	cl09154	MrpF_PhaF superfamily	C	 - 	"Multiple resistance and pH regulation protein F (MrpF / PhaF); Members of the PhaF / MrpF family are predicted to be an integral membrane proteins with three transmembrane regions, involved in regulation of pH. PhaF is part of a potassium efflux system involved in pH regulation. It is also involved in symbiosis in Rhizobium meliloti. MrpF is part of a Na+/H+ antiporter complex, also involved in pH homeostasis. MrpF is thought to be an efflux system for Na+ and cholate. The Mrp system in Bacilli may also have primary energisation capacities."
Q#4371 - 	CGI_10005774	superfamily	241600	220	429	1.90E-88	271.806	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#4373 - 	CGI_10005776	superfamily	246925	270	423	5.53E-12	67.3805	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#4373 - 	CGI_10005776	superfamily	246925	467	708	1.86E-07	53.5134	cl15309	LRR_RI superfamily	C	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#4374 - 	CGI_10005777	superfamily	214507	209	247	5.50E-06	42.8024	cl15307	LRRCT superfamily	C	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#4374 - 	CGI_10005777	superfamily	246925	23	114	0.000562174	39.261	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#4380 - 	CGI_10017381	superfamily	241574	801	978	2.25E-66	223.617	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4380 - 	CGI_10017381	superfamily	241574	1000	1072	4.09E-08	53.7437	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4381 - 	CGI_10017382	superfamily	248264	299	458	3.75E-39	139.68	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#4381 - 	CGI_10017382	superfamily	243161	5	90	9.52E-15	69.7305	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#4381 - 	CGI_10017382	superfamily	222263	218	310	2.56E-08	51.1645	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#4387 - 	CGI_10017389	superfamily	247905	726	870	1.40E-26	106.553	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#4387 - 	CGI_10017389	superfamily	247805	546	670	4.18E-08	52.3396	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#4388 - 	CGI_10017390	superfamily	241596	30	90	7.92E-10	54.1423	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#4389 - 	CGI_10017391	superfamily	241596	4	64	9.91E-11	56.0683	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#4390 - 	CGI_10017392	superfamily	241624	152	408	3.81E-66	222.587	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#4392 - 	CGI_10017394	superfamily	243039	294	423	3.00E-70	228.453	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#4392 - 	CGI_10017394	superfamily	247792	26	69	5.46E-09	53.6036	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4392 - 	CGI_10017394	superfamily	241563	110	144	1.33E-06	46.5115	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4392 - 	CGI_10017394	superfamily	128778	150	275	4.11E-10	58.4303	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#4393 - 	CGI_10017395	superfamily	241802	9	291	3.86E-96	304.41	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#4393 - 	CGI_10017395	superfamily	247775	267	785	2.77E-61	215.283	cl17221	ArsB_NhaD_permease superfamily	 - 	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#4394 - 	CGI_10017396	superfamily	241802	9	319	2.22E-106	315.966	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#4395 - 	CGI_10017397	superfamily	247775	53	91	9.73E-07	44.113	cl17221	ArsB_NhaD_permease superfamily	NC	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#4399 - 	CGI_10017401	superfamily	247723	118	191	3.63E-45	147.244	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4399 - 	CGI_10017401	superfamily	247723	8	78	1.70E-35	122.196	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4400 - 	CGI_10017402	superfamily	243034	398	503	0.000954993	37.7448	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#4401 - 	CGI_10017403	superfamily	247723	43	118	1.97E-45	149.787	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4402 - 	CGI_10017404	superfamily	218333	422	790	1.02E-16	84.1545	cl09347	DNA_pol_phi superfamily	N	 - 	DNA polymerase phi; This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.
Q#4402 - 	CGI_10017404	superfamily	218333	63	243	1.54E-07	54.4942	cl09347	DNA_pol_phi superfamily	C	 - 	DNA polymerase phi; This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.
Q#4403 - 	CGI_10017405	superfamily	202638	148	370	2.77E-38	140.036	cl18230	Anp1 superfamily	 - 	 - 	"Anp1; The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localise within the cis Golgi, and that they are physically associated in two distinct complexes."
Q#4404 - 	CGI_10017406	superfamily	243094	1198	1530	8.58E-178	550.387	cl02569	RasGAP superfamily	 - 	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#4404 - 	CGI_10017406	superfamily	247725	1713	1822	2.13E-59	202.699	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4404 - 	CGI_10017406	superfamily	247069	1572	1712	1.07E-07	53.1578	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#4406 - 	CGI_10001352	superfamily	241600	53	270	5.22E-70	217.493	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#4407 - 	CGI_10003187	superfamily	241600	121	325	3.64E-33	122.771	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#4408 - 	CGI_10008525	superfamily	241574	923	1117	4.07E-84	275.233	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4408 - 	CGI_10008525	superfamily	216363	22	78	2.57E-12	65.5694	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#4408 - 	CGI_10008525	superfamily	241574	1288	1374	1.15E-06	48.5091	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4410 - 	CGI_10008527	superfamily	219821	166	240	4.27E-10	59.307	cl07136	VWA_N superfamily	N	 - 	"VWA N-terminal; This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits."
Q#4410 - 	CGI_10008527	superfamily	217211	770	851	8.03E-07	48.4346	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#4410 - 	CGI_10008527	superfamily	217211	496	556	0.000197317	41.501	cl03691	Cache_1 superfamily	C	 - 	Cache domain; Cache domain.  
Q#4410 - 	CGI_10008527	superfamily	241578	268	450	0.000616739	40.627	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4411 - 	CGI_10008528	superfamily	241649	13	103	7.50E-10	51.2416	cl00159	fer2 superfamily	 - 	 - 	"2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin."
Q#4412 - 	CGI_10008529	superfamily	241563	65	101	6.67E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4413 - 	CGI_10008530	superfamily	241644	8	149	4.38E-41	141.956	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#4414 - 	CGI_10008531	superfamily	241782	28	388	0	530.622	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#4419 - 	CGI_10000487	superfamily	242885	10	172	1.24E-79	236.725	cl02106	IF4E superfamily	 - 	 - 	Eukaryotic initiation factor 4E; Eukaryotic initiation factor 4E.  
Q#4422 - 	CGI_10020102	superfamily	217473	162	327	4.51E-25	107.066	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#4422 - 	CGI_10020102	superfamily	241563	724	759	0.00107707	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4423 - 	CGI_10020103	superfamily	241691	31	147	0.00208988	35.9508	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#4425 - 	CGI_10020105	superfamily	247724	8	173	2.74E-118	336.196	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4426 - 	CGI_10020106	superfamily	207684	30	59	0.00111721	38.514	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#4428 - 	CGI_10020108	superfamily	248264	121	164	0.000217872	39.913	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#4432 - 	CGI_10020112	superfamily	241610	13	65	5.95E-15	63.0378	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#4433 - 	CGI_10020113	superfamily	247639	15	274	1.89E-43	150.689	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#4434 - 	CGI_10020114	superfamily	245205	94	174	2.30E-14	65.7221	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#4437 - 	CGI_10020117	superfamily	246975	139	160	0.0093438	33.4745	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#4439 - 	CGI_10020119	superfamily	245201	407	677	6.65E-28	114.191	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4440 - 	CGI_10020120	superfamily	247068	582	663	1.82E-05	43.8414	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4440 - 	CGI_10020120	superfamily	247068	672	759	0.000240905	40.3746	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4440 - 	CGI_10020120	superfamily	247068	467	528	0.00951269	35.367	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4442 - 	CGI_10020122	superfamily	248054	59	125	5.32E-13	60.9488	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#4444 - 	CGI_10000626	superfamily	245879	26	73	6.19E-09	47.8523	cl12116	DUSP superfamily	C	 - 	DUSP domain; The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Q#4446 - 	CGI_10017929	superfamily	243039	47	148	3.83E-05	41.5959	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#4450 - 	CGI_10017933	superfamily	241636	83	261	2.85E-65	206.285	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#4451 - 	CGI_10017934	superfamily	241636	95	273	2.68E-62	202.047	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#4452 - 	CGI_10017935	superfamily	241636	1	150	9.15E-51	166.609	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#4454 - 	CGI_10017937	superfamily	247741	26	114	1.52E-17	75.809	cl17187	Aldolase_Class_I superfamily	NC	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#4456 - 	CGI_10017939	superfamily	247741	8	62	0.000360827	39.5992	cl17187	Aldolase_Class_I superfamily	N	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#4458 - 	CGI_10017941	superfamily	222150	290	315	5.36E-05	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4458 - 	CGI_10017941	superfamily	222150	234	259	0.00307011	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4458 - 	CGI_10017941	superfamily	222150	318	341	0.00807449	33.9045	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4459 - 	CGI_10017942	superfamily	241578	180	340	5.30E-46	161.305	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4459 - 	CGI_10017942	superfamily	243119	679	729	3.73E-06	45.1273	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#4460 - 	CGI_10017943	superfamily	241776	162	337	3.10E-60	194.338	cl00315	RPS2 superfamily	 - 	 - 	"Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane and subsequent signalling events, and has been linked to several diseases. Some evidence also suggests that the precursor of 67LR, 37LRP is also present in the nucleus in animals, where it appears associated with histones."
Q#4461 - 	CGI_10017944	superfamily	241578	181	340	1.24E-28	109.689	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4463 - 	CGI_10017946	superfamily	217293	39	223	4.16E-35	127.364	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#4464 - 	CGI_10017947	superfamily	247684	12	443	3.32E-103	320.764	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4465 - 	CGI_10017948	superfamily	247724	202	296	2.55E-22	93.2163	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4465 - 	CGI_10017948	superfamily	247724	105	190	2.88E-07	49.6887	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4467 - 	CGI_10017950	superfamily	220695	48	183	0.00112311	39.0991	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#4471 - 	CGI_10017954	superfamily	217853	21	174	2.47E-37	135.094	cl04371	Las1 superfamily	 - 	 - 	Las1-like; Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth.
Q#4475 - 	CGI_10017958	superfamily	242173	6	149	3.59E-63	192.861	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#4477 - 	CGI_10017960	superfamily	247789	18	81	6.10E-07	44.557	cl17235	ABC2_membrane superfamily	NC	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#4478 - 	CGI_10017961	superfamily	243310	1	133	6.20E-43	143.533	cl03120	ELO superfamily	N	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#4479 - 	CGI_10001015	superfamily	247677	576	707	7.24E-39	140.883	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#4479 - 	CGI_10001015	superfamily	243128	89	265	1.30E-22	96.6298	cl02652	MIF4G superfamily	C	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#4479 - 	CGI_10001015	superfamily	243129	390	491	1.13E-16	77.2937	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#4482 - 	CGI_10013509	superfamily	247684	58	463	1.65E-83	269.917	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4485 - 	CGI_10013512	superfamily	215866	7	148	1.75E-32	120.893	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#4485 - 	CGI_10013512	superfamily	243212	173	308	1.06E-16	76.6137	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#4488 - 	CGI_10013515	superfamily	248318	997	1050	4.65E-22	92.4989	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#4488 - 	CGI_10013515	superfamily	221354	1306	1657	0	559.298	cl13422	DUF3480 superfamily	 - 	 - 	Domain of unknown function (DUF3480); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 350 to 362 amino acids in length. This domain is found associated with pfam01363.
Q#4489 - 	CGI_10013516	superfamily	245226	11	190	2.86E-65	201.295	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#4490 - 	CGI_10013517	superfamily	243263	78	329	9.16E-32	123.672	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#4491 - 	CGI_10013518	superfamily	247725	176	281	1.06E-52	177.906	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4491 - 	CGI_10013518	superfamily	247683	658	711	6.10E-27	104.683	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#4491 - 	CGI_10013518	superfamily	243095	274	471	3.02E-105	322.035	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#4491 - 	CGI_10013518	superfamily	245835	3	128	9.53E-56	190.219	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#4492 - 	CGI_10013519	superfamily	191362	77	129	2.55E-23	87.7114	cl05351	zf-nanos superfamily	 - 	 - 	"Nanos RNA binding domain; This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development."
Q#4493 - 	CGI_10013520	superfamily	243141	79	209	1.41E-22	92.7646	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#4494 - 	CGI_10013521	superfamily	218505	29	255	5.12E-79	240.611	cl04994	UNC-50 superfamily	 - 	 - 	UNC-50 family; Gmh1p from S. cerevisiae is located in the Golgi membrane and interacts with ARF exchange factors.
Q#4496 - 	CGI_10013523	superfamily	198867	203	273	5.07E-06	45.0249	cl06652	BACK superfamily	C	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#4496 - 	CGI_10013523	superfamily	243066	119	190	5.07E-06	44.9892	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#4497 - 	CGI_10013524	superfamily	241554	65	199	4.81E-31	118.517	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#4497 - 	CGI_10013524	superfamily	241752	526	654	2.00E-15	73.5077	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#4497 - 	CGI_10013524	superfamily	241554	204	309	1.65E-09	56.1147	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#4498 - 	CGI_10013525	superfamily	247684	249	488	6.09E-37	140.875	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4498 - 	CGI_10013525	superfamily	246680	2	54	0.00163813	37.1812	cl14633	DD_superfamily superfamily	N	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4498 - 	CGI_10013525	superfamily	247684	213	238	0.00483889	38.0272	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4499 - 	CGI_10013526	superfamily	246680	120	186	0.00153846	36.2497	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4500 - 	CGI_10013527	superfamily	247684	93	503	9.98E-86	276.466	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4501 - 	CGI_10013528	superfamily	247684	150	560	2.72E-85	276.851	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4502 - 	CGI_10013529	superfamily	246680	13	89	0.000523317	34.4848	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4503 - 	CGI_10013530	superfamily	247684	127	544	1.56E-71	239.487	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4505 - 	CGI_10013532	superfamily	247684	49	471	4.21E-85	274.155	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4507 - 	CGI_10001470	superfamily	247948	55	108	9.39E-16	68.4746	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#4508 - 	CGI_10001471	superfamily	247755	18	60	3.64E-17	73.7272	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#4509 - 	CGI_10001642	superfamily	243035	140	165	0.000791954	36.4238	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4510 - 	CGI_10011281	superfamily	246918	194	246	3.33E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	23	75	8.20E-11	57.9819	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	422	474	2.11E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	365	416	2.50E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	479	531	2.58E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	308	360	1.74E-09	54.1299	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	251	303	8.56E-09	52.2039	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	137	189	6.81E-08	49.5075	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4510 - 	CGI_10011281	superfamily	246918	80	132	8.83E-08	49.5075	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4511 - 	CGI_10011282	superfamily	191608	692	837	1.86E-75	246.39	cl06029	DUF1227 superfamily	 - 	 - 	Protein of unknown function (DUF1227); This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).
Q#4511 - 	CGI_10011282	superfamily	248014	966	1110	1.41E-58	199.042	cl17460	Csf4_U superfamily	 - 	 - 	CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Q#4511 - 	CGI_10011282	superfamily	219153	452	616	4.14E-43	155.976	cl15854	DEAD_2 superfamily	 - 	 - 	"DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast."
Q#4511 - 	CGI_10011282	superfamily	219199	20	63	6.46E-07	48.1452	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#4512 - 	CGI_10011283	superfamily	241599	397	453	5.91E-09	52.6309	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4514 - 	CGI_10011285	superfamily	247725	8	101	2.40E-38	134.189	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4517 - 	CGI_10011288	superfamily	215754	31	107	6.25E-10	54.952	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#4517 - 	CGI_10011288	superfamily	215754	224	312	3.90E-05	41.0848	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#4517 - 	CGI_10011288	superfamily	215754	112	222	7.80E-05	39.9292	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#4518 - 	CGI_10011289	superfamily	247724	2	174	2.10E-104	309.129	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4518 - 	CGI_10011289	superfamily	243184	273	363	7.28E-30	110.896	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#4518 - 	CGI_10011289	superfamily	243185	182	268	4.48E-27	102.971	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#4519 - 	CGI_10011290	superfamily	226801	647	708	0.000464655	39.4107	cl15486	COG4357 superfamily	C	 - 	Zinc finger domain containing protein (CHY type) [Function unknown]
Q#4519 - 	CGI_10011290	superfamily	245716	142	165	0.000535654	38.3793	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#4519 - 	CGI_10011290	superfamily	245716	83	103	0.00727967	35.2267	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#4522 - 	CGI_10011293	superfamily	247856	154	216	1.21E-19	82.9809	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4522 - 	CGI_10011293	superfamily	247856	311	373	4.17E-19	81.8253	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4522 - 	CGI_10011293	superfamily	247856	384	441	1.50E-18	80.2845	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4522 - 	CGI_10011293	superfamily	247856	227	282	4.99E-18	78.7437	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4522 - 	CGI_10011293	superfamily	247856	64	119	3.33E-15	70.6545	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4522 - 	CGI_10011293	superfamily	247856	2	53	2.13E-13	65.6469	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4523 - 	CGI_10011294	superfamily	247856	25	87	4.68E-18	75.2769	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4523 - 	CGI_10011294	superfamily	247856	98	159	5.11E-09	50.2389	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4524 - 	CGI_10011295	superfamily	247856	19	81	6.88E-20	78.3585	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4524 - 	CGI_10011295	superfamily	247856	55	109	7.53E-07	42.9201	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4524 - 	CGI_10011295	superfamily	247856	92	133	0.00690107	32.1345	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4525 - 	CGI_10011296	superfamily	247856	140	210	4.30E-12	58.3281	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4526 - 	CGI_10011297	superfamily	247856	15	77	1.26E-18	79.8993	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4526 - 	CGI_10011297	superfamily	247856	319	381	8.05E-18	77.9733	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4526 - 	CGI_10011297	superfamily	247856	393	447	7.84E-16	72.1953	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4526 - 	CGI_10011297	superfamily	247856	88	150	6.01E-15	69.8841	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4526 - 	CGI_10011297	superfamily	247856	124	206	5.16E-10	55.6317	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4526 - 	CGI_10011297	superfamily	247856	218	273	5.90E-07	46.7721	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4527 - 	CGI_10011298	superfamily	247856	85	139	3.93E-12	57.9429	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4527 - 	CGI_10011298	superfamily	247856	11	73	8.33E-12	57.1725	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4530 - 	CGI_10011301	superfamily	247856	89	151	8.73E-22	83.7513	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4530 - 	CGI_10011301	superfamily	247856	16	78	4.36E-18	74.1213	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4531 - 	CGI_10011302	superfamily	247856	29	76	1.96E-09	48.6981	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4533 - 	CGI_10001830	superfamily	243085	17	62	8.05E-26	98.1331	cl02557	DM superfamily	 - 	 - 	"DM DNA binding domain; The DM domain is named after dsx and mab-3. dsx contains a single amino-terminal DM domain, whereas mab-3 contains two amino-terminal domains. The DM domain has a pattern of conserved zinc chelating residues C2H2C4. The dsx DM domain has been shown to dimerise and bind palindromic DNA."
Q#4533 - 	CGI_10001830	superfamily	112299	185	221	2.13E-09	52.7966	cl04098	DMA superfamily	 - 	 - 	DMRTA motif; This region is found to the C-terminus of the pfam00751. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Q#4534 - 	CGI_10002110	superfamily	242153	133	306	1.16E-06	46.5232	cl00866	NTPase_I-T superfamily	 - 	 - 	Protein of unknown function DUF84; The function of this prokaryotic protein family is unknown.
Q#4536 - 	CGI_10001795	superfamily	241547	146	273	2.07E-34	128.94	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#4536 - 	CGI_10001795	superfamily	241547	363	465	2.79E-17	80.0195	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#4537 - 	CGI_10003382	superfamily	245213	103	135	1.98E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4537 - 	CGI_10003382	superfamily	214531	551	590	1.33E-11	60.6932	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#4537 - 	CGI_10003382	superfamily	214531	591	635	1.58E-11	60.6932	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#4537 - 	CGI_10003382	superfamily	214531	636	678	6.66E-06	44.1297	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#4537 - 	CGI_10003382	superfamily	205157	236	266	2.73E-05	42.5247	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4537 - 	CGI_10003382	superfamily	205157	441	476	3.12E-05	42.1395	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4537 - 	CGI_10003382	superfamily	241668	2	59	5.84E-05	43.835	cl00186	nidG2 superfamily	N	 - 	"Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a potential role in the assembly and connection of networks. Nidogen consists of 3 globular domains (G1-G3), G3 is the lamin-binding domain, while G2 binds collagen IV and perlecan. Also found in hemicentin, a protein which functions at various cell-cell and cell-matrix junctions and might assist in refining broad regions of cell contact into oriented, line-shaped junctions. Nidogen G2 consists of an N-terminal EGF-like domain (excluded from this alignment model) and an 11-stranded beta-barrel with a central helix, a topology that exhibits high structural similarity to the green flourescent proteins of Cnidaria."
Q#4537 - 	CGI_10003382	superfamily	205157	66	101	0.000141699	40.2135	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4537 - 	CGI_10003382	superfamily	205157	403	434	0.00390957	35.9763	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4537 - 	CGI_10003382	superfamily	205157	354	391	0.00534743	35.5911	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4537 - 	CGI_10003382	superfamily	205157	152	182	0.00780586	35.2059	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#4539 - 	CGI_10003384	superfamily	241570	573	684	3.24E-20	88.9221	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#4539 - 	CGI_10003384	superfamily	243045	65	156	1.04E-10	60.7247	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#4539 - 	CGI_10003384	superfamily	219619	437	491	1.59E-08	53.7507	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#4540 - 	CGI_10003385	superfamily	241574	479	675	6.63E-73	241.336	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4540 - 	CGI_10003385	superfamily	241574	699	931	2.68E-36	138.102	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4542 - 	CGI_10001399	superfamily	204716	74	244	0.00227156	36.8347	cl18257	Git3 superfamily	 - 	 - 	"G protein-coupled glucose receptor regulating Gpa2; Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This is the conserved N-terminus of these proteins, and the C-terminal conserved region is now in family Git3_C."
Q#4543 - 	CGI_10002689	superfamily	247044	39	151	7.54E-59	187.045	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#4543 - 	CGI_10002689	superfamily	247044	165	243	6.00E-22	88.0632	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#4543 - 	CGI_10002689	superfamily	247044	269	323	6.14E-06	43.392	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#4544 - 	CGI_10016336	superfamily	247068	458	554	9.72E-24	97.7693	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4544 - 	CGI_10016336	superfamily	247068	564	660	6.04E-20	86.5985	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4544 - 	CGI_10016336	superfamily	247068	242	341	9.51E-19	83.1317	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4544 - 	CGI_10016336	superfamily	247068	673	763	2.04E-16	76.5833	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4544 - 	CGI_10016336	superfamily	247068	356	450	2.40E-16	76.1981	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4544 - 	CGI_10016336	superfamily	247068	134	234	4.20E-16	75.4277	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4544 - 	CGI_10016336	superfamily	247068	22	124	6.19E-08	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4553 - 	CGI_10016345	superfamily	245814	102	157	7.54E-05	40.468	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4556 - 	CGI_10016348	superfamily	248097	59	185	3.67E-25	95.4098	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4557 - 	CGI_10016349	superfamily	248097	281	390	4.88E-26	101.958	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4557 - 	CGI_10016349	superfamily	248097	397	463	8.17E-12	62.2826	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4558 - 	CGI_10016350	superfamily	248097	289	399	8.37E-26	100.417	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4558 - 	CGI_10016350	superfamily	242079	192	240	0.00172876	38.5365	cl00770	PSP1 superfamily	NC	 - 	PSP1 C-terminal conserved region; This region is present in both eukaryotes and eubacteria. The yeast PSP1 protein is involved in suppressing mutations in the DNA polymerase alpha subunit in yeast.
Q#4559 - 	CGI_10016351	superfamily	241564	81	130	5.10E-14	63.8423	cl00035	BIR superfamily	N	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4560 - 	CGI_10016352	superfamily	248097	636	739	1.23E-21	91.943	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4561 - 	CGI_10016353	superfamily	248097	156	284	4.63E-23	91.943	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4562 - 	CGI_10016354	superfamily	241564	38	100	2.22E-14	65.7682	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4562 - 	CGI_10016354	superfamily	241564	141	205	4.12E-11	56.9087	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4562 - 	CGI_10016354	superfamily	247792	220	262	3.29E-09	51.6116	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4563 - 	CGI_10016355	superfamily	241564	285	350	1.30E-19	81.9283	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4563 - 	CGI_10016355	superfamily	241564	6	73	5.47E-15	69.2167	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4564 - 	CGI_10016356	superfamily	241564	1	52	2.01E-16	69.2167	cl00035	BIR superfamily	N	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4568 - 	CGI_10016361	superfamily	248097	208	334	8.72E-29	108.507	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4569 - 	CGI_10016362	superfamily	248097	244	369	2.64E-22	90.4022	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4570 - 	CGI_10016363	superfamily	241564	41	107	1.47E-23	91.5583	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4570 - 	CGI_10016363	superfamily	247792	250	289	1.38E-05	41.6624	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4571 - 	CGI_10016364	superfamily	241564	99	167	9.79E-22	86.1655	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4571 - 	CGI_10016364	superfamily	241564	15	80	2.50E-21	85.0099	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#4573 - 	CGI_10016366	superfamily	241693	227	375	8.63E-103	303.621	cl00215	Aconitase_swivel superfamily	 - 	 - 	"Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive  element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid."
Q#4573 - 	CGI_10016366	superfamily	241753	2	145	5.02E-94	290.881	cl00285	Aconitase superfamily	N	 - 	"Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Aconitase catalytic domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle.  Cis-aconitate is formed as an intermediate product during the course of the reaction. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. Aconitase, in its active form, contains a 4Fe-4S  iron-sulfur cluster; three cysteine residues have been shown to be ligands of the 4Fe-4S cluster. This is the Aconitase core domain, including structural domains 1, 2 and 3, which binds the Fe-S cluster. The aconitase family also contains the following proteins: - Iron-responsive  element binding protein (IRE-BP), a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in  the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of  transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the  alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid."
Q#4574 - 	CGI_10012136	superfamily	110440	211	237	0.00234461	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#4581 - 	CGI_10012143	superfamily	248264	2	67	4.41E-06	44.1502	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#4582 - 	CGI_10012144	superfamily	248318	758	810	9.33E-22	90.5729	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#4584 - 	CGI_10004798	superfamily	243110	4	181	3.07E-18	79.7809	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#4586 - 	CGI_10004800	superfamily	248458	12	381	1.78E-08	54.2421	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4587 - 	CGI_10004801	superfamily	248458	35	413	7.35E-26	107.4	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4588 - 	CGI_10004802	superfamily	219290	15	156	3.43E-20	82.5489	cl06216	Spot_14 superfamily	 - 	 - 	"Thyroid hormone-inducible hepatic protein Spot 14; This family consists of several thyroid hormone-inducible hepatic protein (Spot 14 or S14) sequences. Mainly expressed in tissues that synthesise triglycerides, the mRNA coding for Spot 14 has been shown to be increased in rat liver by insulin, dietary carbohydrates, glucose in hepatocyte culture medium, as well as thyroid hormone. In contrast, dietary fats and polyunsaturated fatty acids, have been shown to decrease the amount of Spot 14 mRNA, while an elevated level of cAMP acts as a dominant negative factor. In addition, liver-specific factors or chromatin organisation of the gene have been shown to contribute to the regulation of its expression. Spot 14 protein is thought to be required for induction of hepatic lipogenesis."
Q#4589 - 	CGI_10004803	superfamily	243050	103	161	1.45E-27	103.566	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#4589 - 	CGI_10004803	superfamily	243050	284	337	6.21E-27	101.663	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#4589 - 	CGI_10004803	superfamily	243050	164	215	2.83E-26	100.103	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#4589 - 	CGI_10004803	superfamily	243050	228	278	1.41E-21	87.4285	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#4589 - 	CGI_10004803	superfamily	243050	345	398	2.78E-20	83.9369	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#4591 - 	CGI_10004805	superfamily	241563	62	97	1.90E-05	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4595 - 	CGI_10006585	superfamily	220168	15	118	1.79E-46	156.959	cl07802	DUF1969 superfamily	 - 	 - 	"Domain of unknown function (DUF1969); The N-terminal domain of fumarylacetoacetate hydrolase is functionally uncharacterized, and adopts a structure consisting of an SH3-like barrel."
Q#4595 - 	CGI_10006585	superfamily	245608	150	359	1.99E-27	107.784	cl11421	FAA_hydrolase superfamily	 - 	 - 	"Fumarylacetoacetate (FAA) hydrolase family; This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase, encoded by mhpD in E. coli, is involved in the phenylpropionic acid pathway of E. coli and catalyzes the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli is involved in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida is a 4-Oxalocrotonate decarboxylase."
Q#4596 - 	CGI_10006586	superfamily	247899	334	472	1.21E-07	52.2663	cl17345	AccA superfamily	NC	 - 	Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]
Q#4596 - 	CGI_10006586	superfamily	247899	26	180	7.45E-06	46.7236	cl17345	AccA superfamily	NC	 - 	Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]
Q#4597 - 	CGI_10006587	superfamily	243092	703	947	1.59E-09	58.8856	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4597 - 	CGI_10006587	superfamily	243092	923	1118	1.58E-08	56.1892	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4598 - 	CGI_10006588	superfamily	204080	211	395	3.68E-41	145.878	cl18252	BAAT_C superfamily	 - 	 - 	BAAT / Acyl-CoA thioester hydrolase C terminal; This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT).
Q#4598 - 	CGI_10006588	superfamily	218259	15	150	4.74E-35	126.615	cl04742	Bile_Hydr_Trans superfamily	 - 	 - 	"Acyl-CoA thioester hydrolase/BAAT N-terminal region; This family consists of the amino termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT). This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism. For example, in peroxisomes, the hydrolase acts on bile-CoA esters."
Q#4599 - 	CGI_10006589	superfamily	245819	380	556	1.05E-52	180.083	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#4599 - 	CGI_10006589	superfamily	219812	43	287	6.14E-21	92.3692	cl07121	NIT superfamily	 - 	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#4599 - 	CGI_10006589	superfamily	219526	287	366	4.28E-07	49.9251	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#4600 - 	CGI_10006590	superfamily	245819	405	557	6.01E-44	155.815	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#4600 - 	CGI_10006590	superfamily	219812	68	313	8.84E-21	91.984	cl07121	NIT superfamily	 - 	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#4600 - 	CGI_10006590	superfamily	219526	365	390	0.00051014	40.6803	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#4601 - 	CGI_10006591	superfamily	246925	116	387	1.17E-23	100.508	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#4603 - 	CGI_10006593	superfamily	247907	10	45	0.000188162	36.2421	cl17353	LamG superfamily	NC	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#4604 - 	CGI_10006594	superfamily	247907	1	93	3.17E-14	64.3617	cl17353	LamG superfamily	N	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#4605 - 	CGI_10011169	superfamily	241563	65	106	0.00146909	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4606 - 	CGI_10011170	superfamily	110440	111	137	0.00325451	33.5353	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#4607 - 	CGI_10011171	superfamily	110440	561	588	0.00609569	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#4609 - 	CGI_10011173	superfamily	245819	832	1008	2.44E-65	218.217	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#4609 - 	CGI_10011173	superfamily	245225	45	410	6.22E-50	182.511	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#4609 - 	CGI_10011173	superfamily	245201	531	759	1.51E-30	122.26	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4609 - 	CGI_10011173	superfamily	219526	777	818	2.88E-05	44.9175	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#4610 - 	CGI_10011174	superfamily	245819	9	159	2.66E-54	171.993	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#4611 - 	CGI_10011175	superfamily	241578	25	187	4.07E-31	122.015	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4612 - 	CGI_10011176	superfamily	247723	15	88	1.94E-51	168.541	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4612 - 	CGI_10011176	superfamily	247723	99	181	1.31E-43	148.212	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4615 - 	CGI_10011179	superfamily	247805	28	146	3.22E-11	56.5768	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#4617 - 	CGI_10011181	superfamily	241599	111	169	3.05E-24	95.0028	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4617 - 	CGI_10011181	superfamily	146451	291	309	0.00493514	34.6423	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#4619 - 	CGI_10006904	superfamily	190261	122	181	2.62E-22	93.7674	cl03504	RFX_DNA_binding superfamily	 - 	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#4621 - 	CGI_10006906	superfamily	243072	100	222	9.28E-40	140.982	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#4622 - 	CGI_10006907	superfamily	216101	167	767	2.48E-178	527.246	cl08288	Carn_acyltransf superfamily	 - 	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#4630 - 	CGI_10022409	superfamily	245213	45	78	0.000137082	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4630 - 	CGI_10022409	superfamily	245847	84	227	7.93E-17	74.1301	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#4634 - 	CGI_10022414	superfamily	241958	1	392	5.40E-78	249.74	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#4636 - 	CGI_10022416	superfamily	220806	150	208	0.000527998	38.1492	cl12387	MULE superfamily	N	 - 	MULE transposase domain; This domain was identified by Babu and colleagues.
Q#4637 - 	CGI_10022417	superfamily	243161	102	163	0.000357635	36.6442	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#4640 - 	CGI_10022420	superfamily	241563	62	97	0.000821051	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4641 - 	CGI_10022421	superfamily	247896	1	290	8.85E-170	484.51	cl17342	Pyruvate_Kinase superfamily	N	 - 	"Pyruvate kinase (PK):  Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors.  Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state.  PK exists as several different isozymes, depending on organism and tissue type.  In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung.  PK forms a homotetramer, with each subunit containing three domains.  The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer."
Q#4643 - 	CGI_10022423	superfamily	222150	61	85	7.67E-05	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4643 - 	CGI_10022423	superfamily	222150	88	113	0.00304351	32.3638	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4644 - 	CGI_10022424	superfamily	241574	21	136	5.48E-53	175.467	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4644 - 	CGI_10022424	superfamily	241574	137	193	1.38E-12	62.7615	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4644 - 	CGI_10022424	superfamily	241574	231	303	1.53E-05	44.1138	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4646 - 	CGI_10022426	superfamily	246680	149	228	8.56E-05	41.6119	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4647 - 	CGI_10022427	superfamily	241574	1	182	9.63E-69	221.306	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4647 - 	CGI_10022427	superfamily	241574	245	432	3.21E-19	85.7153	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4650 - 	CGI_10017669	superfamily	241578	23	66	3.32E-07	44.9701	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4651 - 	CGI_10017670	superfamily	248012	413	533	1.61E-14	70.7653	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#4651 - 	CGI_10017670	superfamily	214507	291	328	0.000279819	38.9504	cl15307	LRRCT superfamily	C	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#4652 - 	CGI_10017672	superfamily	241584	10804	10888	3.92E-05	46.7207	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#4652 - 	CGI_10017672	superfamily	241584	10939	11008	0.00680466	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#4652 - 	CGI_10017672	superfamily	216566	469	567	1.93E-05	47.5673	cl18370	Peptidase_M23 superfamily	 - 	 - 	"Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Escherichia coli murein hydrolase activator NlpD, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown."
Q#4652 - 	CGI_10017672	superfamily	241584	10328	10405	0.000760293	42.7963	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#4652 - 	CGI_10017672	superfamily	245213	12767	12801	0.00268244	40.308	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4654 - 	CGI_10017675	superfamily	241607	37	63	0.00723219	29.9306	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#4655 - 	CGI_10017676	superfamily	245819	371	546	1.81E-65	215.906	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#4655 - 	CGI_10017676	superfamily	245201	56	297	2.01E-31	122.345	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4655 - 	CGI_10017676	superfamily	219526	310	356	0.00125589	39.5247	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#4656 - 	CGI_10017677	superfamily	247068	654	717	0.00167653	38.0995	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4656 - 	CGI_10017677	superfamily	247068	411	481	0.00299725	37.3291	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4657 - 	CGI_10017678	superfamily	247805	33	151	8.25E-12	59.6584	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#4667 - 	CGI_10017688	superfamily	247068	103	169	0.00566862	35.4031	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4668 - 	CGI_10017690	superfamily	243035	191	281	2.67E-11	58.7853	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4670 - 	CGI_10017692	superfamily	219933	1	204	1.07E-50	165.186	cl07290	Med20 superfamily	 - 	 - 	TATA-binding related factor (TRF) of subunit 20 of Mediator complex; This family of proteins is related to TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex. Human TRF has been shown to associate with an RNA polymerase II-SRB complex. This Med20 subunit of Mediator is found in the non-essential part of the head.
Q#4671 - 	CGI_10017693	superfamily	241733	2	70	6.79E-48	148.514	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#4672 - 	CGI_10023008	superfamily	191362	29	81	1.29E-20	78.4666	cl05351	zf-nanos superfamily	 - 	 - 	"Nanos RNA binding domain; This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development."
Q#4673 - 	CGI_10023009	superfamily	243092	144	385	1.21E-24	101.258	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4673 - 	CGI_10023009	superfamily	243074	49	92	1.70E-06	44.8049	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#4676 - 	CGI_10023012	superfamily	248097	148	223	2.90E-15	69.6014	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4677 - 	CGI_10023013	superfamily	248097	73	151	7.24E-13	61.8974	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4678 - 	CGI_10023014	superfamily	248097	154	282	6.40E-13	63.4382	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4678 - 	CGI_10023014	superfamily	248097	51	134	7.35E-09	51.8822	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4679 - 	CGI_10023015	superfamily	248097	234	360	2.00E-17	76.9202	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4679 - 	CGI_10023015	superfamily	248097	46	172	1.49E-10	57.6602	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4680 - 	CGI_10023016	superfamily	246669	17	151	8.00E-20	85.3098	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#4680 - 	CGI_10023016	superfamily	241578	167	384	1.65E-41	150.215	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4682 - 	CGI_10023018	superfamily	241644	12	119	6.23E-40	141.571	cl00154	UBCc superfamily	C	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#4683 - 	CGI_10023019	superfamily	188051	142	305	5.25E-30	116.027	cl18155	nop2p superfamily	C	 - 	"NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base modification]."
Q#4685 - 	CGI_10023022	superfamily	241578	347	460	4.36E-11	61.4278	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4685 - 	CGI_10023022	superfamily	241578	156	215	1.24E-06	47.5606	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4685 - 	CGI_10023022	superfamily	115363	20	71	1.50E-14	69.3229	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#4685 - 	CGI_10023022	superfamily	115363	94	140	2.28E-12	63.1597	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#4685 - 	CGI_10023022	superfamily	115363	571	617	1.15E-10	58.1522	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#4686 - 	CGI_10023023	superfamily	247068	358	448	6.48E-12	63.1013	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4686 - 	CGI_10023023	superfamily	247068	233	277	1.20E-05	44.6118	cl15786	CA_like superfamily	NC	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4686 - 	CGI_10023023	superfamily	247068	142	201	1.50E-05	44.2266	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4686 - 	CGI_10023023	superfamily	115363	12	73	2.33E-13	66.6265	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#4686 - 	CGI_10023023	superfamily	115363	100	130	0.00110938	38.1218	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#4687 - 	CGI_10023024	superfamily	219533	673	955	1.45E-136	413.357	cl06658	Coatamer_beta_C superfamily	 - 	 - 	Coatamer beta C-terminal region; This family is found at the N-terminus of the coatamer beta subunit proteins (Beta-coat proteins). This C-terminal domain probably adapts the function of the N-terminal pfam01602 domain.
Q#4688 - 	CGI_10023025	superfamily	245208	45	418	0	669.535	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#4689 - 	CGI_10023026	superfamily	216101	202	814	0	653.592	cl08288	Carn_acyltransf superfamily	 - 	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#4690 - 	CGI_10023027	superfamily	245227	30	827	0	1437.25	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#4692 - 	CGI_10023029	superfamily	243077	63	116	3.35E-15	67.5705	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#4693 - 	CGI_10023030	superfamily	241677	4	169	3.17E-95	287.7	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#4693 - 	CGI_10023030	superfamily	247723	237	319	6.42E-58	187.856	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4697 - 	CGI_10023034	superfamily	243061	31	129	7.82E-40	130.925	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4698 - 	CGI_10003202	superfamily	247684	5	200	1.70E-28	110.629	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4702 - 	CGI_10018905	superfamily	242274	2	144	0.000124562	40.4734	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#4704 - 	CGI_10018907	superfamily	247856	207	236	0.00408814	34.4928	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4706 - 	CGI_10018909	superfamily	247743	129	258	0.000242836	41.8016	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#4707 - 	CGI_10018910	superfamily	247743	129	258	0.000151771	42.1868	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#4708 - 	CGI_10018911	superfamily	241719	1	140	9.49E-72	214.333	cl00242	MoaC superfamily	 - 	 - 	"MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis."
Q#4710 - 	CGI_10018913	superfamily	245599	182	368	1.18E-68	228.53	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#4710 - 	CGI_10018913	superfamily	245599	91	181	8.76E-26	106.807	cl11397	NR_LBD superfamily	C	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#4713 - 	CGI_10018916	superfamily	243084	845	952	4.01E-71	235.415	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#4713 - 	CGI_10018916	superfamily	241760	1478	1518	1.32E-21	91.4707	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#4713 - 	CGI_10018916	superfamily	242892	1105	1422	8.35E-97	318.593	cl02120	KAT11 superfamily	 - 	 - 	"Histone acetylation protein; Histone acetylation is required in many cellular processes including transcription, DNA repair, and chromatin assembly. This family contains the fungal KAT11 protein (previously known as RTT109) which is required for H3K56 acetylation. Loss of KAT11 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin. KAT11 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of Pol II in yeast. This family also incorporates the p300/CBP histone acetyltransferase domain which has different catalytic properties and cofactor regulation to KAT11."
Q#4713 - 	CGI_10018916	superfamily	111102	565	644	5.49E-41	148.364	cl03478	KIX superfamily	 - 	 - 	KIX domain; CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.
Q#4713 - 	CGI_10018916	superfamily	243131	359	437	8.98E-29	112.834	cl02660	zf-TAZ superfamily	 - 	 - 	"TAZ zinc finger; The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC."
Q#4713 - 	CGI_10018916	superfamily	243131	1541	1614	2.29E-22	94.3447	cl02660	zf-TAZ superfamily	 - 	 - 	"TAZ zinc finger; The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC."
Q#4713 - 	CGI_10018916	superfamily	191424	950	990	2.25E-20	87.841	cl05510	DUF902 superfamily	 - 	 - 	"Domain of Unknown Function (DUF902); This domain of unknown function is found in several transcriptional co-activators including the CREB-binding protein, which is an acetyltransferase that acetylates histones, giving a specific tag for transcriptional activation. This short domain is found to the C-terminus of bromodomains. The 40 residue domain contains four conserved cysteines suggesting that it may be stabilised by a zinc ion. In CREB this domain is to the N-terminus of another zinc binding PHD domain."
Q#4713 - 	CGI_10018916	superfamily	220093	1793	1843	2.66E-11	63.1626	cl07590	Creb_binding superfamily	N	 - 	"Creb binding; The Creb binding domain assumes a structure comprising of three alpha-helices which pack in a bundle, exposing a hydrophobic groove between alpha-1 and alpha-3 within which complimentary domains found in the protein 'activator for thyroid hormone and retinoid receptors' (ACTR) can dock. Docking of these domains is required for the recruitment of RNA polymerase II and the basal transcription machinery."
Q#4715 - 	CGI_10018918	superfamily	243176	310	679	0	700.192	cl02777	chaperonin_like superfamily	N	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#4715 - 	CGI_10018918	superfamily	243176	12	308	0	549.964	cl02777	chaperonin_like superfamily	C	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#4718 - 	CGI_10018921	superfamily	241647	12	42	1.56E-09	55.6118	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#4718 - 	CGI_10018921	superfamily	246669	694	811	1.14E-37	138.903	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#4718 - 	CGI_10018921	superfamily	241647	58	88	0.000474406	39.5063	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#4719 - 	CGI_10018922	superfamily	247804	446	488	2.65E-10	58.3558	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#4719 - 	CGI_10018922	superfamily	247804	339	381	5.04E-05	42.5626	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#4721 - 	CGI_10018924	superfamily	218376	19	132	5.82E-47	149.706	cl04884	Ocnus superfamily	 - 	 - 	"Janus/Ocnus family (Ocnus); This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster."
Q#4723 - 	CGI_10018926	superfamily	245814	129	191	1.00E-05	41.3207	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4723 - 	CGI_10018926	superfamily	245814	48	109	3.09E-05	40.1651	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#4724 - 	CGI_10009063	superfamily	245213	534	569	0.00116737	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#4724 - 	CGI_10009063	superfamily	243061	691	773	4.07E-13	66.5966	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#4724 - 	CGI_10009063	superfamily	246918	578	632	1.19E-09	55.6707	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4724 - 	CGI_10009063	superfamily	246918	634	687	1.97E-09	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4725 - 	CGI_10009064	superfamily	241642	243	299	3.14E-12	60.587	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#4725 - 	CGI_10009064	superfamily	241634	76	175	1.79E-11	59.6759	cl00143	SynN superfamily	 - 	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#4729 - 	CGI_10009068	superfamily	248458	297	436	0.00543847	37.6785	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4730 - 	CGI_10009069	superfamily	100115	1	147	1.16E-27	106.985	cl18930	StaR_like superfamily	N	 - 	"StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure."
Q#4731 - 	CGI_10009070	superfamily	100115	58	174	1.87E-18	80.0207	cl18930	StaR_like superfamily	C	 - 	"StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure."
Q#4732 - 	CGI_10009071	superfamily	243072	39	136	7.95E-23	88.2094	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#4733 - 	CGI_10009072	superfamily	243072	12	160	2.83E-19	80.5054	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#4735 - 	CGI_10009074	superfamily	215821	245	309	2.62E-06	44.5387	cl18346	FKBP_C superfamily	C	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#4736 - 	CGI_10003734	superfamily	247068	238	334	5.86E-28	110.481	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	953	1049	1.79E-25	103.547	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	744	841	1.49E-23	98.1545	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	853	945	2.82E-23	96.9989	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	1164	1266	1.65E-22	95.0729	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	1059	1156	6.92E-22	93.1469	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	647	735	8.50E-20	86.9837	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	442	539	8.86E-16	75.4277	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	134	229	8.12E-12	63.8717	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	1288	1361	2.25E-09	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	568	637	3.20E-07	50.0046	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	37	120	4.35E-07	49.6194	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4736 - 	CGI_10003734	superfamily	247068	343	415	0.000714303	39.5872	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4738 - 	CGI_10003736	superfamily	217078	110	287	6.27E-65	208.555	cl15643	CoA_transf_3 superfamily	 - 	 - 	"CoA-transferase family III; CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases."
Q#4739 - 	CGI_10003737	superfamily	247692	192	541	5.13E-67	222.782	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#4739 - 	CGI_10003737	superfamily	247692	51	215	1.89E-12	68.056	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#4740 - 	CGI_10003738	superfamily	247692	184	533	4.45E-63	211.996	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#4740 - 	CGI_10003738	superfamily	247692	17	211	9.19E-16	78.8669	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#4741 - 	CGI_10000334	superfamily	203591	86	219	5.29E-37	136.347	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#4741 - 	CGI_10000334	superfamily	226728	184	256	0.000244991	42.2241	cl18775	COG4278 superfamily	NC	 - 	Uncharacterized conserved protein [Function unknown]
Q#4741 - 	CGI_10000334	superfamily	203591	12	89	0.00135406	38.5064	cl06275	DUF1399 superfamily	N	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#4743 - 	CGI_10007438	superfamily	241677	9	176	1.84E-89	273.364	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#4745 - 	CGI_10007440	superfamily	215754	143	230	3.92E-21	86.1532	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#4745 - 	CGI_10007440	superfamily	215754	234	329	8.46E-21	85.3828	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#4745 - 	CGI_10007440	superfamily	215754	7	132	8.61E-18	76.9084	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#4747 - 	CGI_10007442	superfamily	248458	124	259	1.67E-13	68.1093	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4750 - 	CGI_10007445	superfamily	243035	248	352	5.41E-10	56.4741	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4750 - 	CGI_10007445	superfamily	243093	109	177	1.36E-08	51.7622	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#4750 - 	CGI_10007445	superfamily	243035	30	92	0.00286066	36.0586	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4752 - 	CGI_10007447	superfamily	241578	205	358	1.41E-35	128.949	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4752 - 	CGI_10007447	superfamily	241578	34	204	1.62E-30	115.081	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#4753 - 	CGI_10007448	superfamily	241720	8	102	6.18E-49	156.22	cl00245	MGS-like superfamily	C	 - 	"MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site."
Q#4754 - 	CGI_10009966	superfamily	245206	53	313	1.03E-95	289.563	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#4755 - 	CGI_10009967	superfamily	245602	205	569	0	537.137	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#4755 - 	CGI_10009967	superfamily	222390	99	161	2.08E-09	54.8238	cl16409	Gal_mutarotas_2 superfamily	 - 	 - 	"Galactose mutarotase-like; This family is found N-terminal to glycosyl-hydrolase domains, and appears to be similar to the galactose mutarotase superfamily."
Q#4756 - 	CGI_10009968	superfamily	247639	35	361	0	532.962	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#4757 - 	CGI_10009969	superfamily	247856	88	158	7.15E-12	57.1725	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4757 - 	CGI_10009969	superfamily	247856	53	114	1.24E-10	53.7057	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4758 - 	CGI_10009970	superfamily	247792	20	72	7.23E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4759 - 	CGI_10009971	superfamily	247856	65	126	1.30E-11	56.7873	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4759 - 	CGI_10009971	superfamily	247856	100	170	4.91E-11	55.2465	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4760 - 	CGI_10009972	superfamily	222150	516	541	2.62E-05	42.3789	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4760 - 	CGI_10009972	superfamily	222150	461	484	0.0002058	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4760 - 	CGI_10009972	superfamily	222150	347	370	0.000302495	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4760 - 	CGI_10009972	superfamily	222150	544	568	0.000320428	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4760 - 	CGI_10009972	superfamily	222150	601	625	0.00154004	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4760 - 	CGI_10009972	superfamily	222150	374	398	0.00168598	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4760 - 	CGI_10009972	superfamily	222150	488	512	0.00254084	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4761 - 	CGI_10009973	superfamily	245201	53	298	8.35E-69	220.448	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4762 - 	CGI_10009974	superfamily	243034	33	127	2.84E-25	96.6803	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#4764 - 	CGI_10009976	superfamily	247856	102	173	1.16E-13	65.2617	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4764 - 	CGI_10009976	superfamily	247856	69	127	2.28E-13	64.1061	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4764 - 	CGI_10009976	superfamily	247856	42	88	0.00486752	34.4457	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4765 - 	CGI_10009977	superfamily	243072	294	419	3.17E-19	85.1278	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#4765 - 	CGI_10009977	superfamily	247856	65	126	3.92E-17	77.2029	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4765 - 	CGI_10009977	superfamily	247856	100	174	7.16E-15	70.6545	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4765 - 	CGI_10009977	superfamily	244906	595	660	4.00E-28	108.767	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#4765 - 	CGI_10009977	superfamily	244906	476	540	3.74E-25	100.292	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#4765 - 	CGI_10009977	superfamily	244906	737	801	7.38E-23	93.7439	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#4765 - 	CGI_10009977	superfamily	244899	36	86	0.0022496	37.0842	cl08302	S-100 superfamily	N	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#4766 - 	CGI_10009978	superfamily	247068	428	521	1.72E-26	107.014	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	976	1078	9.88E-26	104.703	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	1210	1305	2.82E-21	91.6061	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	88	185	5.52E-21	90.8357	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	639	735	1.33E-20	89.6801	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	194	300	1.47E-16	78.1241	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	530	631	2.16E-15	74.6573	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	870	968	4.65E-11	61.9457	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	744	841	8.93E-11	61.1753	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	1091	1195	1.13E-10	60.7901	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	309	420	3.59E-06	47.3082	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4766 - 	CGI_10009978	superfamily	247068	1338	1451	0.000257356	41.5302	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#4767 - 	CGI_10009979	superfamily	218267	217	429	2.88E-35	136.41	cl04754	LMBR1 superfamily	N	 - 	"LMBR1-like membrane protein; Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought. Vertebrate members of this family may play a role in limb development. A member of this family has been shown to be a lipocalin membrane receptor"
Q#4768 - 	CGI_10009980	superfamily	248264	47	107	3.59E-06	44.5354	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#4770 - 	CGI_10022475	superfamily	247723	12	70	1.35E-29	101.158	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4771 - 	CGI_10022476	superfamily	247723	35	105	1.03E-25	97.3058	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4771 - 	CGI_10022476	superfamily	199156	122	138	0.00185652	35.1225	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#4773 - 	CGI_10022478	superfamily	243142	391	560	4.23E-16	75.3555	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#4774 - 	CGI_10022479	superfamily	245598	1	246	4.54E-130	384.389	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#4775 - 	CGI_10022480	superfamily	241629	16	125	1.73E-35	120.909	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#4776 - 	CGI_10022481	superfamily	241629	41	84	7.87E-08	45.7016	cl00133	SCP superfamily	N	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#4777 - 	CGI_10022482	superfamily	241629	40	127	2.27E-15	68.7008	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#4778 - 	CGI_10022483	superfamily	216368	121	442	7.99E-77	249.357	cl03130	CAP_N superfamily	 - 	 - 	Adenylate cyclase associated (CAP) N terminal; Adenylate cyclase associated (CAP) N terminal.  
Q#4778 - 	CGI_10022483	superfamily	197827	538	575	1.77E-09	54.0609	cl02725	CARP superfamily	 - 	 - 	Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product; Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product.  
Q#4779 - 	CGI_10022484	superfamily	241574	378	558	3.93E-17	79.9373	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4781 - 	CGI_10022486	superfamily	221377	15	55	0.000318394	39.3743	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#4781 - 	CGI_10022486	superfamily	192535	95	194	0.00533635	36.4198	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#4782 - 	CGI_10022487	superfamily	245303	43	411	0	516.727	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#4782 - 	CGI_10022487	superfamily	243119	440	488	2.84E-14	67.844	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#4784 - 	CGI_10022489	superfamily	241867	75	289	3.84E-20	88.3794	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#4786 - 	CGI_10022491	superfamily	247856	19	79	4.96E-18	72.1953	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#4788 - 	CGI_10022493	superfamily	243540	622	848	2.73E-29	116.964	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#4788 - 	CGI_10022493	superfamily	128778	98	212	6.64E-05	42.2519	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#4788 - 	CGI_10022493	superfamily	241563	60	95	0.000165398	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4790 - 	CGI_10022495	superfamily	110440	356	382	9.38E-05	39.6985	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#4792 - 	CGI_10022497	superfamily	241563	38	73	9.12E-06	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4794 - 	CGI_10022500	superfamily	241727	130	184	0.00109484	36.1709	cl00252	NifX_NifB superfamily	C	 - 	"This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme.  This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily.  This conserved domain is represented in two of the three major divisions of life (bacteria and archaea)."
Q#4795 - 	CGI_10022501	superfamily	247854	145	201	9.83E-08	47.3963	cl17300	Herpes_UL52 superfamily	 - 	 - 	"Herpesviridae UL52/UL70 DNA primase; Herpes simplex virus type 1 DNA replication in host cells is known to be mediated by seven viral-encoded proteins, three of which form a heterotrimeric DNA helicase-primase complex. This complex consists of UL5, UL8, and UL52 subunits. Heterodimers consisting of UL5 and UL52 have been shown to retain both helicase and primase activities. Nevertheless, UL8 is still essential for replication: though it lacks any DNA binding or catalytic activities, it is involved in the transport of UL5-UL52 and it also interacts with other replication proteins. The molecular mechanisms of the UL5-UL52 catalytic activities are not known. While UL5 is associated with DNA helicase activity and UL52 with DNA primase activity, the helicase activity requires the interaction of UL5 and UL52. It is not known if the primase activity can be maintained by UL52 alone. The region encompassed by residues 610-636 of HSV1 UL52 is thought to contain a divalent metal cation binding motif. Indeed, this region contains several aspartate and glutamate residues that might be involved in divalent cation binding. The biological significance of UL52-UL8 interaction is not known. Yeast two-hybrid analysis together with immunoprecipitation experiments have shown that the HSV1 UL52 region between residues 366-914 is essential for this interaction, while the first 349 N-terminal residues are dispensable. This family also includes protein UL70 from cytomegalovirus (CMV, a subgroup of the Herpesviridae) strains, which, by analogy with UL52, is thought to have DNA primase activity. Indeed, CMV strains also possess a DNA helicase-primase complex, the other subunits being protein UL105 (with known similarity to HSV1 UL5) and protein UL102."
Q#4796 - 	CGI_10022502	superfamily	247725	1130	1251	3.30E-50	175.532	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4796 - 	CGI_10022502	superfamily	243096	927	1111	4.07E-27	110.85	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#4796 - 	CGI_10022502	superfamily	248318	1278	1332	7.85E-21	89.0321	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#4796 - 	CGI_10022502	superfamily	247725	1424	1489	9.69E-19	83.9639	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4798 - 	CGI_10022504	superfamily	113585	171	281	1.50E-21	88.1499	cl04775	DUF716 superfamily	 - 	 - 	"Family of unknown function (DUF716); This family is equally distributed in both metazoa and plants. Annotation associated with a member from Nicotiana tabacum suggest that it may be involved in response to viral attack in plants. However, no clear function has been assigned to this family."
Q#4799 - 	CGI_10022505	superfamily	243066	1	79	4.37E-08	47.6856	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#4801 - 	CGI_10022507	superfamily	246680	116	160	8.76E-08	46.1746	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4802 - 	CGI_10022508	superfamily	221535	136	233	1.12E-15	73.3991	cl13730	Ipi1_N superfamily	 - 	 - 	"Rix1 complex component involved in 60S ribosome maturation; This domain family is found in eukaryotes, and is typically between 91 and 105 amino acids in length. This family is the N terminal of Ipi1, a component of the Rix1 complex which works in conjunction with Rea1 to mature the 60S ribosome."
Q#4803 - 	CGI_10022509	superfamily	202529	6	42	2.76E-06	39.4668	cl18228	MtN3_slv superfamily	NC	 - 	"Sugar efflux transporter for intercellular exchange; This family includes proteins such as drosophila saliva, MtN3 involved in root nodule development and a protein involved in activation and expression of recombination activation genes (RAGs). Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This family contains a region of two transmembrane helices that is found in two copies in most members of the family. This family also contains specific sugar efflux transporters that are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. In many organisims it meditaes gluose transport; in Arabidopsis it is necessary for pollen viability; and two of the rice homologues are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter."
Q#4805 - 	CGI_10003526	superfamily	242406	4	105	1.62E-08	51.0529	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#4805 - 	CGI_10003526	superfamily	248264	150	198	0.00567579	35.2906	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#4811 - 	CGI_10010493	superfamily	241563	108	141	0.000276856	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4814 - 	CGI_10010496	superfamily	110440	222	246	0.00439341	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#4815 - 	CGI_10010497	superfamily	241733	29	97	6.11E-38	124.56	cl00259	Sm_like superfamily	N	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#4816 - 	CGI_10010498	superfamily	194822	166	277	2.91E-40	141.125	cl04283	Rad10 superfamily	 - 	 - 	"Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex."
Q#4816 - 	CGI_10010498	superfamily	109247	358	437	1.87E-09	54.1201	cl02816	Ribosomal_L2 superfamily	 - 	 - 	"Ribosomal Proteins L2, RNA binding domain; Ribosomal Proteins L2, RNA binding domain.  "
Q#4817 - 	CGI_10010499	superfamily	241563	68	109	3.64E-07	47.474	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4817 - 	CGI_10010499	superfamily	241563	28	59	0.00195103	36.3032	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#4818 - 	CGI_10010500	superfamily	202823	35	100	8.04E-12	57.9341	cl08408	Ribosomal_L2_C superfamily	NC	 - 	"Ribosomal Proteins L2, C-terminal domain; Ribosomal Proteins L2, C-terminal domain.  "
Q#4821 - 	CGI_10010503	superfamily	241570	292	398	8.52E-07	48.091	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#4823 - 	CGI_10010505	superfamily	243035	343	469	6.43E-31	115.41	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#4823 - 	CGI_10010505	superfamily	243051	189	334	2.18E-16	76.2352	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#4824 - 	CGI_10010506	superfamily	248097	145	222	8.11E-12	59.9714	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4824 - 	CGI_10010506	superfamily	222429	8	53	2.24E-09	52.2428	cl18676	Myb_DNA-bind_5 superfamily	C	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#4826 - 	CGI_10010508	superfamily	241613	104	137	4.93E-06	41.0382	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#4826 - 	CGI_10010508	superfamily	246918	41	92	1.00E-11	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#4827 - 	CGI_10010509	superfamily	218273	69	165	1.02E-37	126.874	cl04760	ETC_C1_NDUFA4 superfamily	 - 	 - 	ETC complex I subunit conserved region; Family of pankaryotic NADH-ubiquinone oxidoreductase subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein.
Q#4829 - 	CGI_10010511	superfamily	245595	681	948	2.71E-141	425.749	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#4831 - 	CGI_10010513	superfamily	247799	70	131	1.37E-09	54.8735	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#4831 - 	CGI_10010513	superfamily	247799	190	233	1.34E-06	46.0139	cl17245	KH-I superfamily	N	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#4831 - 	CGI_10010513	superfamily	247792	483	529	0.000446643	38.1956	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4834 - 	CGI_10028588	superfamily	241574	299	450	1.04E-20	88.0492	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4835 - 	CGI_10028589	superfamily	245309	51	134	0.0067617	34.0474	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#4837 - 	CGI_10028591	superfamily	243066	23	121	1.47E-13	68.0277	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#4837 - 	CGI_10028591	superfamily	222412	826	859	0.00326774	36.5797	cl16432	Tnp_zf-ribbon_2 superfamily	 - 	 - 	DDE_Tnp_1-like zinc-ribbon; This zinc-ribbon domain is frequently found at the C-terminal of proteins derived from transposable elements.
Q#4844 - 	CGI_10028598	superfamily	222150	590	615	3.93E-05	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4844 - 	CGI_10028598	superfamily	222150	320	345	0.00258782	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4845 - 	CGI_10028599	superfamily	247684	13	186	3.29E-19	83.7923	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4846 - 	CGI_10028600	superfamily	247684	13	186	1.03E-19	84.9479	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4847 - 	CGI_10028601	superfamily	247684	13	186	1.16E-19	84.9479	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4848 - 	CGI_10028602	superfamily	247684	13	176	2.90E-18	78.0143	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4849 - 	CGI_10028603	superfamily	247684	13	186	5.59E-19	83.0219	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4849 - 	CGI_10028603	superfamily	247684	290	336	0.00916239	36.2527	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4850 - 	CGI_10028604	superfamily	247684	13	178	6.53E-18	78.3995	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#4855 - 	CGI_10028609	superfamily	202685	453	498	0.00280353	36.9628	cl04160	DUF1759 superfamily	NC	 - 	Protein of unknown function (DUF1759); This is a family of proteins of unknown function. Most of the members are gag-polyproteins.
Q#4856 - 	CGI_10028610	superfamily	248097	7	43	1.77E-08	46.4894	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#4857 - 	CGI_10028611	superfamily	243181	213	339	4.96E-28	110.709	cl02783	TopoII_MutL_Trans superfamily	 - 	 - 	"MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2.  MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families."
Q#4857 - 	CGI_10028611	superfamily	241593	30	151	7.21E-06	45.3302	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#4857 - 	CGI_10028611	superfamily	241597	611	659	0.000174845	40.68	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#4858 - 	CGI_10028612	superfamily	248458	75	222	3.63E-06	47.6937	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4858 - 	CGI_10028612	superfamily	248458	324	499	1.63E-05	45.7677	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4861 - 	CGI_10028615	superfamily	248458	74	440	2.12E-05	44.9973	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#4862 - 	CGI_10028616	superfamily	222150	213	240	0.000192583	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4863 - 	CGI_10028617	superfamily	220666	33	253	1.78E-55	182.56	cl10951	Tmemb_185A superfamily	 - 	 - 	"Transmembrane Fragile-X-F protein; This is a family of conserved transmembrane proteins that appear in humans to be expressed from a region upstream of the FragileXF site and to be intimately linked with the Fragile-X syndrome. Absence of TMEM185A does not necessarily lead to developmental delay, but might in combination with other, yet unknown, factors. Otherwise, the lack of the TMEM185A protein is either disposable (redundant) or its function can be complemented by the highly similar chromosome 2 retro-pseudogene product, TMEM185B."
Q#4864 - 	CGI_10028618	superfamily	243072	18	119	4.87E-25	94.7578	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#4865 - 	CGI_10028619	superfamily	222150	139	166	0.000895353	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4868 - 	CGI_10028622	superfamily	150854	68	250	1.30E-32	120.212	cl10929	MRP-S22 superfamily	C	 - 	"Mitochondrial 28S ribosomal protein S22; This is the conserved N-terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them."
Q#4869 - 	CGI_10028623	superfamily	220658	244	360	9.82E-06	46.5769	cl12382	Rogdi_lz superfamily	NC	 - 	Rogdi leucine zipper containing protein; This is a family of conserved proteins which have been suggested as containing leucine-zipper domains. A leucine zipper domain is a region of 30 amino acids with leucines repeating every seven or eight residues; these proteins do have many such leucines. The protein in Drosophila comes from the gene ROGDI.
Q#4873 - 	CGI_10028627	superfamily	241559	405	455	2.24E-13	66.5655	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#4873 - 	CGI_10028627	superfamily	220715	11	164	2.71E-21	90.4671	cl11025	NT-C2 superfamily	 - 	 - 	"N-terminal C2 in EEIG1 and EHBP1 proteins; This version of the C2 domain was initally identified in the vertebrate estrogen early-induced gene 1 (EEIG1), and its Drosophila ortholog required for uptake of dsRNA via the endocytotic machinery to induce RNAi silencing. It is also in C.elegans ortholog Sym-3 (SYnthetic lethal with Mec-3) and the mammalian protein EHBP1 (EH domain Binding Protein-1) that regulates endocytotic recycling and two plant proteins, RPG that regulates Rhizobium-directed polar growth and PMI1 (Plastid Movement Impaired 1) that is essential for intracellular movement of chloroplasts in response to blue light."
Q#4874 - 	CGI_10028628	superfamily	241754	7	316	2.00E-74	245.223	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#4875 - 	CGI_10028629	superfamily	222150	566	591	0.000431184	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4875 - 	CGI_10028629	superfamily	246975	553	574	0.000899292	38.0969	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#4877 - 	CGI_10028631	superfamily	247724	1	151	6.77E-48	155.394	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4878 - 	CGI_10028632	superfamily	247724	6	165	3.09E-50	161.943	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4879 - 	CGI_10028633	superfamily	247724	11	158	2.00E-41	139.216	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4880 - 	CGI_10028634	superfamily	247724	9	165	2.29E-41	138.831	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4882 - 	CGI_10028636	superfamily	247724	9	165	4.26E-45	148.461	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4883 - 	CGI_10028637	superfamily	247724	19	108	3.76E-31	110.326	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4884 - 	CGI_10028638	superfamily	247724	10	170	1.72E-43	144.609	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4886 - 	CGI_10028640	superfamily	247724	1	147	8.13E-31	111.097	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4887 - 	CGI_10028641	superfamily	247724	11	173	1.25E-59	186.21	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4890 - 	CGI_10028644	superfamily	247724	10	166	1.87E-40	137.29	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4891 - 	CGI_10028645	superfamily	217648	28	393	5.44E-75	243.414	cl15557	Glyco_hydro_65m superfamily	 - 	 - 	"Glycosyl hydrolase family 65 central catalytic domain; This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu. The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom. The catalytic domain also forms the majority of the dimerisation interface."
Q#4892 - 	CGI_10028646	superfamily	241941	7	96	3.48E-16	72.2417	cl00551	Acylphosphatase superfamily	 - 	 - 	Acylphosphatase; Acylphosphatase.  
Q#4893 - 	CGI_10028647	superfamily	152354	1706	1795	3.35E-38	140.067	cl13371	DUF3437 superfamily	 - 	 - 	Domain of unknown function (DUF3437); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length.
Q#4894 - 	CGI_10028648	superfamily	245602	375	713	0	636.923	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#4894 - 	CGI_10028648	superfamily	222390	245	315	9.63E-20	85.2546	cl16409	Gal_mutarotas_2 superfamily	 - 	 - 	"Galactose mutarotase-like; This family is found N-terminal to glycosyl-hydrolase domains, and appears to be similar to the galactose mutarotase superfamily."
Q#4895 - 	CGI_10028649	superfamily	245818	47	184	7.63E-43	149.28	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#4895 - 	CGI_10028649	superfamily	221674	222	281	1.59E-09	54.3568	cl14990	PolyA_pol_RNAbd superfamily	 - 	 - 	Probable RNA and SrmB- binding site of polymerase A; This region encompasses much of the RNA and SrmB binding motifs on polymerase A.
Q#4897 - 	CGI_10028651	superfamily	241580	120	196	1.74E-50	166.19	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#4899 - 	CGI_10028653	superfamily	243306	319	531	8.30E-116	348.767	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#4899 - 	CGI_10028653	superfamily	243306	10	226	6.59E-95	294.81	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#4899 - 	CGI_10028653	superfamily	247799	542	599	0.000205222	39.8274	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#4903 - 	CGI_10028657	superfamily	247755	88	296	4.95E-76	244.488	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#4903 - 	CGI_10028657	superfamily	247789	401	574	1.00E-20	90.7809	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#4904 - 	CGI_10028658	superfamily	247755	52	277	5.05E-70	228.695	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#4904 - 	CGI_10028658	superfamily	247789	370	582	2.72E-13	68.4394	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#4905 - 	CGI_10028659	superfamily	245201	38	284	3.41E-66	209.4	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4906 - 	CGI_10028660	superfamily	245201	71	317	3.00E-55	182.051	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4907 - 	CGI_10028661	superfamily	243092	349	561	8.22E-24	103.184	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4907 - 	CGI_10028661	superfamily	243092	875	1006	1.47E-06	50.026	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4907 - 	CGI_10028661	superfamily	243092	140	240	0.000521729	41.9368	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4907 - 	CGI_10028661	superfamily	243092	667	714	0.00347009	39.6256	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4909 - 	CGI_10028663	superfamily	241599	106	154	1.04E-19	80.3652	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#4909 - 	CGI_10028663	superfamily	146451	250	266	2.10E-06	43.5019	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#4911 - 	CGI_10028665	superfamily	222347	234	328	0.00107564	39.1644	cl16365	TraF_2 superfamily	NC	 - 	"F plasmid transfer operon, TraF, protein; F plasmid transfer operon, TraF, protein.  "
Q#4913 - 	CGI_10028667	superfamily	147194	201	243	0.00347237	35.3499	cl04832	RAMP superfamily	N	 - 	Receptor activity modifying family; The calcitonin-receptor-like receptor can function as either a calcitonin-gene-related peptide or an adrenomedullin receptor. The receptors function is modified by receptor-activity-modifying protein or RAMP. RAMPs are single-transmembrane-domain proteins.
Q#4915 - 	CGI_10028669	superfamily	245202	58	149	6.99E-51	161.26	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#4915 - 	CGI_10028669	superfamily	206550	2	40	6.97E-08	46.2344	cl16842	ECR1_N superfamily	 - 	 - 	Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.
Q#4917 - 	CGI_10028671	superfamily	247723	130	178	1.91E-22	87.7615	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#4919 - 	CGI_10028673	superfamily	219225	7	61	0.00803958	31.2795	cl06114	FAIM1 superfamily	N	 - 	"Fas apoptotic inhibitory molecule (FAIM1); This family consists of several fas apoptotic inhibitory molecule (FAIM1) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM1 is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology."
Q#4920 - 	CGI_10028674	superfamily	219225	50	131	0.00166903	35.5167	cl06114	FAIM1 superfamily	N	 - 	"Fas apoptotic inhibitory molecule (FAIM1); This family consists of several fas apoptotic inhibitory molecule (FAIM1) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM1 is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology."
Q#4921 - 	CGI_10028675	superfamily	243092	181	411	1.08E-12	67.36	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4926 - 	CGI_10028680	superfamily	242886	58	161	2.82E-45	148.868	cl02107	Evr1_Alr superfamily	N	 - 	Erv1 / Alr family; Biogenesis of Fe/S clusters involves a number of essential mitochondrial proteins. Erv1p of Saccharomyces cerevisiae mitochondria is required for the maturation of Fe/S proteins in the cytosol. The ALR (augmenter of liver regeneration) represents a mammalian orthologue of yeast Erv1p. Both Erv1p and full-length ALR are located in the mitochondrial intermembrane an d it thought to operate downstream of the mitochondrial ABC transporter.
Q#4928 - 	CGI_10028682	superfamily	148425	14	180	7.96E-09	52.4506	cl06049	NPDC1 superfamily	N	 - 	Neural proliferation differentiation control-1 protein (NPDC1); This family consists of several neural proliferation differentiation control-1 (NPDC1) proteins. NPDC1 plays a role in the control of neural cell proliferation and differentiation. It has been suggested that NPDC1 may be involved in the development of several secretion glands. This family also contains the C-terminal region of the C. elegans protein CAB-1 which is known to interact with AEX-3.
Q#4929 - 	CGI_10028683	superfamily	241559	24	125	4.83E-19	84.2847	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#4929 - 	CGI_10028683	superfamily	221433	805	936	3.32E-35	132.037	cl13553	DUF3585 superfamily	 - 	 - 	Protein of unknown function (DUF3585); This domain is found in eukaryotes. This domain is typically between 135 and 149 amino acids in length and is found associated with pfam00307.
Q#4929 - 	CGI_10028683	superfamily	243050	177	210	7.59E-09	53.5682	cl02475	LIM superfamily	C	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#4932 - 	CGI_10028686	superfamily	111745	554	602	1.24E-23	95.8325	cl17930	zf-MIZ superfamily	 - 	 - 	MIZ/SP-RING zinc finger; This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation.
Q#4933 - 	CGI_10028688	superfamily	201526	126	192	1.04E-28	104.928	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#4933 - 	CGI_10028688	superfamily	222370	28	89	1.08E-14	66.3925	cl16386	Longin superfamily	C	 - 	"Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain."
Q#4934 - 	CGI_10028689	superfamily	245201	34	302	4.05E-58	202.728	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#4934 - 	CGI_10028689	superfamily	220736	563	701	6.66E-23	96.995	cl11068	PTEN_C2 superfamily	 - 	 - 	"C2 domain of PTEN tumour-suppressor protein; This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane."
Q#4934 - 	CGI_10028689	superfamily	241574	466	549	0.00702567	36.5679	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4935 - 	CGI_10028690	superfamily	243555	233	402	0.000901499	40.8374	cl03871	Chitin_bind_3 superfamily	N	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#4937 - 	CGI_10028692	superfamily	216807	3	189	1.94E-48	159.739	cl18379	DUF106 superfamily	 - 	 - 	Integral membrane protein DUF106; This archaebacterial protein family has no known function. Members are predicted to be integral membrane proteins.
Q#4938 - 	CGI_10028693	superfamily	245010	11	142	5.59E-21	83.4331	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#4939 - 	CGI_10028694	superfamily	242611	89	334	7.40E-127	379.541	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#4939 - 	CGI_10028694	superfamily	245606	392	547	7.28E-65	213.072	cl11410	TPP_enzyme_PYR superfamily	 - 	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#4939 - 	CGI_10028694	superfamily	217227	563	685	3.32E-25	101.904	cl08363	Transketolase_C superfamily	 - 	 - 	"Transketolase, C-terminal domain; The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site."
Q#4941 - 	CGI_10028696	superfamily	243015	5	135	5.75E-50	160.775	cl02381	Tim17 superfamily	 - 	 - 	"Tim17/Tim22/Tim23/Pmp24 family; The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane. This family includes Tim17, Tim22 and Tim23. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27 in."
Q#4942 - 	CGI_10028697	superfamily	241896	244	477	8.53E-100	306.908	cl00483	UDG_like superfamily	 - 	 - 	"Uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDG) catalyzes the removal of uracil from DNA, which initiates the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. At least five UDG families have been characterized so far; these families share similar overall folds and common active site motifs. They demonstrate different substrate specificities, but often the function of one enzyme can be complemented by the other. Family 1 enzymes are active against uracil in both ssDNA and dsDNA, and recognize uracil explicitly in an extrahelical conformation via a combination of protein and bound-water interactions. Family 2 enzymes are mismatch specific and explicitly recognize the widowed guanine on the complementary strand, rather than the extrahelical scissile pyrimidine. This allows a broader specificity so that some Family 2 enzymes can excise uracil as well as 3, N(4)-ethenocytosine from mismatches with guanine. A Family 3 UDG from human was first characterized to remove Uracil from ssDNA, hence the name hSMUG (single-strand-selective monofunctional uracil-DNA glycosylase). However, subsequent research has shown that hSMUG1 and its rat ortholog can remove uracil and its oxidized pyrimidine derivatives from both, ssDNA and dsDNA. Enzymes in Families 4 and 5 are both thermostable. Family 4 enzymes specifically recognize uracil in a manner similar to human UDG (Family 1), rather than guanine in the complementary strand DNA, as does E. coli MUG (Family 2). These results suggest that the mechanism by which Family 4 UDGs remove uracils from DNA is similar to that of Family 1 enzyme. Although Family 5 enzymes are close relatives of Family 4, they show different substrate specificities."
Q#4943 - 	CGI_10028698	superfamily	247739	46	238	1.66E-25	100.038	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#4944 - 	CGI_10028699	superfamily	201804	42	223	3.85E-56	179.689	cl03220	MAGE superfamily	 - 	 - 	"MAGE family; The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis."
Q#4946 - 	CGI_10028701	superfamily	248232	1	440	0	684.411	cl17678	MRS6 superfamily	 - 	 - 	"RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational modification, protein turnover, chaperones]"
Q#4947 - 	CGI_10028702	superfamily	243109	99	187	3.46E-51	168.246	cl02614	SPRY superfamily	N	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#4948 - 	CGI_10028703	superfamily	248012	3	57	2.84E-06	42.1797	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#4949 - 	CGI_10028704	superfamily	241555	8	114	1.93E-12	61.0331	cl00020	GAT_1 superfamily	C	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#4950 - 	CGI_10028705	superfamily	243091	122	251	1.78E-29	109.346	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#4950 - 	CGI_10028705	superfamily	243114	17	114	4.25E-12	60.8869	cl02622	Pre-SET superfamily	 - 	 - 	Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.
Q#4951 - 	CGI_10028706	superfamily	243072	27	138	1.53E-27	100.536	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#4952 - 	CGI_10028707	superfamily	243072	30	150	4.69E-37	125.959	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#4953 - 	CGI_10028708	superfamily	248012	4	145	1.41E-16	71.5856	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#4954 - 	CGI_10004706	superfamily	241714	8	198	1.33E-59	187.475	cl00237	Peptidase_C15 superfamily	 - 	 - 	"Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I:  Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from proteolysis by other proteases until the pGlu is removed by a PGP.  PGPs are cysteine proteases with a Cys-His-Glu/Asp catalytic triad. Type I PGPs are found in a wide variety of prokaryotes and eukaryotes. It is not clear whether the functional form is a monomer, a homodimer, or a homotetramer."
Q#4955 - 	CGI_10004707	superfamily	243106	10	90	2.38E-27	107.162	cl02608	BAH superfamily	N	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#4955 - 	CGI_10004707	superfamily	226572	159	203	0.000588065	39.4644	cl18761	COG4087 superfamily	N	 - 	Soluble P-type ATPase [General function prediction only]
Q#4962 - 	CGI_10004714	superfamily	115139	21	147	1.26E-51	163.165	cl05790	Mob_synth_C superfamily	 - 	 - 	Molybdenum Cofactor Synthesis C; This region contains two iron-sulphur (3Fe-4S) binding sites. Mutations in this region of human MOCS1 cause MOCOD (Molybdenum Co-Factor Deficiency) type A.
Q#4964 - 	CGI_10011863	superfamily	245818	75	182	5.49E-22	89.1535	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#4964 - 	CGI_10011863	superfamily	217750	269	328	4.61E-11	57.9742	cl04280	PAP_assoc superfamily	 - 	 - 	Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.
Q#4965 - 	CGI_10011864	superfamily	192286	104	207	3.04E-68	208.433	cl18178	UPF1_Zn_bind superfamily	C	 - 	RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD).
Q#4966 - 	CGI_10011865	superfamily	246680	628	675	6.35E-08	50.797	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#4967 - 	CGI_10011866	superfamily	217783	59	278	8.21E-97	288.594	cl04314	TRAP_alpha superfamily	N	 - 	"Translocon-associated protein (TRAP), alpha subunit; The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane."
Q#4968 - 	CGI_10011867	superfamily	207687	352	466	3.69E-54	180.241	cl02647	AXH superfamily	 - 	 - 	Ataxin-1 and HBP1 module (AXH); AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1). ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression.
Q#4969 - 	CGI_10011868	superfamily	243109	11	185	2.56E-58	195.414	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#4969 - 	CGI_10011868	superfamily	220676	456	555	2.63E-28	109.994	cl18566	DUF2392 superfamily	 - 	 - 	Protein of unknown function (DUF2392); This is a family of proteins conserved from plants to humans. The function is not known. It carries a characteristic GRG sequence motif.
Q#4969 - 	CGI_10011868	superfamily	241758	294	515	0.000458925	40.3084	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#4970 - 	CGI_10011869	superfamily	243092	11	305	3.50E-20	87.3904	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4971 - 	CGI_10011870	superfamily	247724	150	352	1.07E-43	151.788	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#4972 - 	CGI_10011871	superfamily	222150	270	293	0.000184171	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#4973 - 	CGI_10011872	superfamily	146263	4	112	8.84E-24	94.6786	cl04138	SK_channel superfamily	 - 	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#4974 - 	CGI_10011873	superfamily	146263	73	165	3.33E-22	91.597	cl04138	SK_channel superfamily	 - 	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#4974 - 	CGI_10011873	superfamily	219619	259	323	3.04E-11	59.5287	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#4975 - 	CGI_10011874	superfamily	146263	84	193	4.41E-19	83.1227	cl04138	SK_channel superfamily	 - 	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#4975 - 	CGI_10011874	superfamily	219619	304	359	9.60E-12	61.0695	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#4975 - 	CGI_10011874	superfamily	198825	378	449	3.45E-05	42.0157	cl03763	CaMBD superfamily	 - 	 - 	"Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other."
Q#4976 - 	CGI_10011875	superfamily	247058	123	313	3.19E-57	186.997	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#4976 - 	CGI_10011875	superfamily	241699	24	100	2.52E-33	120.123	cl00221	ACBP superfamily	 - 	 - 	Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Q#4977 - 	CGI_10011876	superfamily	247058	433	620	3.66E-52	179.293	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#4978 - 	CGI_10011877	superfamily	243092	306	577	6.06E-39	144.4	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#4978 - 	CGI_10011877	superfamily	247792	25	58	2.65E-05	42.0476	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4978 - 	CGI_10011877	superfamily	190233	115	172	0.00362349	35.893	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#4979 - 	CGI_10011878	superfamily	247792	46	90	9.49E-15	67.4708	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#4980 - 	CGI_10011879	superfamily	245847	55	113	4.11E-07	44.4156	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#4982 - 	CGI_10002435	superfamily	241832	8	133	7.13E-60	184.641	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#4987 - 	CGI_10025633	superfamily	241868	38	224	1.01E-78	237.077	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#4988 - 	CGI_10025634	superfamily	241574	645	876	3.14E-113	348.421	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#4988 - 	CGI_10025634	superfamily	241622	480	567	2.03E-22	93.015	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#4990 - 	CGI_10025636	superfamily	247725	211	333	2.92E-75	233.71	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#4990 - 	CGI_10025636	superfamily	215882	131	236	3.77E-35	127.012	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#4990 - 	CGI_10025636	superfamily	220215	33	125	2.13E-24	96.1402	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#4990 - 	CGI_10025636	superfamily	192138	332	377	1.05E-11	59.9399	cl07378	FA superfamily	 - 	 - 	"FERM adjacent (FA); This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates."
Q#4992 - 	CGI_10025638	superfamily	241593	31	118	2.74E-07	45.3302	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#4993 - 	CGI_10025639	superfamily	128937	84	144	5.36E-14	63.0504	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#4993 - 	CGI_10025639	superfamily	128937	9	74	2.27E-11	55.7316	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#4995 - 	CGI_10025641	superfamily	242406	27	144	8.44E-15	67.2313	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#4997 - 	CGI_10025643	superfamily	241613	2	30	6.42E-09	52.209	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#4997 - 	CGI_10025643	superfamily	247744	269	312	0.00449978	36.6872	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#4999 - 	CGI_10025645	superfamily	218295	2	570	0	757.872	cl15562	TH1 superfamily	 - 	 - 	TH1 protein; TH1 is a highly conserved but uncharacterized metazoan protein. No homologue has been identified in Caenorhabditis elegans. TH1 binds specifically to A-Raf kinase.
Q#5000 - 	CGI_10025646	superfamily	243967	293	542	3.44E-65	212.96	cl05005	TAF4 superfamily	 - 	 - 	"TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. Each TAF, with the help of a specific activator, is required only for the expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID.   Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. TAF4 domain interacts with TAF12 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes."
Q#5000 - 	CGI_10025646	superfamily	198757	133	224	6.65E-33	120.892	cl02658	TAFH superfamily	 - 	 - 	"NHR1 homology to TAF; This corresponds to the region NHR1 that is conserved between the product of the nervy gene in Drosophila and the human mtg8b protein, which is hypothesised to be a transcription factor."
Q#5001 - 	CGI_10025647	superfamily	241733	4	77	4.58E-40	141.186	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#5001 - 	CGI_10025647	superfamily	220282	334	439	1.64E-19	84.843	cl09757	FDF superfamily	 - 	 - 	"FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain."
Q#5002 - 	CGI_10025648	superfamily	247856	102	161	3.34E-05	40.9941	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5003 - 	CGI_10025649	superfamily	243068	5	230	8.55E-19	82.5932	cl02523	Zona_pellucida superfamily	 - 	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#5005 - 	CGI_10025651	superfamily	220692	58	157	0.00107911	39.1097	cl18570	7TM_GPCR_Srw superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#5008 - 	CGI_10025654	superfamily	189870	13	103	1.04E-42	142.269	cl09526	SBDS superfamily	 - 	 - 	"Shwachman-Bodian-Diamond syndrome (SBDS) protein; This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterized by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism. In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition."
Q#5009 - 	CGI_10025655	superfamily	247856	452	530	2.35E-11	59.8689	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5009 - 	CGI_10025655	superfamily	246925	120	415	4.28E-30	119.382	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#5013 - 	CGI_10025659	superfamily	241550	299	428	8.11E-13	65.0048	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#5013 - 	CGI_10025659	superfamily	241872	5	104	7.01E-06	45.0557	cl00453	CDP-OH_P_transf superfamily	C	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#5014 - 	CGI_10025660	superfamily	247907	4281	4440	1.42E-29	119.06	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#5014 - 	CGI_10025660	superfamily	247907	3740	3893	4.17E-25	105.963	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#5014 - 	CGI_10025660	superfamily	247907	3997	4175	2.28E-24	103.652	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#5014 - 	CGI_10025660	superfamily	238012	2502	2551	1.70E-10	60.4458	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#5014 - 	CGI_10025660	superfamily	238012	2081	2130	1.98E-10	60.0606	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#5014 - 	CGI_10025660	superfamily	245814	3009	3069	8.31E-10	59.0399	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	241613	445	480	1.19E-09	57.6018	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	1052	1086	4.46E-09	56.061	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	1012	1047	8.36E-09	55.2906	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	574	605	1.42E-08	54.5202	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	238012	1681	1730	2.45E-08	54.2826	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#5014 - 	CGI_10025660	superfamily	241613	367	401	3.76E-08	53.3646	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	938	973	5.96E-08	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	1195	1227	7.51E-08	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	743	777	1.29E-07	51.8238	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	406	441	1.50E-07	51.4386	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	238012	1796	1841	1.94E-07	51.5862	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#5014 - 	CGI_10025660	superfamily	245814	2635	2700	2.45E-07	51.7211	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	241613	1280	1315	3.83E-07	50.283	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	783	814	6.04E-07	49.8978	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	245213	4236	4272	6.83E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5014 - 	CGI_10025660	superfamily	238012	2195	2244	9.38E-07	49.6602	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#5014 - 	CGI_10025660	superfamily	241613	975	1010	1.67E-06	48.357	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	821	857	4.38E-06	47.2014	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	616	647	6.03E-06	46.8162	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	902	936	1.12E-05	46.0458	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	527	560	1.58E-05	45.6606	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	241613	487	520	4.97E-05	44.1198	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5014 - 	CGI_10025660	superfamily	245213	3913	3949	0.00578951	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5014 - 	CGI_10025660	superfamily	245213	4203	4233	0.00821617	37.6162	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5014 - 	CGI_10025660	superfamily	243080	1503	1630	3.45E-29	116.977	cl02548	Laminin_B superfamily	 - 	 - 	Laminin B (Domain IV); Laminin B (Domain IV).  
Q#5014 - 	CGI_10025660	superfamily	245814	1333	1410	1.97E-27	110.272	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	243080	1911	2035	2.22E-24	103.11	cl02548	Laminin_B superfamily	 - 	 - 	Laminin B (Domain IV); Laminin B (Domain IV).  
Q#5014 - 	CGI_10025660	superfamily	243080	2314	2455	6.04E-24	101.954	cl02548	Laminin_B superfamily	 - 	 - 	Laminin B (Domain IV); Laminin B (Domain IV).  
Q#5014 - 	CGI_10025660	superfamily	245814	2710	2794	2.46E-19	87.2184	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	3434	3510	2.71E-16	78.316	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	3610	3686	4.26E-15	74.8492	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	3099	3166	8.65E-14	70.5133	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	3524	3599	1.47E-13	70.2268	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	3179	3262	1.79E-12	67.1452	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	3345	3419	2.15E-10	60.982	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	243060	82	179	1.88E-09	58.5444	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#5014 - 	CGI_10025660	superfamily	245814	2809	2890	7.38E-09	56.3597	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	3284	3335	6.70E-08	53.1795	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	1101	1179	8.59E-06	47.1576	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	2927	2964	3.15E-05	45.6168	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	245814	655	737	5.85E-05	44.4612	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5014 - 	CGI_10025660	superfamily	238012	1731	1788	0.00625636	38.1042	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#5014 - 	CGI_10025660	superfamily	241613	861	884	0.00887947	37.6129	cl00104	LDLa superfamily	C	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5015 - 	CGI_10025661	superfamily	219251	205	290	2.42E-23	92.8857	cl18503	MRP-L47 superfamily	 - 	 - 	"Mitochondrial 39-S ribosomal protein L47 (MRP-L47); This family represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure."
Q#5017 - 	CGI_10025663	superfamily	243069	37	232	5.63E-108	312.608	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#5018 - 	CGI_10025664	superfamily	241634	1	139	8.70E-46	152.053	cl00143	SynN superfamily	 - 	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#5018 - 	CGI_10025664	superfamily	241642	153	212	1.24E-12	60.587	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#5020 - 	CGI_10025666	superfamily	241913	190	263	0.00228093	35.6597	cl00509	hot_dog superfamily	C	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#5021 - 	CGI_10025667	superfamily	241884	5	213	3.00E-145	407.905	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#5022 - 	CGI_10025668	superfamily	241574	51	285	1.01E-91	279.856	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#5023 - 	CGI_10025669	superfamily	241599	188	240	1.20E-12	61.1052	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#5023 - 	CGI_10025669	superfamily	243050	113	167	4.38E-26	97.8791	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#5023 - 	CGI_10025669	superfamily	243050	52	105	8.40E-18	75.1053	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#5025 - 	CGI_10025671	superfamily	209898	36	56	0.00893719	33.0827	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#5026 - 	CGI_10025672	superfamily	219609	1	140	7.30E-52	165.566	cl06752	Orai-1 superfamily	 - 	 - 	"Mediator of CRAC channel activity; ORAI-1 is a protein homologue of Drosophila Orai and human Orai1, Orai2 and Orai3. ORAI-1 GFP reporters are co- expressed with STIM-1 (ER CA(2+) sensors) in the gonad and intestine. The protein has four predicted transmembrane domains with a highly conserved region between TM2 ad TM3. This conserved domain is thought to function in channel regulation. ORAI1- related proteins are required for the production of the calcium channel, CRAC, along with STIM1-related proteins."
Q#5027 - 	CGI_10025673	superfamily	202085	713	741	2.34E-10	58.1406	cl03401	zf-CXXC superfamily	N	 - 	"CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR."
Q#5027 - 	CGI_10025673	superfamily	202224	298	398	1.17E-08	54.6092	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#5027 - 	CGI_10025673	superfamily	199166	1278	1394	1.99E-05	46.1664	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#5027 - 	CGI_10025673	superfamily	243074	1148	1191	2.62E-05	43.6493	cl02535	F-box-like superfamily	N	 - 	F-box-like; This is an F-box-like family.
Q#5028 - 	CGI_10025674	superfamily	241593	264	403	2.30E-12	63.0494	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#5028 - 	CGI_10025674	superfamily	220754	64	217	1.65E-51	172.022	cl11087	BCDHK_Adom3 superfamily	 - 	 - 	"Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase; Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. This is the butyryl-CoA dehydrogenase, subunit A domain 3, a largely alpha-helical bundle of the enzyme BCDHK. This enzyme is the regulator of the dehydrogenase complex that breaks branched-chain amino-acids down, by phosphorylating and thereby inactivating it when synthesis is required. The domain is associated with family HATPase_c pfam02518 which is towards the C-terminal."
Q#5030 - 	CGI_10025676	superfamily	248458	46	138	0.000109947	42.6861	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5031 - 	CGI_10025677	superfamily	203238	57	218	1.04E-85	253.375	cl12307	GMP_PDE_delta superfamily	 - 	 - 	"GMP-PDE, delta subunit; GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE)(EC:3.1.4.35). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport."
Q#5032 - 	CGI_10025678	superfamily	243072	6	116	9.77E-09	53.9266	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5032 - 	CGI_10025678	superfamily	243072	434	499	4.22E-05	42.3707	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5033 - 	CGI_10025679	superfamily	248312	30	199	0.0020896	36.9477	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#5034 - 	CGI_10025680	superfamily	241750	25	394	2.83E-94	289.999	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#5035 - 	CGI_10025681	superfamily	247723	540	616	5.59E-32	123.151	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5035 - 	CGI_10025681	superfamily	247723	367	440	6.13E-31	120.106	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5035 - 	CGI_10025681	superfamily	247723	466	539	3.73E-29	114.806	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5035 - 	CGI_10025681	superfamily	247723	113	171	4.07E-09	56.6883	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5036 - 	CGI_10025682	superfamily	219549	1212	1336	1.13E-20	90.0474	cl06671	SPOC superfamily	 - 	 - 	SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.
Q#5037 - 	CGI_10025683	superfamily	241777	181	459	1.54E-27	110.083	cl00316	Cation_efflux superfamily	 - 	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#5038 - 	CGI_10025684	superfamily	248313	96	159	0.00679985	34.8994	cl17759	EamA superfamily	N	 - 	EamA-like transporter family; This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.
Q#5039 - 	CGI_10025685	superfamily	242059	1	422	9.46E-28	112.84	cl00738	MBOAT superfamily	 - 	 - 	"MBOAT, membrane-bound O-acyltransferase family; The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue."
Q#5040 - 	CGI_10025686	superfamily	201526	32	98	1.09E-28	102.231	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#5041 - 	CGI_10025687	superfamily	220393	3	289	1.11E-99	310.076	cl10751	Tmem26 superfamily	 - 	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#5045 - 	CGI_10025691	superfamily	243035	8	127	7.44E-20	82.2825	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5046 - 	CGI_10025692	superfamily	245201	338	562	9.81E-55	187.744	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5047 - 	CGI_10025693	superfamily	190614	40	122	1.76E-33	114.58	cl15647	YEATS superfamily	 - 	 - 	"YEATS family; We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity"
Q#5048 - 	CGI_10025694	superfamily	244870	175	389	1.22E-51	179.408	cl08238	PA superfamily	 - 	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#5048 - 	CGI_10025694	superfamily	246748	397	669	2.80E-47	169.696	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#5048 - 	CGI_10025694	superfamily	202944	667	785	5.46E-13	66.9104	cl07854	TFR_dimer superfamily	 - 	 - 	Transferrin receptor-like dimerisation domain; This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
Q#5049 - 	CGI_10025695	superfamily	243859	62	147	1.69E-10	55.799	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#5050 - 	CGI_10012376	superfamily	207642	206	295	5.50E-28	104.881	cl02558	GED superfamily	 - 	 - 	Dynamin GTPase effector domain; Dynamin GTPase effector domain.  
Q#5050 - 	CGI_10012376	superfamily	247725	36	75	1.48E-22	90.4455	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5050 - 	CGI_10012376	superfamily	247725	151	185	8.40E-20	82.7415	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5051 - 	CGI_10012377	superfamily	248469	110	208	8.11E-09	51.2167	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#5053 - 	CGI_10012379	superfamily	241578	409	560	6.03E-38	139.734	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5053 - 	CGI_10012379	superfamily	243051	134	272	2.71E-35	132.116	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#5053 - 	CGI_10012379	superfamily	243061	299	401	7.89E-34	126.303	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5053 - 	CGI_10012379	superfamily	243061	24	126	2.94E-30	115.902	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5054 - 	CGI_10012380	superfamily	247755	580	815	4.54E-136	407.001	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#5054 - 	CGI_10012380	superfamily	216049	244	534	1.05E-11	64.9998	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#5055 - 	CGI_10012381	superfamily	241640	70	303	1.87E-69	218.3	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#5057 - 	CGI_10012383	superfamily	247792	18	55	7.45E-08	47.8256	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5057 - 	CGI_10012383	superfamily	149875	129	271	2.24E-80	242.787	cl07515	USP8_interact superfamily	N	 - 	USP8 interacting; This domain interacts with the UBP deubiquitinating enzyme USP8.
Q#5058 - 	CGI_10012384	superfamily	246675	87	127	0.00802021	36.8788	cl14615	PI-PLCc_GDPD_SF superfamily	NC	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#5059 - 	CGI_10012385	superfamily	243029	40	108	9.75E-17	71.9981	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#5059 - 	CGI_10012385	superfamily	215647	141	215	2.46E-09	54.9221	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#5060 - 	CGI_10012386	superfamily	219619	329	385	2.64E-10	56.4471	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#5060 - 	CGI_10012386	superfamily	243066	6	56	1.91E-09	54.0961	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#5061 - 	CGI_10012387	superfamily	217740	22	222	8.63E-71	218	cl18427	Scramblase superfamily	 - 	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#5062 - 	CGI_10012388	superfamily	219863	493	892	1.20E-159	485.277	cl07203	DUF1744 superfamily	 - 	 - 	Domain of unknown function (DUF1744); This domain is found on the epsilon catalytic subunit of DNA polymerase. It is found C terminal to pfam03104 and pfam00136.
Q#5062 - 	CGI_10012388	superfamily	245235	23	116	1.34E-50	190.195	cl10023	POLBc superfamily	N	 - 	"DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y).  Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis."
Q#5063 - 	CGI_10012389	superfamily	245235	461	992	0	1051.12	cl10023	POLBc superfamily	 - 	 - 	"DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y).  Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis."
Q#5063 - 	CGI_10012389	superfamily	245226	198	401	4.62E-146	435.921	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#5064 - 	CGI_10012390	superfamily	220417	2	142	1.76E-12	60.8706	cl10785	MRP-L28 superfamily	 - 	 - 	Mitochondrial ribosomal protein L28; Members of this family are components of the mitochondrial large ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S).
Q#5065 - 	CGI_10012391	superfamily	149675	4	164	1.70E-115	327.09	cl07351	UFC1 superfamily	 - 	 - 	"Ubiquitin-fold modifier-conjugating enzyme 1; Ubiquitin-like (UBL) post-translational modifiers are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. Ubiquitin-fold modifier 1 (Ufm1) a ubiquitin-like protein is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. This family represents the E2-like enzyme."
Q#5067 - 	CGI_10012393	superfamily	246669	6	117	1.71E-32	119.666	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#5067 - 	CGI_10012393	superfamily	245205	255	334	1.43E-08	51.4697	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#5069 - 	CGI_10012395	superfamily	245814	54	120	3.27E-11	59.4251	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5069 - 	CGI_10012395	superfamily	245814	164	243	3.67E-27	104.53	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5069 - 	CGI_10012395	superfamily	245814	266	359	1.31E-14	69.753	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5072 - 	CGI_10012398	superfamily	247741	25	91	5.06E-12	59.8691	cl17187	Aldolase_Class_I superfamily	N	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#5073 - 	CGI_10005379	superfamily	246902	304	490	2.52E-79	257.505	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#5073 - 	CGI_10005379	superfamily	246902	69	241	3.35E-79	256.321	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#5073 - 	CGI_10005379	superfamily	199166	755	882	2.11E-05	45.396	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#5075 - 	CGI_10005381	superfamily	193251	2416	2686	3.94E-155	485.21	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#5075 - 	CGI_10005381	superfamily	193253	3043	3386	8.56E-155	487.622	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#5075 - 	CGI_10005381	superfamily	193256	2763	3030	1.14E-152	477.903	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#5075 - 	CGI_10005381	superfamily	193257	3404	3631	2.24E-135	426.709	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#5075 - 	CGI_10005381	superfamily	247743	2123	2244	3.97E-08	54.994	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#5077 - 	CGI_10005383	superfamily	241622	137	216	2.80E-11	58.7322	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5077 - 	CGI_10005383	superfamily	221480	22	63	0.007449	35.9323	cl13647	MSA-2c superfamily	N	 - 	Merozoite surface antigen 2c; This family of proteins is found in eukaryotes. Proteins in this family are typically between 263 and 318 amino acids in length. There is a conserved SFT sequence motif. MSA-2 is a plasma membrane glycoprotein which can be found in Babesia bovis species.
Q#5078 - 	CGI_10005384	superfamily	222370	27	97	1.12E-16	71.4001	cl16386	Longin superfamily	 - 	 - 	"Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain."
Q#5078 - 	CGI_10005384	superfamily	201526	117	172	8.47E-16	69.1041	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#5079 - 	CGI_10005385	superfamily	241739	223	481	1.46E-108	324.499	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#5080 - 	CGI_10005386	superfamily	218209	85	299	1.58E-48	162.534	cl12298	DUF607 superfamily	 - 	 - 	"Protein of unknown function, DUF607; This family represents a conserved region found in several uncharacterized eukaryotic proteins."
Q#5081 - 	CGI_10005387	superfamily	242908	6	148	1.76E-64	197.396	cl02155	ER_lumen_recept superfamily	 - 	 - 	ER lumen protein retaining receptor; ER lumen protein retaining receptor.  
Q#5086 - 	CGI_10007651	superfamily	220325	399	579	7.06E-32	123.282	cl09853	Med18 superfamily	 - 	 - 	"Med18 protein; Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators."
Q#5086 - 	CGI_10007651	superfamily	241583	19	61	4.80E-06	46.2593	cl00064	ZnMc superfamily	NC	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#5087 - 	CGI_10007652	superfamily	247057	346	397	1.60E-05	42.1967	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#5087 - 	CGI_10007652	superfamily	221744	46	91	0.00261634	37.8007	cl18614	CABIT superfamily	C	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#5088 - 	CGI_10007653	superfamily	220226	106	363	1.46E-97	292.98	cl09658	XendoU superfamily	 - 	 - 	Endoribonuclease XendoU; This is a family of endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.
Q#5088 - 	CGI_10007653	superfamily	207618	18	58	9.66E-11	56.6746	cl02508	Somatomedin_B superfamily	 - 	 - 	Somatomedin B domain; Somatomedin B domain.  
Q#5088 - 	CGI_10007653	superfamily	207618	58	96	1.83E-10	55.9042	cl02508	Somatomedin_B superfamily	 - 	 - 	Somatomedin B domain; Somatomedin B domain.  
Q#5090 - 	CGI_10007655	superfamily	243098	165	209	1.60E-06	46.0519	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#5090 - 	CGI_10007655	superfamily	247999	677	717	7.12E-08	50.1816	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#5090 - 	CGI_10007655	superfamily	248259	82	146	2.62E-07	49.1702	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#5093 - 	CGI_10007658	superfamily	245213	64	98	9.26E-08	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5093 - 	CGI_10007658	superfamily	245213	148	191	2.74E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5093 - 	CGI_10007658	superfamily	245213	193	228	8.81E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5093 - 	CGI_10007658	superfamily	245213	105	141	0.000217144	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5093 - 	CGI_10007658	superfamily	245213	20	57	0.00391578	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5093 - 	CGI_10007658	superfamily	205157	238	275	0.00524395	35.5911	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#5094 - 	CGI_10007659	superfamily	245213	10	52	1.25E-08	51.4834	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5098 - 	CGI_10007082	superfamily	241563	67	108	2.39E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5098 - 	CGI_10007082	superfamily	241563	27	58	0.00116743	37.0736	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5099 - 	CGI_10007083	superfamily	242536	147	228	2.73E-29	106.027	cl01497	ATase superfamily	 - 	 - 	"The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of the C-terminal domain, suggesting an important structural role for the N-terminal domain in orienting the C-terminal domain for proper catalysis. Some ATase C-terminal domain homologs are either single-domain proteins that lack an N-terminal domain, or have a tryptophan substituted in place of the acceptor cysteine (i.e. the motif PCHR is replaced by PWHR). ATase null mutant mice are viable, fertile, and have a normal lifespan."
Q#5103 - 	CGI_10007087	superfamily	243362	209	250	8.34E-05	41.2567	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#5103 - 	CGI_10007087	superfamily	110440	335	361	0.000255661	38.5429	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#5109 - 	CGI_10003693	superfamily	247744	250	369	4.38E-08	51.5004	cl17190	NK superfamily	N	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#5109 - 	CGI_10003693	superfamily	241782	70	141	0.00501046	36.2063	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#5111 - 	CGI_10003696	superfamily	219843	5	199	2.13E-81	249.078	cl18528	ATP-grasp_2 superfamily	 - 	 - 	ATP-grasp domain; ATP-grasp domain.  
Q#5111 - 	CGI_10003696	superfamily	215988	258	309	1.07E-11	61.1184	cl18355	Ligase_CoA superfamily	C	 - 	"CoA-ligase; This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP."
Q#5112 - 	CGI_10003697	superfamily	247724	23	302	2.99E-130	388.912	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5112 - 	CGI_10003697	superfamily	216255	226	516	8.98E-121	364.943	cl03076	Dynamin_M superfamily	 - 	 - 	"Dynamin central region; This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169."
Q#5112 - 	CGI_10003697	superfamily	207642	593	682	1.79E-25	101.414	cl02558	GED superfamily	 - 	 - 	Dynamin GTPase effector domain; Dynamin GTPase effector domain.  
Q#5113 - 	CGI_10000428	superfamily	247098	7	92	7.38E-20	78.82	cl15841	COG0229 superfamily	N	 - 	"Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]"
Q#5115 - 	CGI_10002622	superfamily	222150	89	114	7.54E-05	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5115 - 	CGI_10002622	superfamily	222150	118	141	0.000168036	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5118 - 	CGI_10012067	superfamily	192566	29	151	1.05E-29	115.094	cl18180	COG5 superfamily	 - 	 - 	"Golgi transport complex subunit 5; The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller, B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7."
Q#5119 - 	CGI_10012068	superfamily	247740	22	251	6.50E-96	285.928	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#5120 - 	CGI_10012069	superfamily	245201	167	416	4.74E-61	210.941	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5120 - 	CGI_10012069	superfamily	221460	443	480	1.88E-12	64.7475	cl12053	OSR1_C superfamily	 - 	 - 	"Oxidative-stress-responsive kinase 1 C terminal; This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00069. There is a single completely conserved residue F that may be functionally important. OSR1 is involved in the signalling cascade which activates Na/K/2Cl cotransporter during osmotic stress. This domain is the C terminal domain of OSR1 which recognises a motif (Arg-Phe-Xaa-Val) on the OSR1-activating protein WNK1."
Q#5123 - 	CGI_10012072	superfamily	247743	488	666	0.000135167	41.7479	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#5123 - 	CGI_10012072	superfamily	221668	83	184	1.56E-05	44.626	cl13991	MCM2_N superfamily	N	 - 	"Mini-chromosome maintenance protein 2; This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function."
Q#5125 - 	CGI_10012074	superfamily	246918	30	89	4.49E-16	69.5379	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5126 - 	CGI_10012075	superfamily	246918	192	252	2.01E-09	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5126 - 	CGI_10012075	superfamily	246918	255	317	1.37E-07	49.5075	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5126 - 	CGI_10012075	superfamily	246918	142	187	0.000110543	41.0331	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5127 - 	CGI_10012076	superfamily	245201	811	1048	4.31E-20	90.3737	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5127 - 	CGI_10012076	superfamily	247724	149	197	6.75E-14	71.0385	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5127 - 	CGI_10012076	superfamily	247724	248	398	5.06E-06	46.771	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5128 - 	CGI_10012077	superfamily	245201	827	986	2.75E-13	69.5729	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5128 - 	CGI_10012077	superfamily	247724	162	226	1.35E-09	57.5566	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5129 - 	CGI_10012078	superfamily	245201	721	994	2.87E-46	166.258	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5129 - 	CGI_10012078	superfamily	247724	232	371	1.19E-08	54.475	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5129 - 	CGI_10012078	superfamily	247724	129	167	1.19E-05	45.6154	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5130 - 	CGI_10012079	superfamily	245201	81	133	0.000111852	39.099	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5131 - 	CGI_10012080	superfamily	245201	13	96	2.62E-10	54.4648	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5132 - 	CGI_10012081	superfamily	247724	124	162	3.66E-07	49.8526	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5132 - 	CGI_10012081	superfamily	247724	227	342	8.70E-05	42.919	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5132 - 	CGI_10012081	superfamily	245814	534	631	0.00207353	37.4849	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5133 - 	CGI_10012082	superfamily	203031	31	90	1.68E-07	43.856	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#5135 - 	CGI_10012084	superfamily	241659	96	174	3.23E-27	99.9018	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#5136 - 	CGI_10012085	superfamily	245602	1439	1610	1.89E-96	318.344	cl11402	GH31 superfamily	N	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#5136 - 	CGI_10012085	superfamily	245602	2079	2571	4.95E-169	529.506	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#5136 - 	CGI_10012085	superfamily	245602	289	783	4.19E-142	453.237	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#5136 - 	CGI_10012085	superfamily	245602	1196	1371	3.15E-62	219.348	cl11402	GH31 superfamily	C	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#5136 - 	CGI_10012085	superfamily	241612	917	961	7.59E-06	46.183	cl00103	Trefoil superfamily	 - 	 - 	"P or trefoil or TFF domain; Trefoil factor family domain peptides are mucin-associated molecules, largely found in epithelia of gastrointestinal tissues. Function is not known but it was originally identified from mucosal tissues, where it may have a regulatory or structural role and has also been implicated as a growth fractor in other tissues.The domain is found in 1 to 6 copies where it occurs."
Q#5136 - 	CGI_10012085	superfamily	241612	1815	1862	0.00128259	39.291	cl00103	Trefoil superfamily	 - 	 - 	"P or trefoil or TFF domain; Trefoil factor family domain peptides are mucin-associated molecules, largely found in epithelia of gastrointestinal tissues. Function is not known but it was originally identified from mucosal tissues, where it may have a regulatory or structural role and has also been implicated as a growth fractor in other tissues.The domain is found in 1 to 6 copies where it occurs."
Q#5140 - 	CGI_10012090	superfamily	241563	75	115	8.21E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5141 - 	CGI_10018432	superfamily	245201	7	212	2.49E-82	250.878	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5142 - 	CGI_10018433	superfamily	245033	162	306	7.31E-26	101.246	cl09208	Tim44 superfamily	 - 	 - 	Tim44-like domain; Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region. This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast. This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane.
Q#5143 - 	CGI_10018434	superfamily	241782	35	370	1.51E-58	206.038	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#5143 - 	CGI_10018434	superfamily	247856	540	601	0.000515278	39.4533	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5143 - 	CGI_10018434	superfamily	215754	779	870	1.57E-26	105.798	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#5143 - 	CGI_10018434	superfamily	215754	965	1054	2.00E-26	105.798	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#5143 - 	CGI_10018434	superfamily	215754	871	962	1.08E-20	89.2348	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#5143 - 	CGI_10018434	superfamily	244899	465	523	0.000324407	40.1658	cl08302	S-100 superfamily	 - 	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#5144 - 	CGI_10018435	superfamily	220729	3	151	8.94E-43	148.181	cl11056	Hat1_N superfamily	 - 	 - 	"Histone acetyl transferase HAT1 N-terminus; This domain is the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of the GNAT Acetyltransf_1 (pfam00583) domain. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyze the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated."
Q#5145 - 	CGI_10018436	superfamily	246749	4	88	2.62E-32	122.221	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#5145 - 	CGI_10018436	superfamily	243098	461	508	0.000100767	41.4295	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#5145 - 	CGI_10018436	superfamily	246749	319	383	1.14E-07	50.5067	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#5146 - 	CGI_10018437	superfamily	243066	7	112	1.71E-15	69.5685	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#5148 - 	CGI_10018439	superfamily	245864	1	93	2.08E-23	93.1118	cl12078	p450 superfamily	NC	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#5149 - 	CGI_10018440	superfamily	245864	190	413	9.41E-53	184.404	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#5149 - 	CGI_10018440	superfamily	245864	39	121	1.57E-15	76.9334	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#5150 - 	CGI_10018441	superfamily	245864	1	419	7.61E-72	236.021	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#5151 - 	CGI_10018442	superfamily	217473	64	334	3.37E-25	105.91	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#5152 - 	CGI_10018443	superfamily	241600	91	300	3.03E-99	293.763	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#5156 - 	CGI_10018447	superfamily	243072	323	501	3.80E-09	55.0822	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5156 - 	CGI_10018447	superfamily	243072	455	551	7.39E-09	54.3118	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5156 - 	CGI_10018447	superfamily	243072	28	119	3.24E-08	52.3858	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5157 - 	CGI_10018448	superfamily	145533	60	154	5.14E-40	140.962	cl03592	Ski_Sno superfamily	 - 	 - 	"SKI/SNO/DAC family; This family contains a presumed domain that is about 100 amino acids long. All members of this family contain a conserved CLPQ motif. The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation. Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli. Dachshund also contains this domain. It is involved in various aspects of development."
Q#5157 - 	CGI_10018448	superfamily	198898	165	257	2.69E-35	127.484	cl07406	c-SKI_SMAD_bind superfamily	 - 	 - 	c-SKI Smad4 binding domain; c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins. This domain binds to Smad4
Q#5158 - 	CGI_10018449	superfamily	241600	301	515	1.50E-97	296.459	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#5159 - 	CGI_10018450	superfamily	247637	211	387	2.49E-91	280.683	cl16912	MDR superfamily	N	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#5160 - 	CGI_10018451	superfamily	216686	68	257	1.47E-54	177.9	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#5163 - 	CGI_10018454	superfamily	243062	305	406	1.02E-56	183.631	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#5163 - 	CGI_10018454	superfamily	216062	15	253	1.40E-49	169.156	cl02928	TGFb_propeptide superfamily	 - 	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#5164 - 	CGI_10018455	superfamily	241645	183	261	5.86E-37	127.08	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#5164 - 	CGI_10018455	superfamily	243133	108	147	2.64E-11	57.5708	cl02662	SEP superfamily	N	 - 	"SEP domain; The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L. Most SEP domains are succeeded closely by a UBX domain."
Q#5165 - 	CGI_10018456	superfamily	247858	395	475	0.000140341	40.4617	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#5166 - 	CGI_10018457	superfamily	245819	267	425	4.38E-20	89.1754	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#5166 - 	CGI_10018457	superfamily	245819	734	811	5.99E-08	52.1963	cl11967	Nucleotidyl_cyc_III superfamily	N	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#5167 - 	CGI_10018458	superfamily	241584	576	667	1.21E-07	50.5727	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5167 - 	CGI_10018458	superfamily	241584	393	437	0.00012122	41.3279	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5167 - 	CGI_10018458	superfamily	245814	160	231	9.80E-16	73.6326	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5167 - 	CGI_10018458	superfamily	245814	257	333	1.14E-15	73.6824	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5167 - 	CGI_10018458	superfamily	245814	64	139	9.63E-13	65.1134	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5167 - 	CGI_10018458	superfamily	245814	2	34	2.82E-06	45.8232	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5169 - 	CGI_10018460	superfamily	243051	596	749	2.63E-37	139.435	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#5169 - 	CGI_10018460	superfamily	241609	1037	1115	4.94E-28	110.16	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#5169 - 	CGI_10018460	superfamily	241609	845	912	5.23E-27	107.464	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#5169 - 	CGI_10018460	superfamily	241609	763	835	5.66E-26	104.382	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#5169 - 	CGI_10018460	superfamily	241609	917	993	9.88E-23	95.1375	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#5169 - 	CGI_10018460	superfamily	241609	1126	1196	1.85E-21	91.2855	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#5169 - 	CGI_10018460	superfamily	241571	429	548	1.46E-10	60.5038	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5169 - 	CGI_10018460	superfamily	245213	988	1029	1.80E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5169 - 	CGI_10018460	superfamily	241583	130	277	4.58E-38	142.325	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#5169 - 	CGI_10018460	superfamily	241583	280	381	2.03E-22	96.8714	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#5172 - 	CGI_10018463	superfamily	247905	573	728	1.50E-13	69.1888	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#5172 - 	CGI_10018463	superfamily	247805	361	501	2.29E-07	50.4136	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#5176 - 	CGI_10022378	superfamily	216363	262	356	3.47E-12	62.1026	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#5178 - 	CGI_10022380	superfamily	241758	4	99	0.00540215	34.2678	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5180 - 	CGI_10022382	superfamily	241758	3	149	2.00E-22	87.4254	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5181 - 	CGI_10022383	superfamily	241758	3	130	6.62E-16	69.321	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5182 - 	CGI_10022384	superfamily	241758	3	140	5.55E-26	96.285	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5183 - 	CGI_10022385	superfamily	183292	2	195	2.69E-05	44.4272	cl18135	PRK11728 superfamily	C	 - 	hydroxyglutarate oxidase; Provisional
Q#5184 - 	CGI_10022386	superfamily	183782	19	55	3.69E-05	44.1187	cl18137	PRK12834 superfamily	C	 - 	putative FAD-binding dehydrogenase; Reviewed
Q#5185 - 	CGI_10022387	superfamily	241758	2	88	6.14E-17	70.8618	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5186 - 	CGI_10022388	superfamily	241758	3	140	2.18E-25	94.7442	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5192 - 	CGI_10022394	superfamily	241563	491	529	0.0023078	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5193 - 	CGI_10022395	superfamily	192604	340	422	1.74E-21	88.125	cl11135	PACT_coil_coil superfamily	 - 	 - 	"Pericentrin-AKAP-450 domain of centrosomal targeting protein; This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly."
Q#5194 - 	CGI_10022396	superfamily	241852	6	433	0	867.066	cl00416	CS_ACL-C_CCL superfamily	 - 	 - 	"Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. Some CS proteins function as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs catalyze an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA; they do this in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate CiCoA, and c) the hydrolysis of CiCoA to produce citrate and CoA. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. There are two types of CSs: type I CS and type II CSs.  Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site.  Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism.  In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL."
Q#5195 - 	CGI_10022397	superfamily	241852	1	47	5.71E-26	96.6664	cl00416	CS_ACL-C_CCL superfamily	N	 - 	"Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. Some CS proteins function as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs catalyze an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA; they do this in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate CiCoA, and c) the hydrolysis of CiCoA to produce citrate and CoA. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. There are two types of CSs: type I CS and type II CSs.  Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site.  Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism.  In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL."
Q#5196 - 	CGI_10022398	superfamily	203881	107	138	3.25E-05	38.6725	cl07024	Spindle_Spc25 superfamily	N	 - 	"Chromosome segregation protein Spc25; This is a family of chromosome segregation proteins. It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex, and in vertebrates it forms part of the Ndc80 complex."
Q#5197 - 	CGI_10022399	superfamily	247724	10	170	8.28E-108	309.241	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5199 - 	CGI_10022401	superfamily	241583	124	277	5.17E-35	133.51	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#5199 - 	CGI_10022401	superfamily	245321	297	374	9.43E-32	120.038	cl10507	Disintegrin superfamily	 - 	 - 	Disintegrin; Disintegrin.  
Q#5199 - 	CGI_10022401	superfamily	246968	375	472	2.65E-28	112.453	cl15456	ADAM_CR superfamily	C	 - 	ADAM cysteine-rich; ADAMs are membrane-anchored proteases that proteolytically modify cell surface and extracellular matrix (ECM) in order to alter cell behaviour. It has been shown that the cysteine-rich domain of ADAM13 regulates the protein's metalloprotease activity.
Q#5199 - 	CGI_10022401	superfamily	216572	74	102	7.69E-06	45.3435	cl03265	Pep_M12B_propep superfamily	NC	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#5201 - 	CGI_10022405	superfamily	248097	65	170	2.67E-18	76.9202	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#5202 - 	CGI_10022406	superfamily	243035	15	124	2.92E-23	89.9865	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5202 - 	CGI_10022406	superfamily	243035	141	179	1.74E-05	41.0662	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5203 - 	CGI_10022407	superfamily	248097	1	86	5.00E-10	51.497	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#5204 - 	CGI_10026995	superfamily	214531	604	644	5.66E-09	53.7597	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5204 - 	CGI_10026995	superfamily	214531	122	165	1.81E-08	52.2189	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5204 - 	CGI_10026995	superfamily	215683	580	619	3.16E-06	45.6239	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#5204 - 	CGI_10026995	superfamily	214531	167	208	5.98E-06	44.9001	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5204 - 	CGI_10026995	superfamily	215683	93	139	0.00500391	35.9939	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#5205 - 	CGI_10026996	superfamily	241874	11	542	0	778.779	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#5206 - 	CGI_10026997	superfamily	241570	412	528	2.48E-20	87.3813	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#5207 - 	CGI_10026998	superfamily	243072	100	224	1.23E-35	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5207 - 	CGI_10026998	superfamily	243072	198	353	5.70E-35	131.737	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5207 - 	CGI_10026998	superfamily	243072	34	158	5.82E-33	125.959	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5207 - 	CGI_10026998	superfamily	243072	294	414	4.60E-31	120.566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5209 - 	CGI_10027000	superfamily	241578	185	342	3.26E-45	160.92	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5209 - 	CGI_10027000	superfamily	245213	671	706	3.79E-09	54.1798	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5209 - 	CGI_10027000	superfamily	245213	632	668	3.79E-09	54.1798	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5209 - 	CGI_10027000	superfamily	245213	594	629	2.27E-08	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5209 - 	CGI_10027000	superfamily	245213	556	592	4.00E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5209 - 	CGI_10027000	superfamily	245213	482	516	1.75E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5209 - 	CGI_10027000	superfamily	243119	822	869	3.01E-08	51.6757	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#5209 - 	CGI_10027000	superfamily	245213	518	540	0.0051631	36.0708	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5209 - 	CGI_10027000	superfamily	243119	770	817	0.0097878	35.1122	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#5211 - 	CGI_10027002	superfamily	242891	26	161	3.30E-57	177.812	cl02117	ORMDL superfamily	 - 	 - 	"ORMDL family; Evidence form suggests that ORMDLs are involved in protein folding in the ER. Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1)."
Q#5212 - 	CGI_10027003	superfamily	241884	1	157	3.34E-92	268.727	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#5213 - 	CGI_10027004	superfamily	241567	162	428	6.43E-44	155.066	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#5214 - 	CGI_10027005	superfamily	247941	117	243	1.12E-11	60.8124	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#5215 - 	CGI_10027006	superfamily	241570	688	799	2.31E-24	100.478	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#5215 - 	CGI_10027006	superfamily	219619	562	611	6.97E-11	60.2991	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#5215 - 	CGI_10027006	superfamily	197509	34	75	0.00580622	36.3921	cl09965	PAC superfamily	 - 	 - 	Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Q#5218 - 	CGI_10027009	superfamily	248264	154	318	2.16E-49	163.947	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#5218 - 	CGI_10027009	superfamily	222263	63	165	4.70E-10	55.4017	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#5220 - 	CGI_10027011	superfamily	217956	242	394	6.92E-34	124.445	cl04443	PDCD2_C superfamily	 - 	 - 	"Programmed cell death protein 2, C-terminal putative domain; Programmed cell death protein 2, C-terminal putative domain.  "
Q#5222 - 	CGI_10027013	superfamily	245225	474	688	8.62E-08	54.0517	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#5222 - 	CGI_10027013	superfamily	247986	186	288	3.79E-06	47.753	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#5222 - 	CGI_10027013	superfamily	247986	718	797	9.99E-05	43.5158	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#5222 - 	CGI_10027013	superfamily	197504	885	995	0.000910305	39.1949	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#5223 - 	CGI_10027014	superfamily	241802	33	334	6.06E-97	292.469	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#5224 - 	CGI_10027015	superfamily	246598	232	446	4.85E-102	308.134	cl13996	MPN superfamily	C	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#5224 - 	CGI_10027015	superfamily	241645	5	76	0.00735452	34.4234	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#5224 - 	CGI_10027015	superfamily	147282	125	264	6.17E-68	215.648	cl04889	zf-NPL4 superfamily	 - 	 - 	"NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. This region of the protein contains possibly two zinc binding motifs (Bateman A pers. obs.). Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing."
Q#5227 - 	CGI_10027018	superfamily	243061	17	118	1.74E-38	127.458	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5228 - 	CGI_10027019	superfamily	248097	15	53	3.02E-08	45.3338	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#5231 - 	CGI_10027022	superfamily	241763	90	336	1.39E-139	398.567	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#5231 - 	CGI_10027022	superfamily	203856	29	73	2.01E-12	61.0676	cl06937	Propeptide_C1 superfamily	 - 	 - 	Peptidase family C1 propeptide; This motif is found at the N terminal of some members of the Peptidase_C1 family (pfam00112) and is involved in activation of this peptidase.
Q#5233 - 	CGI_10027024	superfamily	247802	242	437	7.18E-97	295.958	cl17248	RIO superfamily	 - 	 - 	"RIO kinase family, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They function as non-ribosomal factors necessary for late 18S rRNA processing. RIO1 is also required for proper cell cycle progression and chromosome maintenance. The biological substrates for RIO kinases are still unknown."
Q#5237 - 	CGI_10027028	superfamily	247905	462	617	8.85E-13	66.8776	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#5237 - 	CGI_10027028	superfamily	247805	250	406	8.40E-11	61.1992	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#5237 - 	CGI_10027028	superfamily	214946	728	932	4.00E-32	128.245	cl15345	Sec63 superfamily	C	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#5239 - 	CGI_10027030	superfamily	247949	16	379	7.49E-173	498.773	cl17395	TAF6 superfamily	 - 	 - 	"TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure.  TAF6 is a shared subunit of histone acetyltransferase complex SAGA and TFIID complexes. TAF6 domain interacts with TAF9 and makes a novel histone-like heterodimer that is structurally related to histones H4 and H3. TAF6 may also interact with the downstream core promoter element (DPE)."
Q#5240 - 	CGI_10027031	superfamily	245599	258	434	5.02E-36	131.576	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#5240 - 	CGI_10027031	superfamily	207662	110	203	6.59E-35	125.636	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#5242 - 	CGI_10027033	superfamily	247824	49	309	2.33E-10	59.5455	cl17270	APH_ChoK_like superfamily	 - 	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#5243 - 	CGI_10027034	superfamily	247792	60	110	3.36E-06	45.1292	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5243 - 	CGI_10027034	superfamily	241563	206	237	0.000204361	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5243 - 	CGI_10027034	superfamily	221533	261	337	0.00196906	36.906	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#5244 - 	CGI_10027035	superfamily	241599	195	247	2.81E-17	74.202	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#5245 - 	CGI_10027036	superfamily	243058	1135	1237	3.17E-09	56.5539	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5245 - 	CGI_10027036	superfamily	245201	3	254	7.97E-80	264.36	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5246 - 	CGI_10027037	superfamily	247724	33	270	1.17E-06	46.6808	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5248 - 	CGI_10027039	superfamily	248247	25	450	1.00E-124	380.797	cl17693	Integrin_beta superfamily	 - 	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#5248 - 	CGI_10027039	superfamily	219669	616	679	0.00593744	35.8316	cl06832	Integrin_B_tail superfamily	C	 - 	Integrin beta tail domain; This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
Q#5249 - 	CGI_10027040	superfamily	241750	2	182	3.73E-33	119.986	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#5250 - 	CGI_10004940	superfamily	247692	81	708	0	944.351	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#5252 - 	CGI_10004942	superfamily	246723	55	145	4.85E-32	123.953	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#5254 - 	CGI_10004944	superfamily	245601	91	262	6.59E-30	111.26	cl11399	HP superfamily	 - 	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#5256 - 	CGI_10004946	superfamily	241613	41	75	2.58E-09	50.283	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5256 - 	CGI_10004946	superfamily	241613	1	35	1.39E-07	45.6606	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5257 - 	CGI_10004947	superfamily	214565	34	95	0.00400452	32.5345	cl18312	VWC_out superfamily	 - 	 - 	von Willebrand factor (vWF) type C domain; von Willebrand factor (vWF) type C domain.  
Q#5258 - 	CGI_10004948	superfamily	241636	5	174	1.25E-61	198.966	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#5260 - 	CGI_10017553	superfamily	241574	165	302	1.63E-66	207.846	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#5260 - 	CGI_10017553	superfamily	241626	5	121	1.98E-28	107.368	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#5261 - 	CGI_10017554	superfamily	243072	36	129	2.05E-24	92.0614	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5262 - 	CGI_10017555	superfamily	241622	606	689	7.07E-18	81.459	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5262 - 	CGI_10017555	superfamily	241622	748	835	6.17E-12	64.125	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5262 - 	CGI_10017555	superfamily	241622	392	466	0.000286091	41.0131	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5262 - 	CGI_10017555	superfamily	152488	125	282	2.39E-25	104.998	cl13485	DUF3534 superfamily	 - 	 - 	Domain of unknown function (DUF3534); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 150 amino acids in length. This domain is found associated with pfam00595. This domain has a conserved GILD sequence motif.
Q#5264 - 	CGI_10017557	superfamily	247724	18	176	6.11E-126	354.021	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5266 - 	CGI_10017559	superfamily	215647	209	477	1.04E-63	211.313	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#5266 - 	CGI_10017559	superfamily	243029	49	112	1.18E-21	89.3321	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#5266 - 	CGI_10017559	superfamily	215647	131	191	2.83E-16	77.6488	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#5268 - 	CGI_10017563	superfamily	242095	343	603	3.41E-67	220.455	cl00793	DUF92 superfamily	 - 	 - 	Integral membrane protein DUF92; Members of this family have several predicted transmembrane helices. The function of these prokaryotic proteins is unknown.
Q#5270 - 	CGI_10017565	superfamily	246921	237	293	6.14E-09	53.1481	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#5270 - 	CGI_10017565	superfamily	246921	169	230	7.09E-06	44.2885	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#5272 - 	CGI_10017567	superfamily	217007	48	352	4.30E-65	210.919	cl11995	Syja_N superfamily	C	 - 	SacI homology domain; This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
Q#5274 - 	CGI_10017570	superfamily	241547	15	260	2.41E-80	256.056	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5274 - 	CGI_10017570	superfamily	241547	284	499	4.20E-79	252.589	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5274 - 	CGI_10017570	superfamily	241547	576	592	0.00445609	37.6476	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5277 - 	CGI_10001261	superfamily	245864	54	288	3.37E-51	176.315	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#5278 - 	CGI_10018493	superfamily	241564	152	220	2.73E-29	108.122	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#5278 - 	CGI_10018493	superfamily	241564	21	88	1.57E-20	83.8543	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#5278 - 	CGI_10018493	superfamily	247792	303	341	0.000153156	38.966	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5279 - 	CGI_10018494	superfamily	241564	142	210	8.20E-25	95.0251	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#5279 - 	CGI_10018494	superfamily	241564	21	88	2.88E-20	82.3135	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#5279 - 	CGI_10018494	superfamily	247792	243	281	0.00799904	33.5732	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5280 - 	CGI_10018495	superfamily	220656	39	153	1.12E-39	131.991	cl10939	Erf4 superfamily	 - 	 - 	Golgin subfamily A member 7/ERF4 family; This family of proteins includes Golgin subfamily A member 7 proteins as well as Ras modification protein ERF4.
Q#5284 - 	CGI_10018499	superfamily	247787	112	396	0	586.553	cl17233	RecA-like_NTPases superfamily	 - 	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#5284 - 	CGI_10018499	superfamily	215848	412	503	2.74E-19	83.4833	cl08258	ATP-synt_ab_C superfamily	 - 	 - 	"ATP synthase alpha/beta chain, C terminal domain; ATP synthase alpha/beta chain, C terminal domain.  "
Q#5284 - 	CGI_10018499	superfamily	217261	44	110	3.65E-09	53.6832	cl18399	ATP-synt_ab_N superfamily	 - 	 - 	"ATP synthase alpha/beta family, beta-barrel domain; This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella."
Q#5286 - 	CGI_10018501	superfamily	219738	120	221	6.46E-22	91.3322	cl06980	Anillin superfamily	 - 	 - 	"Cell division protein anillin; Anillin is a protein involved in septin organisation during cell division. It is an actin binding protein that is localised to the cleavage furrow, and it maintains the localisation of active myosin, which ensures the spatial control of concerted contraction during cytokinesis."
Q#5286 - 	CGI_10018501	superfamily	247725	309	414	3.49E-12	63.1533	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5286 - 	CGI_10018501	superfamily	241602	50	103	0.000232239	39.0318	cl00087	HR1 superfamily	 - 	 - 	"Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases; The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and Rho-associated kinase (ROCK). Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 domains may occur in repeat arrangements (PKN contains three HR1 domains), separated by a short linker region."
Q#5290 - 	CGI_10018505	superfamily	243074	959	996	2.90E-09	54.4349	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#5292 - 	CGI_10018507	superfamily	216056	8	146	1.67E-43	155.931	cl08279	Peptidase_M16 superfamily	 - 	 - 	Insulinase (Peptidase family M16); Insulinase (Peptidase family M16).  
Q#5292 - 	CGI_10018507	superfamily	218490	171	350	3.09E-22	96.0063	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#5292 - 	CGI_10018507	superfamily	218490	705	887	3.14E-15	75.2055	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#5293 - 	CGI_10018508	superfamily	241555	682	902	2.78E-118	361.169	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#5293 - 	CGI_10018508	superfamily	241547	390	622	1.07E-44	161.682	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5293 - 	CGI_10018508	superfamily	241547	62	187	2.07E-23	100.05	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5293 - 	CGI_10018508	superfamily	241547	232	272	1.09E-06	49.1923	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5293 - 	CGI_10018508	superfamily	241547	248	336	0.00973974	37.2624	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5294 - 	CGI_10018509	superfamily	245208	65	434	0	575.371	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#5297 - 	CGI_10018512	superfamily	214507	93	146	0.00057949	36.6392	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#5299 - 	CGI_10018514	superfamily	243035	20	136	5.85E-18	75.3489	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5300 - 	CGI_10018515	superfamily	243035	2	105	1.08E-22	86.1345	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5301 - 	CGI_10018516	superfamily	243035	451	569	2.07E-23	96.5349	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5301 - 	CGI_10018516	superfamily	243035	603	715	3.08E-18	81.8973	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5301 - 	CGI_10018516	superfamily	243035	333	433	2.17E-16	76.5045	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5301 - 	CGI_10018516	superfamily	243035	117	209	6.29E-10	57.2445	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5301 - 	CGI_10018516	superfamily	243035	15	141	6.43E-19	83.8933	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5302 - 	CGI_10018517	superfamily	225324	686	845	0.00763769	38.5004	cl11972	COG2604 superfamily	N	 - 	Uncharacterized protein conserved in bacteria [Function unknown]
Q#5304 - 	CGI_10018519	superfamily	241766	23	265	5.60E-94	303.22	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#5305 - 	CGI_10018520	superfamily	241592	62	88	0.00446582	33.0703	cl00074	H2A superfamily	N	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#5306 - 	CGI_10018521	superfamily	203029	72	206	9.51E-81	247.938	cl18233	GRASP55_65 superfamily	 - 	 - 	"GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain."
Q#5306 - 	CGI_10018521	superfamily	203029	15	101	1.68E-22	92.3176	cl18233	GRASP55_65 superfamily	N	 - 	"GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain."
Q#5307 - 	CGI_10018522	superfamily	215859	513	717	2.31E-56	192.046	cl18347	Peptidase_S9 superfamily	 - 	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#5309 - 	CGI_10018524	superfamily	244859	26	153	6.52E-06	44.4597	cl08171	HtrL_YibB superfamily	N	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#5312 - 	CGI_10007812	superfamily	243061	135	238	1.04E-35	130.54	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5312 - 	CGI_10007812	superfamily	214531	356	399	1.45E-08	51.8337	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5312 - 	CGI_10007812	superfamily	214531	537	578	6.29E-08	49.9077	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5312 - 	CGI_10007812	superfamily	214531	579	621	7.31E-06	44.1297	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5312 - 	CGI_10007812	superfamily	214531	450	490	0.00048674	38.7369	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5312 - 	CGI_10007812	superfamily	214531	497	534	0.00074875	37.9665	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5312 - 	CGI_10007812	superfamily	214531	274	311	0.00417239	35.6553	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5312 - 	CGI_10007812	superfamily	214531	328	354	0.0062425	35.2701	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#5314 - 	CGI_10007814	superfamily	243134	28	152	1.64E-29	109.661	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#5314 - 	CGI_10007814	superfamily	243134	171	294	9.21E-24	93.8679	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#5316 - 	CGI_10007816	superfamily	243134	36	159	4.40E-33	119.291	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#5316 - 	CGI_10007816	superfamily	243134	191	293	1.73E-25	98.8755	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#5317 - 	CGI_10007817	superfamily	243134	31	154	1.87E-33	120.062	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#5317 - 	CGI_10007817	superfamily	243134	169	287	4.10E-29	108.506	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#5318 - 	CGI_10007818	superfamily	247684	45	250	5.95E-36	135.868	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#5318 - 	CGI_10007818	superfamily	247724	12	45	4.91E-06	44.7542	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5319 - 	CGI_10007819	superfamily	245323	310	540	3.56E-80	267.572	cl10511	Beach superfamily	 - 	 - 	"BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins."
Q#5319 - 	CGI_10007819	superfamily	243092	1533	1782	1.42E-33	133.229	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5320 - 	CGI_10007820	superfamily	241622	157	225	2.71E-10	58.347	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5321 - 	CGI_10007821	superfamily	247792	206	249	0.000167588	38.1956	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5321 - 	CGI_10007821	superfamily	202367	2	164	9.20E-32	116.485	cl18226	3HCDH_N superfamily	 - 	 - 	"3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda crystallin."
Q#5322 - 	CGI_10007822	superfamily	220679	135	274	8.22E-09	53.0997	cl18567	Methyltransf_16 superfamily	 - 	 - 	Putative methyltransferase; Putative methyltransferase.  
Q#5323 - 	CGI_10007823	superfamily	243555	27	215	0.000981595	38.9114	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#5325 - 	CGI_10003572	superfamily	241578	302	479	5.04E-46	163.155	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5325 - 	CGI_10003572	superfamily	207701	57	174	2.32E-31	120.092	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#5325 - 	CGI_10003572	superfamily	148333	679	860	8.15E-11	61.143	cl05947	ITI_HC_C superfamily	 - 	 - 	"Inter-alpha-trypsin inhibitor heavy chain C-terminus; This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix. All family members contain the pfam00092 domain."
Q#5326 - 	CGI_10003573	superfamily	241868	153	241	1.91E-18	78.5627	cl00447	Nudix_Hydrolase superfamily	C	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#5327 - 	CGI_10003574	superfamily	152704	309	543	6.51E-116	346.384	cl13675	zf-CpG_bind_C superfamily	 - 	 - 	"CpG binding protein zinc finger C terminal domain; This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA."
Q#5327 - 	CGI_10003574	superfamily	202085	123	162	1.65E-13	65.8446	cl03401	zf-CXXC superfamily	 - 	 - 	"CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR."
Q#5327 - 	CGI_10003574	superfamily	247999	30	74	1.42E-07	48.7474	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#5328 - 	CGI_10003575	superfamily	248012	62	191	1.84E-10	54.9721	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#5329 - 	CGI_10003576	superfamily	248012	103	216	5.22E-11	57.2833	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#5330 - 	CGI_10003577	superfamily	248012	13	142	1.23E-10	54.9721	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#5337 - 	CGI_10023702	superfamily	241832	25	147	3.03E-31	113.404	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#5341 - 	CGI_10023706	superfamily	245864	1	402	2.34E-93	313.061	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#5341 - 	CGI_10023706	superfamily	244881	1404	1731	9.67E-53	189.711	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#5341 - 	CGI_10023706	superfamily	203720	1851	1943	5.74E-19	84.9073	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#5341 - 	CGI_10023706	superfamily	216731	539	631	1.80E-17	80.7659	cl12258	A2M_N superfamily	 - 	 - 	MG2 domain; This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin.
Q#5341 - 	CGI_10023706	superfamily	215788	1160	1253	6.98E-15	72.9823	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#5342 - 	CGI_10023707	superfamily	246680	1034	1082	0.00017526	41.167	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#5342 - 	CGI_10023707	superfamily	219405	175	342	0.00443099	39.1154	cl06450	PCEMA1 superfamily	N	 - 	Acidic phosphoprotein precursor PCEMA1; This family consists of several acidic phosphoprotein precursor PCEMA1 sequences which appear to be found exclusively in Plasmodium chabaudi. PCEMA1 is an antigen that is associated with the membrane of the infected erythrocyte throughout the entire intraerythrocytic cycle. The exact function of this family is unclear.
Q#5342 - 	CGI_10023707	superfamily	246680	609	681	0.00788726	35.8645	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#5343 - 	CGI_10023708	superfamily	149414	1	54	1.33E-18	81.1638	cl07091	TRP_2 superfamily	 - 	 - 	Transient receptor ion channel II; This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023).
Q#5344 - 	CGI_10023709	superfamily	216897	8	86	1.13E-28	103.53	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#5344 - 	CGI_10023709	superfamily	216897	105	183	1.02E-27	100.834	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#5345 - 	CGI_10023710	superfamily	216897	30	101	7.79E-21	81.9589	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#5346 - 	CGI_10023711	superfamily	222150	243	267	0.00192984	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5346 - 	CGI_10023711	superfamily	246975	231	251	0.00827773	33.4745	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#5347 - 	CGI_10023712	superfamily	206040	36	220	4.13E-115	329.177	cl16444	NUDIX_2 superfamily	 - 	 - 	"Nucleotide hydrolase; Nudix hydrolases are found in all classes of organism and hydrolyse a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, di-nucleoside and diphospho-inositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity."
Q#5348 - 	CGI_10023713	superfamily	242793	364	523	2.01E-70	225.78	cl01947	MT-A70 superfamily	 - 	 - 	"MT-A70; MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A methyl-transferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs."
Q#5349 - 	CGI_10023714	superfamily	243077	3	56	3.56E-16	69.8817	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#5351 - 	CGI_10023716	superfamily	241578	223	387	1.41E-58	203.228	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5351 - 	CGI_10023716	superfamily	241578	25	181	9.69E-34	131.26	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5351 - 	CGI_10023716	superfamily	247097	471	507	0.000260657	42.053	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#5352 - 	CGI_10023717	superfamily	241578	992	1152	4.29E-55	192.121	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5352 - 	CGI_10023717	superfamily	241578	592	752	5.61E-55	191.736	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5352 - 	CGI_10023717	superfamily	241578	326	490	9.03E-48	170.872	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5352 - 	CGI_10023717	superfamily	241578	792	958	2.80E-50	178.249	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5352 - 	CGI_10023717	superfamily	240521	62	281	1.52E-33	137.824	cl18940	Syo1_like superfamily	N	 - 	"Fungal symportin 1 (syo1) and similar proteins; This family of eukaryotic proteins includes Saccharomyces cerevisiae Ydl063c and Chaetomium thermophilum Syo1, which mediate the co-import of two ribosomal proteins, Rpl5 and Rpl11 (which both interact with 5S rRNA) into the nucleus. Import precedes their association with rRNA and subsequent ribosome assembly in the nucleolus. The primary structure of syo1 is a mixture of Armadillo- (ARM, N-terminal part of syo1) and HEAT-repeats (C-terminal part of syo1)."
Q#5352 - 	CGI_10023717	superfamily	246918	511	562	3.24E-16	76.0863	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5352 - 	CGI_10023717	superfamily	247097	1466	1501	0.000200647	41.6678	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#5352 - 	CGI_10023717	superfamily	247097	2118	2152	0.00619077	36.9737	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#5352 - 	CGI_10023717	superfamily	248289	1739	1797	0.00811917	36.7252	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#5352 - 	CGI_10023717	superfamily	247097	2006	2040	0.00819115	36.6602	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#5353 - 	CGI_10023718	superfamily	215647	216	458	3.49E-39	143.133	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#5353 - 	CGI_10023718	superfamily	243029	147	203	1.57E-11	60.4421	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#5354 - 	CGI_10023719	superfamily	145416	106	254	2.78E-79	238.322	cl03502	PA28_beta superfamily	 - 	 - 	Proteasome activator pa28 beta subunit; PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the beta subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.
Q#5354 - 	CGI_10023719	superfamily	145415	17	71	1.31E-11	58.0596	cl03501	PA28_alpha superfamily	 - 	 - 	Proteasome activator pa28 alpha subunit; PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the alpha subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.
Q#5356 - 	CGI_10023721	superfamily	216731	137	232	1.10E-23	98.0999	cl12258	A2M_N superfamily	 - 	 - 	MG2 domain; This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin.
Q#5356 - 	CGI_10023721	superfamily	248289	953	1002	0.0049445	36.7252	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#5359 - 	CGI_10023724	superfamily	241597	98	161	2.20E-15	67.6529	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#5359 - 	CGI_10023724	superfamily	241597	8	75	9.40E-15	65.7269	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#5360 - 	CGI_10023725	superfamily	206037	123	189	1.95E-23	91.1512	cl16442	zf-SAP30 superfamily	 - 	 - 	"SAP30 zinc-finger; SAP30 is a subunit of the histone deacetylase complex, and this domain is a zinc-finger. Solution of the structure shows a novel fold comprising two beta-strands and two alpha-helices with the zinc organising centre showing remote resemblance to the treble clef motif. In silico analysis of the structure revealed a highly conserved surface dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 zn-finger motif indicated a strong preference for nucleic acid substrates. The zinc-finger of SAP3 probably functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 co-repressor complex."
Q#5360 - 	CGI_10023725	superfamily	206038	212	262	5.90E-23	89.2364	cl16443	SAP30_Sin3_bdg superfamily	 - 	 - 	Sin3 binding region of histone deacetylase complex subunit SAP30; This C-terminal domain of the SAP30 proteins appears to be the binding region for Sin3.
Q#5361 - 	CGI_10023726	superfamily	246598	7	271	3.81E-143	405.821	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#5362 - 	CGI_10023727	superfamily	242881	8	184	6.78E-117	337.623	cl02099	CK_II_beta superfamily	 - 	 - 	Casein kinase II regulatory subunit; Casein kinase II regulatory subunit.  
Q#5363 - 	CGI_10023728	superfamily	206630	433	534	3.94E-31	119.762	cl16900	NFRKB_winged superfamily	 - 	 - 	NFRKB Winged Helix-like; This domain covers regions 370-495 of human nuclear factor related to kappaB binding (NFRKB) protein.
Q#5364 - 	CGI_10023729	superfamily	241874	46	624	0	583.372	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#5376 - 	CGI_10001571	superfamily	243175	88	210	1.34E-68	209.725	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#5376 - 	CGI_10001571	superfamily	241832	4	78	3.23E-32	114.273	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#5378 - 	CGI_10024023	superfamily	243072	823	948	1.76E-36	135.589	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5378 - 	CGI_10024023	superfamily	243072	988	1113	7.59E-36	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5378 - 	CGI_10024023	superfamily	243072	745	882	6.55E-31	119.411	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5378 - 	CGI_10024023	superfamily	243072	960	988	0.000247807	40.23	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5380 - 	CGI_10024025	superfamily	247999	178	222	8.96E-10	53.755	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#5382 - 	CGI_10024027	superfamily	243066	98	189	7.38E-29	108.794	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#5382 - 	CGI_10024027	superfamily	219619	389	459	3.72E-11	59.1435	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#5385 - 	CGI_10024030	superfamily	246680	2	60	6.75E-06	43.7296	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#5388 - 	CGI_10024033	superfamily	246616	73	332	2.07E-28	112.4	cl14105	MetH superfamily	 - 	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#5389 - 	CGI_10024034	superfamily	248097	5	127	3.75E-23	88.4762	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#5391 - 	CGI_10024036	superfamily	247057	323	371	0.00611668	34.4657	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#5392 - 	CGI_10024037	superfamily	203324	57	174	5.06E-57	181.295	cl18240	UEV superfamily	 - 	 - 	"UEV domain; This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic transformation and tumorigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but that this gene is not a tumour suppressor for sporadic forms of breast cancer. This family is related to the ubiquitin conjugating enzymes."
Q#5392 - 	CGI_10024037	superfamily	247057	240	282	0.00197856	35.3489	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#5393 - 	CGI_10024038	superfamily	152683	72	170	5.07E-07	46.8973	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#5394 - 	CGI_10024039	superfamily	215647	786	935	3.13E-11	63.3964	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#5394 - 	CGI_10024039	superfamily	243029	196	241	9.65E-08	50.4269	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#5394 - 	CGI_10024039	superfamily	245814	402	490	0.000361267	40.1813	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5394 - 	CGI_10024039	superfamily	245814	108	189	0.00154451	38.2553	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5396 - 	CGI_10024041	superfamily	152683	111	212	2.11E-11	61.1497	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#5397 - 	CGI_10024042	superfamily	152683	2	95	2.69E-08	46.8973	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#5398 - 	CGI_10024043	superfamily	248458	329	508	3.41E-11	63.4869	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5398 - 	CGI_10024043	superfamily	248458	158	221	0.0080562	37.2933	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5399 - 	CGI_10024044	superfamily	203446	112	177	1.47E-14	70.0611	cl05764	Sec2p superfamily	 - 	 - 	"GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion."
Q#5399 - 	CGI_10024044	superfamily	243092	396	593	7.52E-06	46.9444	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5400 - 	CGI_10024045	superfamily	183292	40	72	0.00762391	35.5676	cl18135	PRK11728 superfamily	C	 - 	hydroxyglutarate oxidase; Provisional
Q#5401 - 	CGI_10024046	superfamily	218493	218	361	9.12E-35	125.933	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#5405 - 	CGI_10024051	superfamily	204914	79	228	1.15E-43	156.285	cl13809	Condensin2nSMC superfamily	 - 	 - 	"Condensin II non structural maintenance of chromosomes subunit; This domain family is found in eukaryotes, and is approximately 150 amino acids in length. This family is part of a non-SMC subunit of condensin II which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II."
Q#5409 - 	CGI_10024055	superfamily	241596	46	86	1.95E-05	41.0455	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#5410 - 	CGI_10024056	superfamily	243205	97	388	2.63E-174	493.37	cl02823	phosphagen_kinases superfamily	 - 	 - 	"Phosphagen (guanidino) kinases; Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) and hypotaurocyamine kinase (HTK). The majority of bacterial phosphagen kinases appear to lack the N-terminal domain and have not been functionally characterized."
Q#5412 - 	CGI_10024058	superfamily	110440	310	336	7.02E-05	40.4689	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#5414 - 	CGI_10001888	superfamily	217311	1	351	3.26E-112	342.009	cl18402	DUF229 superfamily	N	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#5417 - 	CGI_10001510	superfamily	243061	41	141	5.22E-36	122.451	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5417 - 	CGI_10001510	superfamily	243061	3	37	2.41E-10	53.885	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5418 - 	CGI_10001511	superfamily	243061	150	191	3.42E-18	76.2266	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5420 - 	CGI_10002284	superfamily	247805	31	129	1.84E-11	57.3472	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#5422 - 	CGI_10018012	superfamily	247856	18	74	8.76E-16	65.6469	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5423 - 	CGI_10018013	superfamily	110440	188	215	0.00334021	33.9205	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#5424 - 	CGI_10018014	superfamily	242523	80	230	4.36E-10	58.0589	cl01472	DUF2236 superfamily	C	 - 	"Uncharacterized protein conserved in bacteria (DUF2236); This domain, found in various hypothetical bacterial proteins, has no known function. This family contains a highly conserved arginine and histidine that may be active site residues for an as yet unknown catalytic activity."
Q#5427 - 	CGI_10018017	superfamily	247724	5	152	1.78E-79	236.457	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5429 - 	CGI_10018019	superfamily	217206	216	377	5.68E-72	229.879	cl03682	SKIP_SNW superfamily	 - 	 - 	SKIP/SNW domain; This domain is found in chromatin proteins.
Q#5430 - 	CGI_10018020	superfamily	248067	138	254	8.91E-43	152.362	cl17513	ABC1 superfamily	 - 	 - 	"ABC1 family; This family includes ABC1 from yeast and AarF from E. coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex and E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins."
Q#5430 - 	CGI_10018020	superfamily	248067	528	644	3.34E-42	150.821	cl17513	ABC1 superfamily	 - 	 - 	"ABC1 family; This family includes ABC1 from yeast and AarF from E. coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex and E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins."
Q#5431 - 	CGI_10018021	superfamily	222439	1	192	1.77E-61	195.921	cl16461	Glyco_transf_49 superfamily	N	 - 	"Glycosyl-transferase for dystroglycan; This glycosyl-transferase brings about the glycosylation of the alpha-dystroglycan subunit. Dystroglycan is an integral member of the skeletal muscular dystrophin glycoprotein complex, which links dystrophin to proteins in the extracellular matrix."
Q#5432 - 	CGI_10018022	superfamily	243034	832	929	9.01E-14	68.9459	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5432 - 	CGI_10018022	superfamily	243034	762	861	3.11E-13	67.4052	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5432 - 	CGI_10018022	superfamily	241568	169	233	1.99E-11	61.3248	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#5432 - 	CGI_10018022	superfamily	243034	702	787	2.13E-08	53.1528	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5432 - 	CGI_10018022	superfamily	243034	904	978	8.15E-05	41.982	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5432 - 	CGI_10018022	superfamily	241568	42	95	0.000197334	40.524	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#5432 - 	CGI_10018022	superfamily	241568	243	300	0.00138864	38.2128	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#5433 - 	CGI_10018023	superfamily	243179	124	249	4.95E-27	104.438	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#5435 - 	CGI_10018025	superfamily	222090	105	309	7.19E-13	66.1422	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#5436 - 	CGI_10018026	superfamily	241600	77	290	1.20E-78	240.22	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#5437 - 	CGI_10018027	superfamily	241600	66	279	3.23E-93	277.199	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#5438 - 	CGI_10018028	superfamily	243119	59	99	0.000221554	35.8826	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#5439 - 	CGI_10018029	superfamily	246908	18	104	1.51E-31	115.317	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#5439 - 	CGI_10018029	superfamily	245201	133	381	9.48E-153	434.198	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5440 - 	CGI_10018030	superfamily	241584	61	151	2.87E-14	65.9807	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5440 - 	CGI_10018030	superfamily	245814	176	236	0.00241415	35.1575	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5440 - 	CGI_10018030	superfamily	216647	7	53	2.86E-07	46.7761	cl03309	DB superfamily	N	 - 	"DB module; This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657."
Q#5443 - 	CGI_10018033	superfamily	154924	105	211	3.42E-38	129.817	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#5443 - 	CGI_10018033	superfamily	154924	32	91	1.28E-21	86.1964	cl02467	C4 superfamily	N	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#5447 - 	CGI_10018037	superfamily	154924	124	204	3.48E-28	104.686	cl02467	C4 superfamily	C	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#5449 - 	CGI_10018039	superfamily	154924	1375	1477	8.68E-49	170.94	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#5449 - 	CGI_10018039	superfamily	154924	1491	1597	7.59E-38	139.833	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#5452 - 	CGI_10018042	superfamily	154924	1405	1511	2.21E-56	192.897	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#5452 - 	CGI_10018042	superfamily	154924	1512	1627	1.26E-42	153.7	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#5453 - 	CGI_10018043	superfamily	248458	348	524	6.40E-09	56.5533	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5453 - 	CGI_10018043	superfamily	248458	137	238	4.06E-07	50.7753	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5455 - 	CGI_10018045	superfamily	248289	30	86	0.000113784	40.0999	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#5456 - 	CGI_10018046	superfamily	245201	268	456	7.63E-52	177.429	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5456 - 	CGI_10018046	superfamily	246680	9	126	8.44E-23	94.0021	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#5457 - 	CGI_10018047	superfamily	248305	196	573	7.62E-93	296.957	cl17751	Glyco_transf_22 superfamily	 - 	 - 	Alg9-like mannosyltransferase family; Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Q#5457 - 	CGI_10018047	superfamily	248305	42	189	1.44E-43	161.752	cl17751	Glyco_transf_22 superfamily	C	 - 	Alg9-like mannosyltransferase family; Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Q#5458 - 	CGI_10018048	superfamily	243161	4	93	6.84E-15	65.5342	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#5459 - 	CGI_10018049	superfamily	248236	72	242	1.22E-16	78.8804	cl17682	PRK07189 superfamily	C	 - 	malonate decarboxylase subunit beta; Reviewed
Q#5459 - 	CGI_10018049	superfamily	247899	344	513	8.55E-11	62.1315	cl17345	AccA superfamily	N	 - 	Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]
Q#5460 - 	CGI_10018050	superfamily	245596	210	427	7.12E-36	133.761	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#5463 - 	CGI_10018053	superfamily	242281	79	350	1.33E-45	159.462	cl01067	Dyp_perox superfamily	N	 - 	Dyp-type peroxidase family; This family of dye-decolourising peroxidases lack a typical heme-binding region.
Q#5464 - 	CGI_10003895	superfamily	243035	792	918	1.43E-14	71.4969	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5464 - 	CGI_10003895	superfamily	216276	681	772	0.000150261	40.9943	cl15639	Activin_recp superfamily	 - 	 - 	"Activin types I and II receptor domain; This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box."
Q#5465 - 	CGI_10003896	superfamily	217598	437	547	2.63E-50	173.424	cl04130	KCNQ_channel superfamily	N	 - 	KCNQ voltage-gated potassium channel; This family matches to the C-terminal tail of KCNQ type potassium channels.
Q#5465 - 	CGI_10003896	superfamily	219619	218	294	3.50E-12	62.6103	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#5466 - 	CGI_10003897	superfamily	245201	333	582	9.75E-59	197.844	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5466 - 	CGI_10003897	superfamily	245201	1	290	0	569.052	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5467 - 	CGI_10014894	superfamily	243309	1	134	1.39E-28	109.426	cl03119	FpgNei_N superfamily	 - 	 - 	"N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins."
Q#5467 - 	CGI_10014894	superfamily	219199	408	451	1.31E-14	68.1756	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#5467 - 	CGI_10014894	superfamily	115485	157	200	6.61E-09	53.0966	cl06065	H2TH superfamily	NC	 - 	Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.
Q#5467 - 	CGI_10014894	superfamily	219199	360	406	6.62E-07	46.2192	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#5473 - 	CGI_10014900	superfamily	242406	230	370	3.95E-22	91.8841	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#5480 - 	CGI_10009463	superfamily	241571	283	396	3.14E-22	92.4754	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5480 - 	CGI_10009463	superfamily	241571	151	258	5.67E-08	50.8739	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5483 - 	CGI_10009466	superfamily	243109	53	101	1.27E-28	102.252	cl02614	SPRY superfamily	C	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#5485 - 	CGI_10009468	superfamily	215827	68	241	2.47E-38	138.37	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#5487 - 	CGI_10009470	superfamily	245304	160	414	7.44E-179	520.859	cl10459	Peptidases_S8_S53 superfamily	 - 	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#5489 - 	CGI_10009472	superfamily	241680	13	229	4.36E-49	164.007	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#5490 - 	CGI_10009473	superfamily	242046	437	599	2.80E-62	204.796	cl00718	TOPRIM superfamily	 - 	 - 	"Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function."
Q#5490 - 	CGI_10009473	superfamily	190973	323	390	1.23E-17	78.3311	cl04502	TP6A_N superfamily	 - 	 - 	"Type IIB DNA topoisomerase; Type II DNA topoisomerases are ubiquitous enzymes that catalyze the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases. TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP)."
Q#5491 - 	CGI_10009474	superfamily	241749	15	156	1.43E-29	106.701	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#5492 - 	CGI_10002616	superfamily	245213	34	68	5.52E-06	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5492 - 	CGI_10002616	superfamily	245213	71	105	5.52E-06	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5492 - 	CGI_10002616	superfamily	245213	182	216	3.79E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5492 - 	CGI_10002616	superfamily	245213	108	142	8.31E-05	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5492 - 	CGI_10002616	superfamily	245213	293	327	0.000136017	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5492 - 	CGI_10002616	superfamily	245213	145	180	0.000856256	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5492 - 	CGI_10002616	superfamily	245213	219	254	0.0021895	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5492 - 	CGI_10002616	superfamily	245213	256	291	0.00223631	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5494 - 	CGI_10002749	superfamily	247792	215	260	4.58E-11	56.6852	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5494 - 	CGI_10002749	superfamily	222714	15	43	3.11E-06	43.3152	cl16832	zf-RING_3 superfamily	 - 	 - 	zinc-finger; zinc-finger.  
Q#5495 - 	CGI_10002750	superfamily	220796	243	401	8.15E-08	52.3582	cl15661	DUF2454 superfamily	N	 - 	Protein of unknown function (DUF2454); A Schizosaccharomyces pombe member of this family is known to interact with Tel2. Tel2 is a component of the TOR complexes.
Q#5496 - 	CGI_10002751	superfamily	241802	32	339	8.01E-106	315.195	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#5498 - 	CGI_10001934	superfamily	218797	10	236	3.34E-38	136.322	cl05454	Ebp2 superfamily	 - 	 - 	Eukaryotic rRNA processing protein EBP2; This family consists of several Eukaryotic rRNA processing protein EBP2 sequences. Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis. This family also plays a role in chromosome segregation.
Q#5500 - 	CGI_10001936	superfamily	245206	41	346	0	554.999	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#5504 - 	CGI_10002653	superfamily	241832	4	76	1.05E-18	77.2268	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#5504 - 	CGI_10002653	superfamily	243175	89	164	1.54E-13	63.6223	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#5505 - 	CGI_10002654	superfamily	245009	133	261	0.000137742	39.5733	cl09109	NTF2_like superfamily	 - 	 - 	"Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example,  nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and  binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea and eukaryotes."
Q#5506 - 	CGI_10002655	superfamily	243088	19	115	2.13E-10	53.9007	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#5507 - 	CGI_10002656	superfamily	248012	430	571	8.59E-26	103.557	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#5507 - 	CGI_10002656	superfamily	214507	312	371	0.000231547	39.3356	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#5508 - 	CGI_10003344	superfamily	245847	133	174	0.00473519	34.7856	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#5509 - 	CGI_10003345	superfamily	246751	31	330	5.61E-120	351.546	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#5511 - 	CGI_10003347	superfamily	246918	93	145	4.89E-10	57.5967	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	260	310	5.06E-09	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	1138	1188	6.37E-09	54.5151	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	918	968	7.98E-09	54.1299	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	1193	1243	1.05E-08	53.7447	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	480	530	1.32E-08	53.7447	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	536	585	1.79E-08	53.3595	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	1249	1298	2.24E-08	52.9743	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	150	200	2.52E-08	52.5891	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	315	365	3.04E-08	52.5891	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	590	640	6.39E-08	51.4335	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	1084	1133	7.36E-08	51.4335	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	812	860	8.44E-08	51.0483	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	1028	1078	1.15E-07	50.6631	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	370	420	1.52E-07	50.6631	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	755	805	2.44E-07	49.8927	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	645	695	4.19E-07	49.1223	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	425	474	7.45E-07	48.3519	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	1358	1409	9.56E-07	47.9667	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	205	255	9.79E-07	47.9667	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	701	750	1.20E-05	44.8851	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	867	912	1.47E-05	44.4999	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	1303	1353	0.00278421	37.9515	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5511 - 	CGI_10003347	superfamily	246918	973	1000	0.00533752	36.7959	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5512 - 	CGI_10003348	superfamily	193253	303	546	1.87E-20	94.3333	cl15084	MT superfamily	N	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#5512 - 	CGI_10003348	superfamily	193256	7	180	5.85E-12	66.8948	cl18189	AAA_8 superfamily	N	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#5512 - 	CGI_10003348	superfamily	193257	856	1010	8.05E-05	44.9763	cl15086	AAA_9 superfamily	N	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#5514 - 	CGI_10007120	superfamily	247724	9	215	3.43E-22	90.7471	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5515 - 	CGI_10007121	superfamily	243066	27	125	1.11E-21	89.9841	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#5520 - 	CGI_10004025	superfamily	243061	506	606	4.32E-32	121.68	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5520 - 	CGI_10004025	superfamily	243061	403	504	2.72E-31	119.369	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5520 - 	CGI_10004025	superfamily	243061	147	247	1.30E-30	117.443	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5520 - 	CGI_10004025	superfamily	243061	302	400	1.36E-29	114.361	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5520 - 	CGI_10004025	superfamily	243061	715	815	5.41E-25	101.265	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5520 - 	CGI_10004025	superfamily	243061	45	142	2.65E-23	96.257	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5520 - 	CGI_10004025	superfamily	243061	609	712	2.11E-17	79.3082	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5520 - 	CGI_10004025	superfamily	243061	818	911	8.38E-17	77.7674	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#5521 - 	CGI_10004026	superfamily	242565	68	167	5.99E-05	39.4846	cl01535	Repair_PSII superfamily	 - 	 - 	"Repair protein; In plants, this domain plays a role in the photosystem II (PSII) repair cycle. It may be involved in the regulation of synthesis/degradation of the D1 protein of the PSII core and in the assembly of PSII monomers into dimers in the grana stacks. Its function in other organisms is unknown."
Q#5522 - 	CGI_10004027	superfamily	243130	254	286	0.00651757	33.5927	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#5525 - 	CGI_10015726	superfamily	245814	149	207	6.44E-09	52.1063	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5525 - 	CGI_10015726	superfamily	245814	232	303	6.72E-10	54.7578	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5525 - 	CGI_10015726	superfamily	245814	43	127	7.82E-08	49.3079	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5526 - 	CGI_10015727	superfamily	243054	78	274	2.34E-13	70.5523	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5526 - 	CGI_10015727	superfamily	243054	182	390	1.00E-07	53.2184	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5526 - 	CGI_10015727	superfamily	243054	404	603	0.00208863	40.1216	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5526 - 	CGI_10015727	superfamily	243054	1364	1506	0.0025735	39.7364	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5527 - 	CGI_10015728	superfamily	243054	107	250	4.92E-06	46.2848	cl02488	SPEC superfamily	N	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	5401	5610	4.02E-16	80.9527	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	241559	154	257	6.17E-16	78.1215	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#5528 - 	CGI_10015729	superfamily	243054	1494	1703	2.28E-13	72.4783	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	241559	282	386	2.13E-12	67.7211	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#5528 - 	CGI_10015729	superfamily	243054	2773	2981	1.57E-11	66.7004	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	4079	4261	1.77E-11	66.7004	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	4757	4970	1.33E-10	63.6188	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	5186	5399	2.28E-10	62.8484	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	2883	3092	1.35E-09	60.5372	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	3414	3625	2.25E-09	59.7668	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	2456	2669	2.54E-09	59.7668	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	4972	5184	3.33E-09	59.3816	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	5827	6034	4.08E-09	58.9964	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	2671	2865	9.53E-09	57.8408	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	1280	1492	1.21E-08	57.4556	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	4188	4401	4.28E-08	55.9148	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	4542	4755	1.95E-07	53.9888	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	3061	3198	2.50E-07	53.6036	cl02488	SPEC superfamily	N	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	5613	5822	4.96E-07	52.8332	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	3532	3736	7.41E-07	52.0628	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	1953	2132	2.66E-06	50.522	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	3864	4075	7.18E-06	49.3664	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	3322	3403	0.00365939	39.6094	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5528 - 	CGI_10015729	superfamily	243054	1816	2025	0.00896203	40.1216	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#5530 - 	CGI_10015731	superfamily	243179	2	48	4.69E-11	53.9772	cl02781	tetraspanin_LEL superfamily	NC	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#5533 - 	CGI_10015734	superfamily	207662	169	244	5.57E-23	94.9488	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#5533 - 	CGI_10015734	superfamily	245599	816	986	1.56E-14	73.0259	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#5533 - 	CGI_10015734	superfamily	207662	85	162	3.06E-13	66.8292	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#5534 - 	CGI_10015735	superfamily	241563	7	27	0.000740692	37.4588	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5536 - 	CGI_10003949	superfamily	243056	38	255	3.98E-45	158.291	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#5537 - 	CGI_10003950	superfamily	241983	42	349	3.19E-38	141.341	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#5538 - 	CGI_10003951	superfamily	241563	26	55	0.00151068	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5539 - 	CGI_10003109	superfamily	245847	27	142	5.30E-11	56.7419	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#5541 - 	CGI_10003501	superfamily	248264	198	250	1.08E-15	71.1141	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#5541 - 	CGI_10003501	superfamily	243161	4	68	2.69E-08	49.3558	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#5542 - 	CGI_10003706	superfamily	243092	123	206	0.00902331	36.1588	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5543 - 	CGI_10003707	superfamily	241609	131	219	1.50E-26	99.3746	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#5543 - 	CGI_10003707	superfamily	241609	51	133	9.78E-22	86.2779	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#5546 - 	CGI_10003903	superfamily	220695	31	147	0.00211045	37.9435	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#5547 - 	CGI_10003904	superfamily	204985	3	89	6.88E-11	61.4187	cl14987	Chorein_N superfamily	C	 - 	"N-terminal region of Chorein, a TM vesicle-mediated sorter; Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport."
Q#5550 - 	CGI_10003907	superfamily	247941	164	302	6.09E-09	53.1085	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#5551 - 	CGI_10003908	superfamily	177822	102	297	1.61E-10	59.9337	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#5552 - 	CGI_10003909	superfamily	177822	7	215	5.12E-05	42.2145	cl18088	PLN02164 superfamily	 - 	 - 	sulfotransferase
Q#5553 - 	CGI_10003910	superfamily	221997	10	85	5.30E-08	46.2762	cl18631	Complex1_LYR_2 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#5554 - 	CGI_10004560	superfamily	242059	655	866	3.33E-15	76.3478	cl00738	MBOAT superfamily	N	 - 	"MBOAT, membrane-bound O-acyltransferase family; The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue."
Q#5554 - 	CGI_10004560	superfamily	245206	8	108	2.51E-05	45.7229	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#5555 - 	CGI_10004561	superfamily	243156	17	70	2.71E-15	65.484	cl02717	RNA_POL_M_15KD superfamily	 - 	 - 	RNA polymerases M/15 Kd subunit; RNA polymerases M/15 Kd subunit.  
Q#5555 - 	CGI_10004561	superfamily	207668	86	127	4.64E-10	51.1759	cl02609	TFIIS_C superfamily	 - 	 - 	Transcription factor S-II (TFIIS); Transcription factor S-II (TFIIS).  
Q#5558 - 	CGI_10004564	superfamily	222003	194	262	7.71E-07	45.7606	cl17871	Hydrolase_like superfamily	 - 	 - 	HAD-hyrolase-like; HAD-hyrolase-like.  
Q#5559 - 	CGI_10004565	superfamily	147298	1769	1964	1.70E-103	333.333	cl04904	Pecanex_C superfamily	 - 	 - 	Pecanex protein (C-terminus); This family consists of C terminal region of the pecanex protein homologues. The pecanex protein is a maternal-effect neurogenic gene found in Drosophila.
Q#5563 - 	CGI_10004569	superfamily	217473	143	319	1.33E-28	115.925	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#5564 - 	CGI_10002454	superfamily	245230	1	359	0	740.645	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#5565 - 	CGI_10002455	superfamily	245230	52	408	0	784.558	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#5566 - 	CGI_10002456	superfamily	245230	142	275	1.02E-110	330.022	cl10017	Tubulin_FtsZ superfamily	N	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#5566 - 	CGI_10002456	superfamily	245230	2	141	4.76E-105	315.77	cl10017	Tubulin_FtsZ superfamily	C	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#5567 - 	CGI_10002457	superfamily	247755	405	644	5.54E-157	454.69	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#5567 - 	CGI_10002457	superfamily	216049	87	358	3.50E-49	173.626	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#5571 - 	CGI_10013554	superfamily	247905	85	202	2.81E-17	77.278	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#5572 - 	CGI_10013555	superfamily	247805	34	143	5.46E-07	44.6356	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#5575 - 	CGI_10013558	superfamily	245213	147	182	5.26E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	185	221	1.13E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	109	145	1.28E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	603	639	2.21E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	375	410	3.39E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	337	372	3.96E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	451	486	3.99E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	413	448	4.88E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	299	335	5.14E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	223	258	5.75E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	489	525	9.30E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	565	601	1.21E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	261	296	2.33E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	35	69	3.05E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	72	106	9.98E-05	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	245213	527	562	0.000100968	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5575 - 	CGI_10013558	superfamily	221370	770	930	1.59E-06	48.9069	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#5575 - 	CGI_10013558	superfamily	215647	956	1015	0.00038564	41.8253	cl18338	7tm_2 superfamily	NC	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#5576 - 	CGI_10013559	superfamily	243029	35	87	1.01E-05	43.1081	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#5576 - 	CGI_10013559	superfamily	221370	107	267	8.50E-05	42.3585	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#5577 - 	CGI_10013560	superfamily	243124	93	188	1.59E-25	99.8088	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#5578 - 	CGI_10013561	superfamily	247903	215	416	1.20E-43	152.451	cl17349	Peptidase_M54 superfamily	 - 	 - 	"Peptidase family M54, also called archaemetzincins or archaelysins; Peptidase M54 (archaemetzincin or archaelysin) is a zinc-dependent aminopeptidase that contains the consensus zinc-binding sequence HEXXHXXGXXH/D and a conserved Met residue at the active site, and is thus classified as a metzincin. Archaemetzincins, first identified in archaea, are also found in bacteria and eukaryotes, including two human members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1 is mainly found in the liver and heart while AMZ2 is primarily expressed in testis and heart; both have been reported to degrade synthetic substrates and peptides. The Peptidase M54 family contains an extended metzincin concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that a second zinc ion is bound to four cysteines, thus resembling a zinc finger. Phylogenetic analysis of this family reveals a complex evolutionary process involving a series of lateral gene transfer, gene loss and genetic duplication events."
Q#5579 - 	CGI_10013562	superfamily	202894	126	193	2.94E-20	81.113	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#5582 - 	CGI_10004013	superfamily	245010	10	115	3.05E-18	74.9618	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#5583 - 	CGI_10004014	superfamily	241599	122	179	8.68E-19	81.906	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#5584 - 	CGI_10004015	superfamily	241874	3	513	0	751.815	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#5585 - 	CGI_10004016	superfamily	241874	1	178	7.76E-81	252.212	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#5586 - 	CGI_10004017	superfamily	241874	5	184	7.32E-103	309.606	cl00456	SLC5-6-like_sbd superfamily	NC	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#5587 - 	CGI_10006103	superfamily	241739	95	309	2.56E-79	246.688	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#5587 - 	CGI_10006103	superfamily	244928	329	420	2.75E-28	106.741	cl08386	FDX-ACB superfamily	 - 	 - 	Ferredoxin-fold anticodon binding domain; This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold.
Q#5588 - 	CGI_10006104	superfamily	243072	412	529	1.47E-30	117.87	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5588 - 	CGI_10006104	superfamily	243072	470	596	2.60E-22	94.3726	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5588 - 	CGI_10006104	superfamily	243072	580	683	3.53E-11	61.6306	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5588 - 	CGI_10006104	superfamily	241752	784	895	8.25E-28	110.102	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#5588 - 	CGI_10006104	superfamily	241760	71	114	5.46E-10	56.6979	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#5588 - 	CGI_10006104	superfamily	115363	142	214	7.54E-10	56.6114	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#5588 - 	CGI_10006104	superfamily	115363	6	62	8.32E-05	41.5886	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#5591 - 	CGI_10006107	superfamily	241578	31	192	1.90E-46	166.698	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5591 - 	CGI_10006107	superfamily	241578	232	389	4.36E-46	165.542	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5593 - 	CGI_10006109	superfamily	243039	489	591	2.13E-09	55.463	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#5593 - 	CGI_10006109	superfamily	247792	92	139	1.06E-06	46.2848	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5593 - 	CGI_10006109	superfamily	241563	241	270	0.00668268	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5595 - 	CGI_10016233	superfamily	245814	302	375	3.50E-05	41.7059	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5596 - 	CGI_10016234	superfamily	242104	208	277	0.00685346	37.054	cl00803	Cas7_I superfamily	NC	 - 	CRISPR/Cas system-associated RAMP superfamily protein Cas7; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as MJ0381 family
Q#5597 - 	CGI_10016235	superfamily	220692	49	314	1.34E-22	94.5785	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#5599 - 	CGI_10016237	superfamily	147218	22	245	6.50E-69	214.621	cl04854	SIP1 superfamily	 - 	 - 	Survival motor neuron (SMN) interacting protein 1 (SIP1); Survival motor neuron (SMN) interacting protein 1 (SIP1) interacts with SMN protein and plays a crucial role in the biogenesis of spliceosomes. There is evidence that the protein is linked to spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis(ALS) in humans.
Q#5600 - 	CGI_10016238	superfamily	215859	373	575	7.40E-30	116.547	cl18347	Peptidase_S9 superfamily	 - 	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#5604 - 	CGI_10016242	superfamily	241600	1091	1309	3.18E-65	221.345	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#5605 - 	CGI_10016243	superfamily	215733	113	339	4.97E-62	209.729	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#5605 - 	CGI_10016243	superfamily	216063	725	897	1.03E-54	187.826	cl02929	Cation_ATPase_C superfamily	 - 	 - 	"Cation transporting ATPase, C-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices."
Q#5605 - 	CGI_10016243	superfamily	222006	408	492	2.56E-19	84.5814	cl16182	Hydrolase_like2 superfamily	 - 	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#5605 - 	CGI_10016243	superfamily	243244	23	92	7.27E-14	68.3782	cl02930	Cation_ATPase_N superfamily	 - 	 - 	"Cation transporter/ATPase, N-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport."
Q#5605 - 	CGI_10016243	superfamily	226572	615	687	0.00015277	41.7756	cl18761	COG4087 superfamily	N	 - 	Soluble P-type ATPase [General function prediction only]
Q#5606 - 	CGI_10016244	superfamily	247740	10	355	1.31E-124	364.917	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#5607 - 	CGI_10016245	superfamily	187403	109	490	2.19E-173	501.487	cl14649	BRO1_Alix_like superfamily	 - 	 - 	"Protein-interacting Bro1-like domain of mammalian Alix and related domains; This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, HD-PTP, and Brox) and Snf7 (in the case of yeast Bro1, and Rim20). The single domain protein human Brox, and the isolated Bro1-like domains of Alix, HD-PTP and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V) domain, which in the case of Alix, has been shown to be a dimerization domain and to contain a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in this superfamily. Alix, HD-PTP and Bro1 also have a proline-rich region (PRR); the Alix PRR binds multiple partners. Rhophilin-1, and -2, in addition to this Bro1-like domain, have an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This protein has a C-terminal, catalytically inactive tyrosine phosphatase domain."
Q#5607 - 	CGI_10016245	superfamily	241602	21	103	1.96E-36	131.88	cl00087	HR1 superfamily	 - 	 - 	"Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases; The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and Rho-associated kinase (ROCK). Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 domains may occur in repeat arrangements (PKN contains three HR1 domains), separated by a short linker region."
Q#5607 - 	CGI_10016245	superfamily	241622	508	585	7.47E-21	88.0074	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5608 - 	CGI_10016246	superfamily	247038	7	85	3.90E-09	55.1533	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#5608 - 	CGI_10016246	superfamily	246936	103	194	0.002982	37.0848	cl15354	CBS_pair superfamily	C	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#5614 - 	CGI_10016252	superfamily	222150	1495	1519	1.67E-06	47.0013	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5614 - 	CGI_10016252	superfamily	222150	51	76	0.000231244	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5614 - 	CGI_10016252	superfamily	222150	679	703	0.000402703	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5614 - 	CGI_10016252	superfamily	222150	1160	1185	0.00133379	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5616 - 	CGI_10016254	superfamily	216970	1	96	6.11E-42	137.182	cl03529	CBF_beta superfamily	C	 - 	"Core binding factor beta subunit; Core binding factor (CBF) is a heterodimeric transcription factor essential for genetic regulation of hematopoiesis and osteogenesis. The beta subunit enhances DNA-binding ability of the alpha subunit in vitro, and has been show to have a structure related to the OB fold."
Q#5618 - 	CGI_10012241	superfamily	247856	94	144	0.000707837	37.9125	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5620 - 	CGI_10012243	superfamily	216212	465	966	0	655.131	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#5621 - 	CGI_10012244	superfamily	216212	478	979	0	672.465	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#5625 - 	CGI_10012248	superfamily	245213	575	611	6.13E-10	56.1058	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5625 - 	CGI_10012248	superfamily	245213	491	533	3.43E-09	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5625 - 	CGI_10012248	superfamily	245213	452	489	9.23E-09	52.639	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5625 - 	CGI_10012248	superfamily	245213	535	572	1.01E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5625 - 	CGI_10012248	superfamily	110440	363	390	0.000233122	39.6985	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#5627 - 	CGI_10012250	superfamily	241600	27	50	0.00123287	35.6791	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#5629 - 	CGI_10020305	superfamily	194545	49	137	5.10E-64	192.33	cl03131	Dynein_light superfamily	 - 	 - 	Dynein light chain type 1; Dynein light chain type 1.  
Q#5629 - 	CGI_10020305	superfamily	247724	1	58	2.34E-05	40.6078	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5630 - 	CGI_10020306	superfamily	247727	114	192	2.03E-09	53.2027	cl17173	AdoMet_MTases superfamily	N	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#5631 - 	CGI_10020307	superfamily	147539	22	172	8.42E-69	208.791	cl05128	TRAP-delta superfamily	 - 	 - 	"Translocon-associated protein, delta subunit precursor (TRAP-delta); This family consists of several eukaryotic translocon-associated protein, delta subunit precursors (TRAP-delta or SSR-delta). The exact function of this protein is unknown."
Q#5632 - 	CGI_10020308	superfamily	215648	1242	1431	1.15E-19	90.3475	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#5632 - 	CGI_10020308	superfamily	245225	719	1082	4.41E-13	71.8903	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#5632 - 	CGI_10020308	superfamily	245225	395	668	6.89E-09	58.4083	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#5633 - 	CGI_10020309	superfamily	222150	281	306	7.27E-05	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5634 - 	CGI_10020310	superfamily	243082	1176	1507	8.09E-122	389.087	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#5634 - 	CGI_10020310	superfamily	241645	2062	2165	4.61E-34	129.431	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#5635 - 	CGI_10020311	superfamily	245839	357	458	8.55E-16	73.767	cl12020	Anticodon_Ia_like superfamily	C	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#5636 - 	CGI_10020312	superfamily	245201	3	289	0	541.108	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5637 - 	CGI_10020313	superfamily	243146	835	880	5.47E-07	48.0414	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#5637 - 	CGI_10020313	superfamily	198867	645	720	0.000142807	41.5581	cl06652	BACK superfamily	C	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#5637 - 	CGI_10020313	superfamily	243146	886	929	0.00584378	36.2722	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#5638 - 	CGI_10020314	superfamily	248097	86	209	2.75E-19	80.387	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#5639 - 	CGI_10020315	superfamily	248012	1049	1157	5.50E-29	113.442	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#5639 - 	CGI_10020315	superfamily	141623	3	120	5.18E-25	102.774	cl02685	Neuralized superfamily	 - 	 - 	Neuralized; This family contains a conserved region approximately 60 residues long within eukaryotic neuralized and neuralized-like proteins. Neuralized belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the Drosophila nervous system. Some family members contain multiple copies of this region.
Q#5639 - 	CGI_10020315	superfamily	247724	405	524	1.15E-18	85.4655	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5639 - 	CGI_10020315	superfamily	246680	964	1036	1.16E-12	65.462	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#5639 - 	CGI_10020315	superfamily	247724	186	225	7.11E-06	46.1752	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5640 - 	CGI_10020316	superfamily	247875	70	131	5.39E-08	48.5786	cl17321	2OG-FeII_Oxy_2 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; 2OG-Fe(II) oxygenase superfamily.  
Q#5642 - 	CGI_10020318	superfamily	243092	364	644	3.48E-35	137.081	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5642 - 	CGI_10020318	superfamily	243092	22	165	0.000291873	42.7072	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5643 - 	CGI_10020319	superfamily	248024	9	114	5.81E-08	50.7446	cl17470	SBF superfamily	NC	 - 	"Sodium Bile acid symporter family; This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae, this is a putative transmembrane protein involved in resistance to arsenic compounds."
Q#5645 - 	CGI_10020321	superfamily	247856	100	171	2.63E-12	58.7133	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5645 - 	CGI_10020321	superfamily	247856	65	126	7.55E-11	54.4761	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5645 - 	CGI_10020321	superfamily	244899	37	90	0.000255515	37.0842	cl08302	S-100 superfamily	N	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#5646 - 	CGI_10020322	superfamily	220414	3	242	7.58E-45	153.055	cl10780	DUF2348 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2348); Members of this family of putative uncharacterized proteins have no known function.
Q#5647 - 	CGI_10020323	superfamily	217737	3	145	6.32E-24	96.5217	cl04266	Nuf2 superfamily	 - 	 - 	"Nuf2 family; Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, Arabidopsis thaliana T7P1.14. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region."
Q#5648 - 	CGI_10020324	superfamily	246713	65	235	3.04E-46	158.559	cl14786	ENDO3c superfamily	 - 	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#5648 - 	CGI_10020324	superfamily	241868	325	430	1.09E-16	75.8363	cl00447	Nudix_Hydrolase superfamily	N	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#5648 - 	CGI_10020324	superfamily	210074	239	255	0.00371552	35.0969	cl15304	EndIII_4Fe-2S superfamily	 - 	 - 	"Iron-sulfur binding domain of endonuclease III; Escherichia coli endonuclease III (EC 4.2.99.18) is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidized pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site from which the damaged base was removed. Endonuclease III is an iron-sulfur protein that binds a single 4Fe-4S cluster. The 4Fe-4S cluster does not seem to be important for catalytic activity, but is probably involved in the proper positioning of the enzyme along the DNA strand. The 4Fe-4S cluster is bound by four cysteines which are all located in a 17 amino acid region at the C-terminal end of endonuclease III. A similar region is also present in the central section of mutY and in the C-terminus of ORF-10 and of the Micro-coccus UV endonuclease."
Q#5649 - 	CGI_10020325	superfamily	241574	1391	1620	3.25E-116	368.452	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#5649 - 	CGI_10020325	superfamily	241574	1672	1900	1.07E-109	349.962	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#5649 - 	CGI_10020325	superfamily	241584	408	499	1.91E-16	77.5367	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	311	403	2.24E-15	74.4551	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	806	896	2.75E-13	68.2919	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	606	705	6.17E-13	67.5215	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	710	799	2.22E-11	62.8991	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	518	601	5.49E-11	61.7435	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	234	303	8.83E-10	58.2767	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	1000	1100	1.96E-07	50.9579	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	241584	901	980	3.56E-06	47.1059	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#5649 - 	CGI_10020325	superfamily	245814	167	230	2.98E-20	88.0216	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5649 - 	CGI_10020325	superfamily	245814	72	146	1.07E-15	75.0804	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5651 - 	CGI_10020327	superfamily	248458	68	249	9.87E-27	110.481	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5651 - 	CGI_10020327	superfamily	248458	303	517	2.98E-07	51.1605	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5652 - 	CGI_10020328	superfamily	241750	18	342	4.36E-104	310.35	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#5653 - 	CGI_10020329	superfamily	243130	463	503	1.06E-05	43.6079	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#5654 - 	CGI_10020330	superfamily	245936	138	365	1.76E-46	158.482	cl12283	IPK superfamily	 - 	 - 	Inositol polyphosphate kinase; ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
Q#5655 - 	CGI_10020331	superfamily	241782	695	1048	1.16E-104	338.923	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#5655 - 	CGI_10020331	superfamily	243092	408	683	3.24E-57	202.18	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5655 - 	CGI_10020331	superfamily	243072	1482	1577	1.17E-26	108.24	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5655 - 	CGI_10020331	superfamily	247792	149	183	5.44E-05	42.818	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5655 - 	CGI_10020331	superfamily	190233	240	296	6.02E-07	48.9898	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#5655 - 	CGI_10020331	superfamily	213458	299	340	0.00762037	36.4829	cl17044	DD_cGKI superfamily	 - 	 - 	"Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I; Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a  soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing their targeting to different subcellular compartments and intracellular substrates."
Q#5656 - 	CGI_10020332	superfamily	241596	112	155	2.13E-08	48.7495	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#5657 - 	CGI_10020333	superfamily	242686	6	379	8.08E-113	339.653	cl01750	PhoPQ_related superfamily	 - 	 - 	PhoPQ-activated pathogenicity-related protein; Members of this family of bacterial proteins are involved in the virulence of some pathogenic proteobacteria.
Q#5658 - 	CGI_10020334	superfamily	243034	987	1058	4.40E-05	43.5228	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5658 - 	CGI_10020334	superfamily	243092	64	355	8.29E-09	57.3448	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5659 - 	CGI_10020335	superfamily	246598	22	287	5.93E-153	432.447	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#5660 - 	CGI_10020336	superfamily	222269	149	348	5.88E-08	51.9406	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#5663 - 	CGI_10020339	superfamily	246908	35	136	2.75E-44	144.72	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#5663 - 	CGI_10020339	superfamily	247683	139	193	2.46E-18	75.6524	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#5663 - 	CGI_10020339	superfamily	247683	6	32	5.42E-12	57.7517	cl17036	SH3 superfamily	N	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#5664 - 	CGI_10020340	superfamily	215754	217	308	2.27E-24	95.0128	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#5664 - 	CGI_10020340	superfamily	215754	115	213	5.22E-21	85.3828	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#5664 - 	CGI_10020340	superfamily	215754	16	111	5.70E-18	76.9084	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#5665 - 	CGI_10020341	superfamily	247723	237	305	3.01E-30	111.205	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5666 - 	CGI_10020342	superfamily	243072	183	294	1.16E-21	91.6762	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5666 - 	CGI_10020342	superfamily	243072	574	627	0.00104338	38.1335	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5667 - 	CGI_10020343	superfamily	247856	86	148	8.20E-21	81.0549	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5667 - 	CGI_10020343	superfamily	247856	13	75	2.80E-19	77.2029	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5668 - 	CGI_10020344	superfamily	247856	155	217	3.87E-17	72.5805	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5668 - 	CGI_10020344	superfamily	247856	87	139	9.34E-05	38.6829	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5669 - 	CGI_10020345	superfamily	241583	85	280	1.07E-129	391.419	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#5669 - 	CGI_10020345	superfamily	241571	392	503	9.71E-38	137.929	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5669 - 	CGI_10020345	superfamily	241571	547	658	8.76E-34	126.758	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5669 - 	CGI_10020345	superfamily	241571	707	815	1.31E-31	120.595	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5669 - 	CGI_10020345	superfamily	241571	817	932	3.18E-27	108.269	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5669 - 	CGI_10020345	superfamily	241571	282	390	1.68E-20	88.6234	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5669 - 	CGI_10020345	superfamily	241578	483	541	3.94E-08	53.5427	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5669 - 	CGI_10020345	superfamily	241578	652	695	3.26E-07	50.8464	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5670 - 	CGI_10020346	superfamily	210118	193	211	0.000109381	38.4607	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#5673 - 	CGI_10009197	superfamily	219425	383	501	9.21E-14	67.5667	cl06494	Hydrolase_2 superfamily	 - 	 - 	"Cell Wall Hydrolase; These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance B. subtilis sleB is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex. A similar role is carried out by the partially redundant B. subtilis cwlJ. It is not clear whether these enzymes are amidases or peptidases."
Q#5677 - 	CGI_10009201	superfamily	219425	334	452	6.29E-14	67.9519	cl06494	Hydrolase_2 superfamily	 - 	 - 	"Cell Wall Hydrolase; These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance B. subtilis sleB is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex. A similar role is carried out by the partially redundant B. subtilis cwlJ. It is not clear whether these enzymes are amidases or peptidases."
Q#5682 - 	CGI_10009207	superfamily	241563	59	97	2.73E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5684 - 	CGI_10005294	superfamily	243133	106	177	3.07E-15	69.8972	cl02662	SEP superfamily	 - 	 - 	"SEP domain; The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L. Most SEP domains are succeeded closely by a UBX domain."
Q#5684 - 	CGI_10005294	superfamily	241645	291	366	5.35E-09	52.2735	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#5685 - 	CGI_10005295	superfamily	217380	809	1081	5.13E-81	269.965	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#5686 - 	CGI_10005296	superfamily	248139	591	1052	0	759.027	cl17585	RNA_pol_B_RPB2 superfamily	N	 - 	"RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation."
Q#5686 - 	CGI_10005296	superfamily	248139	38	468	3.93E-110	364.968	cl17585	RNA_pol_B_RPB2 superfamily	C	 - 	"RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation."
Q#5686 - 	CGI_10005296	superfamily	191029	562	602	1.39E-12	64.1405	cl04595	RNA_pol_Rpb2_5 superfamily	 - 	 - 	"RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain."
Q#5686 - 	CGI_10005296	superfamily	113341	504	535	2.12E-07	49.599	cl04594	RNA_pol_Rpb2_4 superfamily	C	 - 	"RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain."
Q#5687 - 	CGI_10005297	superfamily	245201	17	112	6.96E-13	62.0324	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5688 - 	CGI_10020485	superfamily	241566	1255	1303	5.41E-10	57.8872	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#5688 - 	CGI_10020485	superfamily	243036	1483	1736	4.96E-29	119.65	cl02434	CNH superfamily	 - 	 - 	"CNH domain; Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations."
Q#5688 - 	CGI_10020485	superfamily	247725	1335	1448	3.87E-07	50.5433	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5689 - 	CGI_10020486	superfamily	245819	44	190	8.52E-64	197.031	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#5689 - 	CGI_10020486	superfamily	219526	1	31	0.000153018	39.9099	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#5691 - 	CGI_10020488	superfamily	202184	16	106	2.30E-19	77.3194	cl03509	UCR_14kD superfamily	 - 	 - 	"Ubiquinol-cytochrome C reductase complex 14kD subunit; The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex."
Q#5693 - 	CGI_10020490	superfamily	241574	235	371	1.72E-61	196.676	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#5693 - 	CGI_10020490	superfamily	241626	78	206	1.64E-29	111.22	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#5694 - 	CGI_10020491	superfamily	243146	127	174	4.64E-09	49.4791	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#5694 - 	CGI_10020491	superfamily	243146	79	126	9.09E-08	46.0123	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#5694 - 	CGI_10020491	superfamily	243146	160	194	0.000110023	37.5915	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#5695 - 	CGI_10020492	superfamily	243146	77	116	0.00119248	34.5595	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#5696 - 	CGI_10020493	superfamily	243072	40	151	1.07E-06	46.993	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5697 - 	CGI_10020494	superfamily	199899	206	251	1.75E-30	110.692	cl18199	TFIIA_alpha_beta_like superfamily	N	 - 	"Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage)."
Q#5697 - 	CGI_10020494	superfamily	199899	7	61	1.45E-24	94.5135	cl18199	TFIIA_alpha_beta_like superfamily	C	 - 	"Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage)."
Q#5699 - 	CGI_10020496	superfamily	246925	97	179	0.00525342	35.409	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#5700 - 	CGI_10020497	superfamily	241775	78	163	4.19E-11	56.756	cl00314	Ribosomal_S10 superfamily	 - 	 - 	Ribosomal protein S10p/S20e; This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.
Q#5703 - 	CGI_10020500	superfamily	212559	1450	1494	6.77E-10	57.2391	cl18297	SANT_MTA3_like superfamily	 - 	 - 	"Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle.  MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis."
Q#5703 - 	CGI_10020500	superfamily	216509	1353	1408	4.38E-06	46.0778	cl03218	ELM2 superfamily	 - 	 - 	"ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a member from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain."
Q#5703 - 	CGI_10020500	superfamily	197676	259	281	0.0098124	35.9045	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#5704 - 	CGI_10020501	superfamily	205451	83	176	1.27E-06	44.8767	cl16203	DUF4062 superfamily	 - 	 - 	"Domain of unknown function (DUF4062); This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif."
Q#5705 - 	CGI_10020502	superfamily	208568	171	222	7.80E-27	99.8888	cl06890	NOSIC superfamily	 - 	 - 	NOSIC (NUC001) domain; This is the central domain in Nop56/SIK1-like proteins.
Q#5705 - 	CGI_10020502	superfamily	219731	5	71	2.90E-21	84.9259	cl06964	NOP5NT superfamily	 - 	 - 	NOP5NT (NUC127) domain; This N terminal domain is found in RNA-binding proteins of the NOP5 family.
Q#5706 - 	CGI_10020503	superfamily	247792	65	108	6.57E-09	50.1368	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5707 - 	CGI_10020504	superfamily	248458	108	460	7.15E-19	86.5989	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5708 - 	CGI_10020505	superfamily	248458	113	496	7.52E-27	110.481	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5709 - 	CGI_10020506	superfamily	241752	941	1148	5.67E-130	398.504	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#5709 - 	CGI_10020506	superfamily	243072	515	640	6.58E-37	136.745	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5709 - 	CGI_10020506	superfamily	243072	668	782	3.73E-34	129.041	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5709 - 	CGI_10020506	superfamily	243072	47	161	1.51E-32	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5709 - 	CGI_10020506	superfamily	243072	115	294	3.44E-29	114.788	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5709 - 	CGI_10020506	superfamily	247057	869	929	1.42E-27	108.184	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#5709 - 	CGI_10020506	superfamily	243072	357	474	7.51E-25	102.077	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5711 - 	CGI_10020508	superfamily	243035	8	76	0.00047513	37.3556	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5712 - 	CGI_10020509	superfamily	220692	76	187	0.00205725	36.7986	cl18570	7TM_GPCR_Srw superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#5714 - 	CGI_10020511	superfamily	241992	823	1057	1.01E-149	456.69	cl00628	Piwi-like superfamily	N	 - 	"Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism."
Q#5714 - 	CGI_10020511	superfamily	241765	338	458	7.62E-40	144.767	cl00301	PAZ superfamily	 - 	 - 	"PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain."
Q#5714 - 	CGI_10020511	superfamily	241992	544	765	7.23E-76	257.156	cl00628	Piwi-like superfamily	C	 - 	"Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism."
Q#5714 - 	CGI_10020511	superfamily	219976	286	338	8.54E-21	87.9985	cl07356	DUF1785 superfamily	 - 	 - 	Domain of unknown function (DUF1785); This region is found in argonaute proteins and often co-occurs with pfam02179 and pfam02171.
Q#5717 - 	CGI_10020514	superfamily	192997	298	423	7.57E-20	87.6371	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#5718 - 	CGI_10020515	superfamily	243072	41	150	1.48E-36	131.352	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5723 - 	CGI_10020520	superfamily	241777	91	410	2.76E-75	237.888	cl00316	Cation_efflux superfamily	 - 	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#5723 - 	CGI_10020520	superfamily	241884	50	120	0.005871	36.5396	cl00467	Ntn_hydrolase superfamily	C	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#5724 - 	CGI_10020521	superfamily	241777	182	329	2.24E-42	149.293	cl00316	Cation_efflux superfamily	N	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#5724 - 	CGI_10020521	superfamily	241777	1	114	1.32E-30	117.321	cl00316	Cation_efflux superfamily	C	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#5727 - 	CGI_10020524	superfamily	245213	1423	1457	7.86E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#5727 - 	CGI_10020524	superfamily	242173	438	593	5.91E-18	83.0702	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#5727 - 	CGI_10020524	superfamily	242173	292	429	1.28E-12	67.2771	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#5727 - 	CGI_10020524	superfamily	242173	611	760	2.79E-10	59.9583	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#5729 - 	CGI_10020526	superfamily	245814	2	87	2.96E-10	56.3597	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5730 - 	CGI_10020527	superfamily	247727	48	126	7.86E-10	55.5138	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#5732 - 	CGI_10001776	superfamily	243072	17	131	2.67E-10	55.8526	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5732 - 	CGI_10001776	superfamily	243073	211	250	0.00272897	34.3935	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#5733 - 	CGI_10001777	superfamily	243072	36	166	1.56E-22	88.5946	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5736 - 	CGI_10008500	superfamily	243074	4	48	7.46E-11	57.1313	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#5736 - 	CGI_10008500	superfamily	192915	227	274	2.18E-07	48.5185	cl13451	DUF3506 superfamily	C	 - 	Domain of unknown function (DUF3506); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 131 to 148 amino acids in length. This domain has a conserved KLTGD sequence motif.
Q#5737 - 	CGI_10008501	superfamily	247724	163	327	9.08E-75	230.389	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5737 - 	CGI_10008501	superfamily	110047	9	161	2.25E-14	68.8896	cl03072	GTP1_OBG superfamily	 - 	 - 	"GTP1/OBG; The N-terminal domain of B. subtilis GTPase obgE has the OBG fold, which is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich these regions form six left-handed collagen-like helices packed and H-bonded together."
Q#5738 - 	CGI_10008502	superfamily	220795	94	272	3.55E-100	293.487	cl11156	Kua-UEV1_localn superfamily	 - 	 - 	"Kua-ubiquitin conjugating enzyme hybrid localisation domain; This domain is part of the transcript of the fusion of two genes, the UEV1, an enzymatically inactive variant of the E2 ubiquitin-conjugating enzymes that regulate non-canonical elongation of ubiquitin chains, and Kua, an otherwise unknown gene. UEV1A is a nuclear protein, whereas both Kua and Kua-UEV localise to cytoplasmic structures, indicating that the addition of a Kua domain to UEV confers new biological properties. UEV1-Kua carries the B domain with its characteristic double histidine motif, and it is probably this domain which determines the cytoplasmic localisation. It is postulated that this hybrid transcript could preferentially direct the variant polyubiquitination of substrates closely associated with the cytoplasmic face of the endoplasmic reticulum, possibly, although not necessarily, in conjunction with membrane-bound ubiquitin-conjugating enzymes."
Q#5739 - 	CGI_10008503	superfamily	222150	1117	1142	3.43E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	1064	1089	5.31E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	1735	1759	0.000210966	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	1246	1270	0.000222736	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	712	737	0.000257426	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	1762	1787	0.000470304	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	768	793	0.000866332	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	298	322	0.000890099	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	1303	1328	0.00093678	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	595	620	0.0013929	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5741 - 	CGI_10008505	superfamily	222150	325	350	0.00301204	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5742 - 	CGI_10008506	superfamily	243072	228	358	1.72E-24	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5742 - 	CGI_10008506	superfamily	243072	305	425	8.17E-18	80.1202	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5742 - 	CGI_10008506	superfamily	243072	134	255	7.22E-12	62.7862	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5742 - 	CGI_10008506	superfamily	243073	463	501	4.89E-06	43.9981	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#5743 - 	CGI_10008507	superfamily	241657	79	556	0	535.799	cl00170	eu-GS superfamily	 - 	 - 	Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily.
Q#5744 - 	CGI_10008508	superfamily	241900	11	158	4.91E-05	40.7883	cl00490	EEP superfamily	N	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#5745 - 	CGI_10008509	superfamily	211463	792	917	7.93E-50	172.417	cl13463	FAT-like_CAS_C superfamily	 - 	 - 	"C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding proteins; a protein interaction module; CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where they localize, and thus, regulate cell invasion and survival. Over-expression of these proteins is implicated in poor prognosis, increased metastasis, and resistance to chemotherapeutics in many cancers such as breast, lung, melanoma, and glioblastoma. CAS proteins have also been linked to the pathogenesis of inflammatory disorders, Alzheimer's, Parkinson's, and developmental defects. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. Vertebrates contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or HEF1), EFS (or SIN), and CASS4 (or HEPL). The FAT-like C-terminal domain of CAS proteins binds to the C-terminal domain of NSPs (novel SH2-containing proteins) to form multidomain signaling modules that mediate cell migration and invasion."
Q#5745 - 	CGI_10008509	superfamily	247683	9	64	6.35E-32	119.758	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#5745 - 	CGI_10008509	superfamily	211451	433	579	3.84E-43	155.061	cl07433	Serine_rich_CAS superfamily	 - 	 - 	"Serine rich Four helix bundle domain of CAS (Crk-Associated Substrate) scaffolding proteins; a protein interaction module; CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where they localize, and thus, regulate cell invasion and survival. Over-expression of these proteins is implicated in poor prognosis, increased metastasis, and resistance to chemotherapeutics in many cancers such as breast, lung, melanoma, and glioblastoma. CAS proteins have also been linked to the pathogenesis of inflammatory disorders, Alzheimer's, Parkinson's, and developmental defects. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. Vertebrates contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or HEF1), EFS (or SIN), and CASS4 (or HEPL). CAS proteins associate with the 14-3-3 family; this interaction is regulated by integrin-mediated cell adhesion. The serine rich four helix bundle domain of BCAR1 has been shown to bind 14-3-3 in a phosphorylation-dependent manner. This domain is structurally similar to other helical bundles found in cell adhesion components such as alpha-catenin, vinculin, and FAK, and may bind other proteins in addition to the 14-3-3 family."
Q#5747 - 	CGI_10008511	superfamily	247723	168	240	5.05E-19	79.2251	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5748 - 	CGI_10008512	superfamily	243058	635	737	5.06E-08	51.9315	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5748 - 	CGI_10008512	superfamily	243058	202	318	6.11E-08	51.5463	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5748 - 	CGI_10008512	superfamily	243058	291	407	1.70E-05	44.2276	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5748 - 	CGI_10008512	superfamily	243072	16	111	8.36E-05	41.9855	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5748 - 	CGI_10008512	superfamily	243058	124	237	0.000236863	40.3756	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5748 - 	CGI_10008512	superfamily	243058	381	491	0.000359328	39.9904	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5749 - 	CGI_10008513	superfamily	227462	39	154	3.23E-44	145.524	cl18814	COG5133 superfamily	N	 - 	Uncharacterized conserved protein [Function unknown]
Q#5750 - 	CGI_10008514	superfamily	241572	258	347	1.67E-17	77.664	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#5750 - 	CGI_10008514	superfamily	241572	372	444	5.77E-11	59.1744	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#5752 - 	CGI_10004958	superfamily	219075	237	413	7.11E-43	151.468	cl05845	RGM_C superfamily	 - 	 - 	"Repulsive guidance molecule (RGM) C-terminus; This family consists of several mammalian and one bird sequence from Gallus gallus (Chicken). This family represents the C-terminal region of several sequences but in others it represents the full protein. All of the mammalian proteins are hypothetical and have no known function but RGMA from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum."
Q#5752 - 	CGI_10004958	superfamily	219076	41	234	2.39E-35	130.709	cl05846	RGM_N superfamily	 - 	 - 	"Repulsive guidance molecule (RGM) N-terminus; This family consists of the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but RGMA from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum."
Q#5754 - 	CGI_10004960	superfamily	247724	22	162	2.08E-24	97.2955	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5757 - 	CGI_10019151	superfamily	241572	82	166	0.00109135	37.1867	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#5759 - 	CGI_10019153	superfamily	245201	162	246	4.68E-09	54.3912	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5761 - 	CGI_10019155	superfamily	242122	1988	2131	4.02E-07	50.7085	cl00824	HEPN superfamily	 - 	 - 	HEPN domain; HEPN domain.  
Q#5765 - 	CGI_10019159	superfamily	192987	21	98	5.55E-20	78.7683	cl13724	TMF_TATA_bd superfamily	N	 - 	"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family."
Q#5767 - 	CGI_10019161	superfamily	243072	43	168	1.12E-33	121.337	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5767 - 	CGI_10019161	superfamily	243072	109	241	1.45E-31	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5768 - 	CGI_10019162	superfamily	247057	445	515	9.61E-34	125.87	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#5768 - 	CGI_10019162	superfamily	247057	379	444	3.23E-30	115.434	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#5768 - 	CGI_10019162	superfamily	247683	22	74	1.13E-06	47.6876	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#5768 - 	CGI_10019162	superfamily	242211	205	293	0.00197241	39.2137	cl00944	KdpC superfamily	C	 - 	"K+-transporting ATPase, c chain; This family consists of K+-transporting ATPase, c chain, KdpC. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+-transporting subunit KdpA. The K+ transport system actively transports K+ ions via ATP hydrolysis."
Q#5769 - 	CGI_10019163	superfamily	246726	28	99	0.000553341	36.734	cl14821	DUF3792 superfamily	C	 - 	Protein of unknown function (DUF3792); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. These proteins are integral membrane proteins.
Q#5772 - 	CGI_10019166	superfamily	247725	28	133	1.25E-46	153.053	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5772 - 	CGI_10019166	superfamily	220708	99	196	1.43E-09	53.5611	cl11017	WWbp superfamily	 - 	 - 	"WW-domain ligand protein; The WWbp domain is characterized by several short PY and PT-like motifs of the PPPPY form. These appear to bind directly to the WW domains of WWP1 and WWP2 and other such diverse proteins as dystrophin and YAP (Yes-associated protein). This is the WW-domain binding protein WWbp via PY and PY_like motifs. The presence of a phosphotyrosine residue in the pWBP-1 peptide abolishes WW domain binding which suggests a potential regulatory role for tyrosine phosphorylation in modulating WW domain-ligand interactions. Given the likelihood that WWP1 and WWP2 function as E3 ubiquitin-protein ligases, it is possible that initial substrate-specific recognition occurs via WW domain-substrate protein interaction followed by ubiquitin transfer and subsequent proteolysis. This domain lies just downstream of the GRAM (pfam02893) in many members."
Q#5773 - 	CGI_10019167	superfamily	241550	59	343	1.53E-101	307.225	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#5774 - 	CGI_10019168	superfamily	218454	250	366	1.93E-26	102.352	cl04950	RNA_pol_Rpc4 superfamily	 - 	 - 	"RNA polymerase III RPC4; Specific subunit for Pol III, the tRNA specific polymerase."
Q#5775 - 	CGI_10019169	superfamily	245201	15	206	1.53E-35	131.59	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5776 - 	CGI_10019170	superfamily	241983	429	751	9.07E-39	145.578	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#5776 - 	CGI_10019170	superfamily	241983	10	334	5.96E-34	132.096	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#5777 - 	CGI_10019171	superfamily	241983	10	127	2.43E-12	61.9902	cl00614	ADP_ribosyl_GH superfamily	C	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#5779 - 	CGI_10019173	superfamily	150870	122	199	2.27E-27	107.455	cl10946	Stork_head superfamily	 - 	 - 	Winged helix Storkhead-box1 domain; This is the conserved N-terminal winged helix domain of Storkhead-box1 protein which is likely to be a DNA binding domain. In humans the full-length protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia.
Q#5780 - 	CGI_10019174	superfamily	247723	12	82	3.57E-29	105.78	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5781 - 	CGI_10019175	superfamily	216881	1	203	3.40E-83	248.016	cl03454	Rho_GDI superfamily	 - 	 - 	RHO protein GDP dissociation inhibitor; RHO protein GDP dissociation inhibitor.  
Q#5783 - 	CGI_10019177	superfamily	203750	989	1123	1.69E-45	161.709	cl18248	Sad1_UNC superfamily	 - 	 - 	"Sad1 / UNC-like C-terminal; The C. elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development. The S. pombe Sad1 protein localises at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2. The SUN domain of Sun2 has been demonstrated to be in the periplasm."
Q#5785 - 	CGI_10001654	superfamily	219610	25	89	1.14E-19	81.3108	cl06753	DUF1632 superfamily	N	 - 	CEO family (DUF1632); These sequences are found in hypothetical eukaryotic proteins of unknown function. The region concerned is approximately 280 residues long. This family has been termed the CEO family for C. elegans ORF.
Q#5787 - 	CGI_10018928	superfamily	141815	13	109	4.64E-36	127.865	cl04275	Mtc superfamily	C	 - 	Tricarboxylate carrier; Tricarboxylate carrier.  
Q#5788 - 	CGI_10018929	superfamily	247724	72	241	2.15E-98	287.756	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5789 - 	CGI_10018930	superfamily	245230	8	436	0	949.038	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#5790 - 	CGI_10018931	superfamily	247725	51	182	4.27E-70	229.063	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5790 - 	CGI_10018931	superfamily	243056	464	672	2.02E-64	216.404	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#5790 - 	CGI_10018931	superfamily	221593	213	343	1.77E-30	118.631	cl13857	DUF3694 superfamily	 - 	 - 	"Kinesin protein; This domain family is found in eukaryotes, and is typically between 131 and 151 amino acids in length. The family is found in association with pfam00225, pfam00498. There is a single completely conserved residue W that may be functionally important."
Q#5792 - 	CGI_10018933	superfamily	247723	191	268	4.93E-35	125.975	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5792 - 	CGI_10018933	superfamily	247723	427	501	2.52E-31	115.496	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5792 - 	CGI_10018933	superfamily	247723	277	355	1.76E-21	88.5111	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5793 - 	CGI_10018934	superfamily	247723	6	83	8.34E-38	132.138	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5793 - 	CGI_10018934	superfamily	247723	250	313	6.98E-29	107.792	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5793 - 	CGI_10018934	superfamily	247723	94	170	2.70E-18	78.4959	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5794 - 	CGI_10018935	superfamily	241889	24	185	9.03E-58	182.859	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#5795 - 	CGI_10018936	superfamily	241846	7	377	1.14E-179	507.719	cl00409	tgt superfamily	 - 	 - 	queuine tRNA-ribosyltransferase; Provisional
Q#5796 - 	CGI_10018937	superfamily	243072	118	241	7.14E-18	78.5794	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5796 - 	CGI_10018937	superfamily	243072	52	170	2.27E-07	48.1486	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5796 - 	CGI_10018937	superfamily	243073	321	361	9.12E-06	42.4573	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#5797 - 	CGI_10018938	superfamily	247724	5	106	1.13E-29	108.767	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5797 - 	CGI_10018938	superfamily	247724	102	163	3.47E-16	72.1731	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5798 - 	CGI_10018939	superfamily	247724	46	164	4.16E-31	113.004	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5799 - 	CGI_10018940	superfamily	243306	6	257	6.93E-140	397.352	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#5800 - 	CGI_10018941	superfamily	216554	144	305	3.41E-36	129.907	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#5801 - 	CGI_10018942	superfamily	215648	316	560	4.63E-29	116.156	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#5802 - 	CGI_10018943	superfamily	243072	503	619	3.02E-34	128.27	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5802 - 	CGI_10018943	superfamily	243072	236	353	7.24E-31	118.64	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5803 - 	CGI_10018944	superfamily	244951	79	340	9.27E-78	241.927	cl08428	Mannosyl_trans superfamily	 - 	 - 	Mannosyltransferase (PIG-M); PIG-M has a DXD motif. The DXD motif is found in many glycosyltransferases that utilise nucleotide sugars. It is thought that the motif is involved in the binding of a manganese ion that is required for association of the enzymes with nucleotide sugar substrates.
Q#5804 - 	CGI_10018945	superfamily	243130	77	114	7.58E-05	38.9855	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#5806 - 	CGI_10018947	superfamily	247792	304	326	0.0010556	36.602	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5807 - 	CGI_10018948	superfamily	245206	179	473	2.80E-109	328.419	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#5807 - 	CGI_10018948	superfamily	243072	57	173	2.07E-27	105.929	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5808 - 	CGI_10018949	superfamily	220226	1	256	1.16E-94	281.424	cl09658	XendoU superfamily	 - 	 - 	Endoribonuclease XendoU; This is a family of endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.
Q#5809 - 	CGI_10018950	superfamily	243072	453	572	6.67E-32	121.722	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5809 - 	CGI_10018950	superfamily	243072	514	676	2.46E-27	108.625	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5809 - 	CGI_10018950	superfamily	243072	620	748	5.43E-24	98.995	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5809 - 	CGI_10018950	superfamily	115363	4	66	9.94E-19	82.0345	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#5809 - 	CGI_10018950	superfamily	241760	77	119	9.81E-09	52.8459	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#5809 - 	CGI_10018950	superfamily	247792	794	835	1.92E-07	48.9152	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5809 - 	CGI_10018950	superfamily	115363	182	209	0.00795652	35.4254	cl05972	MIB_HERC2 superfamily	N	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#5810 - 	CGI_10018951	superfamily	243521	749	857	4.64E-29	112.722	cl03759	Alpha_adaptinC2 superfamily	 - 	 - 	"Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins."
Q#5812 - 	CGI_10018953	superfamily	247792	447	488	5.70E-09	52.448	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5812 - 	CGI_10018953	superfamily	222330	1	416	5.08E-115	352.841	cl16356	TRC8_N superfamily	 - 	 - 	TRC8 N-terminal domain; This region is found at the N-terminus of the TRC8 protein. TRC8 is an E3 ubiquitin-protein ligase also known as RNF139. This region contains 12 transmembrane domains. This region has been suggested to contain a sterol sensing domain. It has been found that TRC8 protein levels are sterol responsive and that it binds and stimulates ubiquitylation of the endoplasmic reticulum anchor protein INSIG.
Q#5814 - 	CGI_10018955	superfamily	241613	103	134	5.78E-05	37.5714	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5814 - 	CGI_10018955	superfamily	241571	57	91	1.20E-05	40.8587	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5814 - 	CGI_10018955	superfamily	241613	9	39	0.00150811	34.1046	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5815 - 	CGI_10018956	superfamily	243161	31	56	0.000839092	33.907	cl02739	THAP superfamily	N	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#5817 - 	CGI_10018958	superfamily	241571	52	147	1.13E-16	73.9858	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#5817 - 	CGI_10018958	superfamily	241613	153	187	7.97E-11	56.4462	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#5818 - 	CGI_10018959	superfamily	243107	422	468	1.87E-10	56.7468	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#5819 - 	CGI_10018960	superfamily	241646	27	75	0.000199009	35.5042	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#5821 - 	CGI_10012401	superfamily	199939	2	50	1.66E-24	89.1619	cl03508	TFIIA_gamma_N superfamily	 - 	 - 	"Gamma subunit of transcription initiation factor IIA, N-terminal helical domain; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The N-terminal domain of the gamma subunit forms a 4-helix bundle together with the alpha subunit."
Q#5821 - 	CGI_10012401	superfamily	199942	56	101	2.71E-22	83.0659	cl08356	TFIIA_gamma_C superfamily	 - 	 - 	"Gamma subunit of transcription initiation factor IIA, C-terminal domain; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The C-terminal domain of the gamma (TFIIA_gamma_C) subunit forms a beta-barrel structure together with TFIIA beta."
Q#5822 - 	CGI_10012402	superfamily	241615	39	81	3.15E-07	45.5541	cl00107	LysM superfamily	 - 	 - 	"Lysine Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes."
Q#5823 - 	CGI_10012403	superfamily	243182	1	158	4.56E-56	182.77	cl02784	Chelatase_Class_II superfamily	 - 	 - 	"Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III)."
Q#5823 - 	CGI_10012403	superfamily	243182	163	299	4.37E-47	158.462	cl02784	Chelatase_Class_II superfamily	 - 	 - 	"Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III)."
Q#5825 - 	CGI_10012405	superfamily	247724	145	273	6.79E-23	97.9118	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5825 - 	CGI_10012405	superfamily	241972	1110	1196	4.08E-08	52.9667	cl00600	Ribosomal_L7Ae superfamily	 - 	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#5826 - 	CGI_10012406	superfamily	247724	6	172	5.20E-121	343.096	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5827 - 	CGI_10012407	superfamily	247724	89	241	2.91E-75	229.746	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5827 - 	CGI_10012407	superfamily	247724	2	89	3.06E-42	144.521	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5828 - 	CGI_10012408	superfamily	241705	16	118	1.63E-56	173.132	cl00228	HIT_like superfamily	 - 	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#5829 - 	CGI_10012409	superfamily	241563	61	99	7.08E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5832 - 	CGI_10009690	superfamily	247041	50	278	5.75E-39	139.009	cl15692	CE4_SF superfamily	 - 	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#5833 - 	CGI_10009691	superfamily	243035	75	188	2.63E-13	63.0225	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5834 - 	CGI_10009692	superfamily	243035	75	188	1.69E-13	63.4077	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5835 - 	CGI_10009693	superfamily	243034	108	194	8.28E-11	59.316	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5835 - 	CGI_10009693	superfamily	243034	434	515	3.64E-09	54.3084	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5835 - 	CGI_10009693	superfamily	243034	337	480	3.92E-06	45.4488	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5835 - 	CGI_10009693	superfamily	243034	484	551	0.000699942	38.5152	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5835 - 	CGI_10009693	superfamily	243034	296	368	0.00902121	35.0484	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5836 - 	CGI_10009694	superfamily	248458	21	169	4.68E-06	46.9233	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5837 - 	CGI_10009695	superfamily	248458	21	166	1.17E-06	48.4641	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#5838 - 	CGI_10009696	superfamily	245201	377	627	2.25E-70	231.64	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5838 - 	CGI_10009696	superfamily	241645	190	266	1.14E-23	96.1044	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#5838 - 	CGI_10009696	superfamily	241645	67	148	2.07E-23	95.334	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#5841 - 	CGI_10009699	superfamily	247684	43	264	1.52E-61	209.056	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#5841 - 	CGI_10009699	superfamily	247684	246	368	3.44E-22	97.3479	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#5842 - 	CGI_10009700	superfamily	159569	269	307	3.90E-05	40.3941	cl11598	Thymosin superfamily	 - 	 - 	Thymosin beta-4 family; Thymosin beta-4 family.  
Q#5842 - 	CGI_10009700	superfamily	159569	231	271	0.00281321	35.0013	cl11598	Thymosin superfamily	 - 	 - 	Thymosin beta-4 family; Thymosin beta-4 family.  
Q#5842 - 	CGI_10009700	superfamily	159569	201	233	0.00306137	35.0013	cl11598	Thymosin superfamily	 - 	 - 	Thymosin beta-4 family; Thymosin beta-4 family.  
Q#5843 - 	CGI_10009701	superfamily	217293	20	216	4.82E-25	103.481	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#5843 - 	CGI_10009701	superfamily	217293	290	470	3.99E-24	100.785	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#5847 - 	CGI_10009705	superfamily	243034	212	311	1.42E-22	93.5987	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5847 - 	CGI_10009705	superfamily	243034	280	379	1.84E-22	93.5987	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5847 - 	CGI_10009705	superfamily	243034	76	175	6.55E-21	88.9763	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5847 - 	CGI_10009705	superfamily	243034	352	447	5.10E-20	86.6651	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5847 - 	CGI_10009705	superfamily	243034	177	210	0.000208	39.7084	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5849 - 	CGI_10009707	superfamily	248022	95	364	5.41E-51	176.699	cl17468	Aa_trans superfamily	C	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#5850 - 	CGI_10009708	superfamily	100115	77	440	2.51E-106	323.467	cl18930	StaR_like superfamily	 - 	 - 	"StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure."
Q#5851 - 	CGI_10009709	superfamily	241832	30	117	1.36E-42	142.492	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#5851 - 	CGI_10009709	superfamily	243175	131	255	1.02E-29	109.718	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#5853 - 	CGI_10009712	superfamily	243124	61	219	4.20E-39	138.714	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#5853 - 	CGI_10009712	superfamily	247038	232	305	0.000510048	38.2112	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#5867 - 	CGI_10025093	superfamily	241572	64	148	8.92E-09	52.2409	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#5870 - 	CGI_10025096	superfamily	145792	5	25	0.00741293	29.9215	cl10597	Antistasin superfamily	 - 	 - 	Antistasin family; Members of this family are inhibitors of trypsin family proteases. This domain is highly disulphide bonded. The domain is also found in some large extracellular proteins in multiple copies.
Q#5871 - 	CGI_10025097	superfamily	247724	81	126	1.14E-25	102.578	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5873 - 	CGI_10025101	superfamily	217410	25	78	1.41E-08	50.0452	cl18409	DDE_1 superfamily	NC	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere."
Q#5877 - 	CGI_10025105	superfamily	207684	128	157	0.0049646	33.2288	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#5878 - 	CGI_10025106	superfamily	241832	13	155	3.95E-31	111.838	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#5879 - 	CGI_10025107	superfamily	241578	796	1038	2.09E-109	346.568	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5879 - 	CGI_10025107	superfamily	219707	1039	1123	2.91E-33	125.321	cl06871	Sec23_BS superfamily	 - 	 - 	Sec23/Sec24 beta-sandwich domain; Sec23/Sec24 beta-sandwich domain.  
Q#5879 - 	CGI_10025107	superfamily	218277	1135	1236	1.29E-22	95.2902	cl04773	Sec23_helical superfamily	 - 	 - 	"Sec23/Sec24 helical domain; COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices."
Q#5879 - 	CGI_10025107	superfamily	203092	723	760	2.17E-14	69.8967	cl04769	zf-Sec23_Sec24 superfamily	 - 	 - 	"Sec23/Sec24 zinc finger; COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain."
Q#5879 - 	CGI_10025107	superfamily	247044	1257	1326	0.000179589	41.5164	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#5881 - 	CGI_10025109	superfamily	241754	83	852	0	1279.45	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#5881 - 	CGI_10025109	superfamily	111612	35	77	4.41E-14	68.6618	cl03686	Myosin_N superfamily	 - 	 - 	Myosin N-terminal SH3-like domain; This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown.
Q#5881 - 	CGI_10025109	superfamily	151039	1016	1153	0.000893146	39.3963	cl11115	Cenp-F_leu_zip superfamily	 - 	 - 	"Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance."
Q#5881 - 	CGI_10025109	superfamily	210118	855	877	0.0016863	37.6903	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#5884 - 	CGI_10025112	superfamily	241578	1	77	1.62E-09	50.753	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#5886 - 	CGI_10025114	superfamily	243092	249	319	2.39E-15	77.3752	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5886 - 	CGI_10025114	superfamily	243092	501	690	2.35E-09	58.8856	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5886 - 	CGI_10025114	superfamily	243092	286	387	3.11E-05	46.174	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5887 - 	CGI_10025115	superfamily	219125	393	584	8.65E-82	257.256	cl05941	C5-epim_C superfamily	 - 	 - 	D-glucuronyl C5-epimerase C-terminus; This family represents the C-terminus of D-glucuronyl C5-epimerase (EC:5.1.3.-). Glucuronyl C5-epimerases catalyze the conversion of D-glucuronic acid (GlcUA) to L-iduronic acid (IdceA) units during the biosynthesis of glycosaminoglycans.
Q#5889 - 	CGI_10025117	superfamily	247725	445	595	3.20E-63	210.595	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5889 - 	CGI_10025117	superfamily	243096	244	433	9.82E-35	131.651	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#5890 - 	CGI_10025118	superfamily	243555	74	259	3.17E-21	88.6022	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#5891 - 	CGI_10025119	superfamily	243555	16	201	1.81E-22	91.6838	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#5892 - 	CGI_10025120	superfamily	248097	7	124	4.31E-13	61.127	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#5894 - 	CGI_10025122	superfamily	110440	331	352	0.00410926	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#5896 - 	CGI_10025124	superfamily	247743	478	623	2.57E-06	47.9111	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#5896 - 	CGI_10025124	superfamily	243092	1381	1607	8.60E-13	69.6712	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5896 - 	CGI_10025124	superfamily	243092	1001	1309	4.95E-09	58.1152	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5898 - 	CGI_10025126	superfamily	220080	265	395	6.11E-61	199.312	cl07526	DUF1900 superfamily	 - 	 - 	"Domain of unknown function (DUF1900); This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It has no known function."
Q#5898 - 	CGI_10025126	superfamily	149883	10	73	6.07E-35	125.814	cl07525	DUF1899 superfamily	 - 	 - 	Domain of unknown function (DUF1899); This set of domains is found in various eukaryotic proteins. Function is unknown.
Q#5898 - 	CGI_10025126	superfamily	243092	81	224	1.08E-17	82.3828	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5900 - 	CGI_10025128	superfamily	241758	194	518	6.44E-108	335.645	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5900 - 	CGI_10025128	superfamily	241555	20	163	5.83E-66	218.559	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#5900 - 	CGI_10025128	superfamily	241758	541	613	0.00418141	38.656	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5901 - 	CGI_10025129	superfamily	243092	259	545	1.55E-21	97.0204	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5901 - 	CGI_10025129	superfamily	243092	707	806	0.000178197	44.248	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5902 - 	CGI_10025130	superfamily	218284	20	187	1.63E-57	180.913	cl04786	SOUL superfamily	 - 	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#5904 - 	CGI_10025132	superfamily	247724	50	255	1.98E-70	217.574	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5907 - 	CGI_10025135	superfamily	241758	13	159	2.19E-26	97.8258	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5911 - 	CGI_10027701	superfamily	242889	329	427	1.22E-21	89.5845	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#5911 - 	CGI_10027701	superfamily	149439	434	464	2.50E-09	53.8682	cl07120	Rpn3_C superfamily	C	 - 	Proteasome regulatory subunit C-terminal; This eukaryotic domain is found at the C-terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function. It occurs together with the PCI/PINT domain (pfam01399).
Q#5911 - 	CGI_10027701	superfamily	243034	255	288	0.00679977	34.4123	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#5915 - 	CGI_10027705	superfamily	207627	1288	1382	5.21E-13	67.6599	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#5915 - 	CGI_10027705	superfamily	207627	925	1023	3.05E-12	65.3535	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#5915 - 	CGI_10027705	superfamily	207627	1055	1143	2.46E-11	63.0375	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#5915 - 	CGI_10027705	superfamily	207627	805	898	3.67E-10	59.5755	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#5915 - 	CGI_10027705	superfamily	207627	1169	1260	3.85E-08	53.4123	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#5916 - 	CGI_10027706	superfamily	247792	11	55	0.00819407	35.114	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#5916 - 	CGI_10027706	superfamily	241563	155	187	0.000994962	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#5917 - 	CGI_10027707	superfamily	247723	91	168	2.98E-25	99.7417	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5917 - 	CGI_10027707	superfamily	247723	462	537	2.88E-13	65.7618	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#5917 - 	CGI_10027707	superfamily	207717	25	77	2.71E-07	48.3836	cl02755	LAM superfamily	N	 - 	"LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes."
Q#5918 - 	CGI_10027708	superfamily	243072	60	184	4.18E-29	112.092	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5918 - 	CGI_10027708	superfamily	243072	126	255	2.26E-21	90.1354	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#5918 - 	CGI_10027708	superfamily	216554	368	530	1.64E-24	100.247	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#5919 - 	CGI_10027709	superfamily	243053	863	1068	9.75E-66	224.054	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#5919 - 	CGI_10027709	superfamily	241622	538	619	1.56E-19	85.6962	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5919 - 	CGI_10027709	superfamily	243067	430	535	2.27E-15	74.7563	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#5919 - 	CGI_10027709	superfamily	241570	291	393	1.12E-12	66.5806	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#5919 - 	CGI_10027709	superfamily	241645	756	840	5.04E-37	136.147	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#5921 - 	CGI_10027711	superfamily	245819	1067	1243	1.05E-61	210.128	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#5921 - 	CGI_10027711	superfamily	245201	751	925	7.66E-30	119.649	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5921 - 	CGI_10027711	superfamily	245225	166	542	1.57E-75	257.644	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#5921 - 	CGI_10027711	superfamily	219526	1012	1053	1.12E-05	46.4583	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#5923 - 	CGI_10027713	superfamily	245225	27	117	3.64E-06	43.7707	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#5924 - 	CGI_10027714	superfamily	201526	18	61	1.20E-08	47.1477	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#5925 - 	CGI_10027715	superfamily	201526	231	291	1.81E-13	65.2521	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#5925 - 	CGI_10027715	superfamily	201526	7	51	1.46E-11	59.8593	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#5926 - 	CGI_10027716	superfamily	201526	424	492	9.74E-14	67.1781	cl09522	Synaptobrevin superfamily	 - 	 - 	Synaptobrevin; Synaptobrevin.  
Q#5928 - 	CGI_10027719	superfamily	192535	59	277	3.36E-07	49.9018	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#5930 - 	CGI_10027721	superfamily	247683	52	106	1.69E-21	87.638	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#5930 - 	CGI_10027721	superfamily	245201	230	436	9.71E-145	417.107	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#5930 - 	CGI_10027721	superfamily	246908	114	215	4.08E-47	159.285	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#5931 - 	CGI_10027722	superfamily	241695	174	356	6.21E-68	215.033	cl00217	pyrophosphatase superfamily	 - 	 - 	Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
Q#5931 - 	CGI_10027722	superfamily	241695	2	151	1.68E-55	186.499	cl00217	pyrophosphatase superfamily	C	 - 	Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
Q#5932 - 	CGI_10027723	superfamily	241597	179	250	3.27E-36	128.185	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#5932 - 	CGI_10027723	superfamily	219805	24	75	4.54E-05	42.9668	cl07093	CTNNB1_binding superfamily	N	 - 	"N-terminal CTNNB1 binding; This region tends to appear at the N-terminus of proteins also containing DNA-binding HMG (high mobility group) boxes (pfam00505) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signaling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation. Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfill their role as transcriptional activators in T-cell differentiation."
Q#5935 - 	CGI_10027726	superfamily	219805	1	47	6.28E-11	54.5228	cl07093	CTNNB1_binding superfamily	C	 - 	"N-terminal CTNNB1 binding; This region tends to appear at the N-terminus of proteins also containing DNA-binding HMG (high mobility group) boxes (pfam00505) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signaling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation. Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfill their role as transcriptional activators in T-cell differentiation."
Q#5936 - 	CGI_10027727	superfamily	243092	136	247	1.24E-13	67.36	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5937 - 	CGI_10027728	superfamily	243058	32	150	2.44E-09	55.3983	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5937 - 	CGI_10027728	superfamily	243058	435	557	4.03E-08	51.9315	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5937 - 	CGI_10027728	superfamily	243058	369	469	8.30E-05	41.5312	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5937 - 	CGI_10027728	superfamily	243058	544	633	0.000195873	40.3756	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#5938 - 	CGI_10027729	superfamily	243859	5	97	6.72E-17	70.4366	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#5941 - 	CGI_10027732	superfamily	243092	68	401	6.90E-49	169.438	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5942 - 	CGI_10027733	superfamily	247683	67	129	7.87E-33	120.075	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#5942 - 	CGI_10027733	superfamily	247744	238	409	5.09E-22	93.5115	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#5943 - 	CGI_10027734	superfamily	246710	4	105	1.19E-18	82.9355	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#5943 - 	CGI_10027734	superfamily	217685	292	450	2.49E-50	171.748	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#5943 - 	CGI_10027734	superfamily	216290	146	277	1.45E-40	143.583	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#5946 - 	CGI_10027737	superfamily	217414	439	840	3.40E-93	301.556	cl03927	Otopetrin superfamily	 - 	 - 	"Protein of unknown function, DUF270; Protein of unknown function, DUF270.  "
Q#5946 - 	CGI_10027737	superfamily	247944	186	244	0.00137181	40.819	cl17390	Herpes_UL37_2 superfamily	C	 - 	Betaherpesvirus immediate-early glycoprotein UL37; This family consists of several Betaherpesvirus immediate-early glycoprotein UL37 sequences. The human cytomegalovirus (HCMV) UL37 immediate-early regulatory protein is a type I integral membrane N-glycoprotein which traffics through the ER and the Golgi network.
Q#5948 - 	CGI_10027739	superfamily	243035	22	134	1.91E-13	64.1781	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5951 - 	CGI_10027742	superfamily	241547	33	260	9.03E-99	291.109	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#5952 - 	CGI_10027743	superfamily	247743	1032	1124	0.00475791	37.66	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#5953 - 	CGI_10027744	superfamily	203031	72	132	0.00109785	35.3816	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#5954 - 	CGI_10027745	superfamily	193256	465	736	3.84E-71	242.161	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#5954 - 	CGI_10027745	superfamily	193257	1249	1479	5.10E-60	208.686	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#5954 - 	CGI_10027745	superfamily	193251	113	376	9.09E-42	157.405	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#5954 - 	CGI_10027745	superfamily	193253	885	1226	4.68E-39	151.343	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#5954 - 	CGI_10027745	superfamily	193256	797	871	7.94E-07	51.872	cl18189	AAA_8 superfamily	N	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#5954 - 	CGI_10027745	superfamily	193253	750	796	0.00610745	40.0201	cl15084	MT superfamily	C	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#5955 - 	CGI_10027746	superfamily	248020	28	441	1.02E-43	162.531	cl17466	Sulfatase superfamily	C	 - 	Sulfatase; Sulfatase.  
Q#5956 - 	CGI_10027747	superfamily	241832	60	172	1.16E-63	195.485	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#5957 - 	CGI_10027748	superfamily	247781	5	192	1.36E-91	278.866	cl17227	Arginosuc_synth superfamily	C	 - 	Arginosuccinate synthase; This family contains a PP-loop motif.
Q#5957 - 	CGI_10027748	superfamily	241758	189	259	9.74E-29	112.242	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#5959 - 	CGI_10027750	superfamily	222370	131	215	6.32E-31	112.231	cl16386	Longin superfamily	 - 	 - 	"Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain."
Q#5959 - 	CGI_10027750	superfamily	201526	230	285	4.51E-13	63.3261	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#5960 - 	CGI_10027751	superfamily	246721	1081	1403	7.90E-103	331.145	cl14807	ACE1-Sec16-like superfamily	 - 	 - 	"Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16; COPII coat complex plays an important role in vesicular traffic of newly synthezised proteins from the endoplasmatic reticulum (ER) to the Golgi apparatus by mediating the formation of transport vesicles. COPII consists of an outer coat, made up of the scaffold proteins Sec31 and Sec13, and the cargo adaptor complex, Sec23 and Sec24, which are recruited by the small GTPase Sar1. Sec16 is involved in the early steps of the assembly process. Sec16 forms elongated heterotetramers with Sec13, Sec13-(Sec16)2-Sec13. It interacts with Sec13 by insertion of a single beta-blade to close the six-bladded beta propeller of Sec13. In the same way Sec13 interacts with Sec31 and Nup145C, a nuclear pore protein, all of these contain a structurally related ancestral coatomer element 1 (ACE1). Sec16 is believed to be a key component in maintaining the integrity of the ER exit site."
Q#5965 - 	CGI_10027756	superfamily	241770	147	274	1.17E-23	93.9996	cl00309	PRTases_typeI superfamily	 - 	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#5965 - 	CGI_10027756	superfamily	222383	4	120	2.44E-69	213.812	cl16402	Pribosyltran_N superfamily	 - 	 - 	"N-terminal domain of ribose phosphate pyrophosphokinase; This family is frequently found N-terminal to the Pribosyltran, pfam00156."
Q#5966 - 	CGI_10027757	superfamily	241644	8	149	2.74E-54	171.616	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#5966 - 	CGI_10027757	superfamily	241643	163	199	1.41E-10	53.6171	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#5967 - 	CGI_10027758	superfamily	241622	661	745	2.84E-13	68.3622	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#5967 - 	CGI_10027758	superfamily	241559	37	115	8.01E-10	58.4763	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#5967 - 	CGI_10027758	superfamily	243050	1961	2019	1.22E-09	56.9391	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#5968 - 	CGI_10027759	superfamily	243092	347	621	5.10E-86	274.212	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#5968 - 	CGI_10027759	superfamily	243074	252	296	1.68E-12	63.2945	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#5970 - 	CGI_10027761	superfamily	218440	882	1158	1.85E-18	89.9809	cl14936	AF-4 superfamily	N	 - 	"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila."
Q#5971 - 	CGI_10027762	superfamily	243083	5	90	4.83E-29	110.237	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#5971 - 	CGI_10027762	superfamily	236582	258	313	5.17E-09	56.2955	cl18895	PRK09599 superfamily	C	 - 	6-phosphogluconate dehydrogenase-like protein; Reviewed
Q#5972 - 	CGI_10027763	superfamily	245814	210	243	0.00124729	37.3745	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#5973 - 	CGI_10027764	superfamily	246597	59	354	0	518.479	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#5973 - 	CGI_10027764	superfamily	247856	474	539	3.70E-11	59.4837	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#5974 - 	CGI_10027765	superfamily	243045	266	361	1.06E-16	75.7475	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#5974 - 	CGI_10027765	superfamily	241596	30	80	1.57E-08	51.4459	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#5974 - 	CGI_10027765	superfamily	243045	120	170	3.49E-06	44.9315	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#5976 - 	CGI_10027767	superfamily	243992	8	64	1.81E-06	41.82	cl05087	Complex1_LYR_1 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#5977 - 	CGI_10027768	superfamily	220695	72	194	0.00181333	38.7139	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#5978 - 	CGI_10027769	superfamily	222526	332	551	4.48E-51	179.853	cl16591	UBN_AB superfamily	 - 	 - 	"Ubinuclein conserved middle domain; Ubinuclein 1 and 2 (UBN1, UBN2) are members of a histone chaperone complex involved in the formation of a certain type of facultative heterochromatin, called senescence-associated heterochromatin foci (SAHF). The domain described here is conserved in many eukaryotes such as human, rat, drosophila, and zebra-fish and has been targeted for protein structure determination by the Joint Center for Structural Genomics."
Q#5978 - 	CGI_10027769	superfamily	219992	117	161	2.40E-09	55.0184	cl16007	HRD superfamily	 - 	 - 	"Hpc2-related domain; HPC2 (Histone promoter control 2) is required for cell-cycle regulation of histone transcription. It regulates transcription of the histone genes during the S-phase of the cell cycle by repressing transcription at other cell cycle stages. HPC2 mutants display synthetic interactions with FACT complex which allows RNA Pol II to elongate through nucleosomes. This short domain is referred to as the HRD or Hpc2-related domain and is found in both human, yeast and Sch. pombe sequences. Hpc2 is one of the proteins of one of the multi-subunit complexes that mediate replication-independent nucleosome assembly, along with histone chaperone proteins. the Hip4 sequence from SCH. pombe is an integral component of this complex that is required for transcriptional silencing at multiple loci."
Q#5979 - 	CGI_10027770	superfamily	242350	3	160	6.98E-35	122.819	cl01182	SprT superfamily	 - 	 - 	"SprT homologues; Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function."
Q#5979 - 	CGI_10027770	superfamily	241597	175	214	0.00274472	34.5987	cl00082	HMG-box superfamily	C	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#5980 - 	CGI_10027771	superfamily	247725	347	483	1.24E-89	279.941	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5980 - 	CGI_10027771	superfamily	247725	529	661	2.76E-47	163.926	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#5980 - 	CGI_10027771	superfamily	241647	236	264	0.00101803	37.9332	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#5981 - 	CGI_10027772	superfamily	188051	318	553	0.00908705	37.0611	cl18155	nop2p superfamily	 - 	 - 	"NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base modification]."
Q#5984 - 	CGI_10027775	superfamily	241867	1	241	8.80E-109	316.739	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#5985 - 	CGI_10027776	superfamily	147799	1	74	1.50E-08	46.4219	cl05422	Apc13p superfamily	 - 	 - 	Apc13p protein; The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc13p.
Q#5986 - 	CGI_10027777	superfamily	241739	45	173	8.87E-52	170.054	cl00268	class_II_aaRS-like_core superfamily	N	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#5987 - 	CGI_10027778	superfamily	243035	1	112	1.01E-12	59.9409	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#5988 - 	CGI_10027779	superfamily	241607	47	79	0.00220342	33.7826	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#5989 - 	CGI_10027780	superfamily	222150	7	31	3.02E-05	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#5990 - 	CGI_10027781	superfamily	215648	20	280	8.20E-19	85.3399	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#5993 - 	CGI_10027785	superfamily	246918	51	95	1.13E-07	44.4999	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5993 - 	CGI_10027785	superfamily	246918	3	48	4.70E-07	42.9591	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#5994 - 	CGI_10027786	superfamily	247724	10	44	2.48E-14	63.1167	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#5995 - 	CGI_10004272	superfamily	247941	222	387	3.35E-08	51.7445	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#5995 - 	CGI_10004272	superfamily	247941	27	124	0.00083597	39.0329	cl17387	Methyltransf_21 superfamily	N	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#5996 - 	CGI_10004273	superfamily	241575	1451	1512	2.37E-11	61.9047	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#5996 - 	CGI_10004273	superfamily	241575	1373	1405	0.000781322	39.5631	cl00054	DSRM superfamily	N	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#5998 - 	CGI_10004275	superfamily	241874	36	143	8.98E-17	77.5213	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#5999 - 	CGI_10004276	superfamily	241874	1	343	1.76E-62	210.489	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#6000 - 	CGI_10004277	superfamily	243035	228	342	4.21E-15	71.8821	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6000 - 	CGI_10004277	superfamily	243035	447	504	8.95E-06	44.1478	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6001 - 	CGI_10009317	superfamily	245819	194	368	1.12E-70	222.84	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#6001 - 	CGI_10009317	superfamily	219526	96	181	1.14E-18	83.0522	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#6001 - 	CGI_10009317	superfamily	203730	16	98	2.06E-16	76.154	cl18246	HNOB superfamily	N	 - 	"Heme NO binding; The HNOB (Heme NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#6002 - 	CGI_10009318	superfamily	215827	187	365	2.10E-30	120.266	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#6003 - 	CGI_10009319	superfamily	215827	136	314	4.97E-41	149.926	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#6004 - 	CGI_10009320	superfamily	220170	18	172	1.84E-20	85.8764	cl08542	XLF superfamily	 - 	 - 	"XLF (XRCC4-like factor); XLF (also called Cernunnos) interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated downregulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining. This family contains Nej1 (non-homologous end-joining factor), and Lif1."
Q#6005 - 	CGI_10009321	superfamily	243072	37	99	1.22E-08	51.6154	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6007 - 	CGI_10009323	superfamily	243077	10	47	8.35E-13	63.3333	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#6009 - 	CGI_10009325	superfamily	202894	106	171	1.80E-26	98.447	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#6010 - 	CGI_10009326	superfamily	248472	6	65	4.23E-28	101.244	cl17918	Ribosomal_P1_P2_L12p superfamily	C	 - 	"Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have two copies each of P1 and P2 (two heterodimers). Bacteria may have four or six copies (two or three homodimers), depending on the species. As in bacteria, the stalk is crucial for binding of initiation, elongation, and release factors in eukaryotes and archaea."
Q#6011 - 	CGI_10009327	superfamily	241832	147	247	8.10E-52	170.158	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#6011 - 	CGI_10009327	superfamily	241832	285	382	4.06E-46	155.52	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#6011 - 	CGI_10009327	superfamily	241832	25	128	1.56E-39	137.801	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#6012 - 	CGI_10009328	superfamily	243092	20	213	2.23E-07	52.7224	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6012 - 	CGI_10009328	superfamily	220045	619	702	0.00102807	38.8524	cl07455	DUF1829 superfamily	 - 	 - 	Domain of unknown function DUF1829; This short domain is usually associated with pfam08861.
Q#6016 - 	CGI_10011604	superfamily	245864	16	486	4.54E-94	295.727	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#6017 - 	CGI_10011606	superfamily	191430	14	189	2.88E-07	49.0114	cl05523	Gly_acyl_tr_N superfamily	 - 	 - 	Aralkyl acyl-CoA:amino acid N-acyltransferase; This family consists of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins EC:2.3.1.13.
Q#6017 - 	CGI_10011606	superfamily	247736	197	265	1.87E-05	41.9314	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#6019 - 	CGI_10011608	superfamily	238191	34	133	0.000967545	38.082	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6020 - 	CGI_10011609	superfamily	238191	30	133	3.21E-10	56.1864	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6021 - 	CGI_10011610	superfamily	238191	35	141	1.76E-06	45.0156	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6022 - 	CGI_10011611	superfamily	238191	1	90	2.04E-06	43.86	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6023 - 	CGI_10011612	superfamily	238191	4	540	2.26E-87	288.462	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6024 - 	CGI_10007145	superfamily	215754	13	107	3.90E-24	94.2424	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#6024 - 	CGI_10007145	superfamily	215754	112	194	2.98E-18	77.6788	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#6024 - 	CGI_10007145	superfamily	215754	221	295	1.85E-14	67.6636	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#6025 - 	CGI_10007146	superfamily	201844	204	234	8.15E-12	60.7722	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#6027 - 	CGI_10007148	superfamily	245864	35	528	4.48E-78	254.896	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#6028 - 	CGI_10007149	superfamily	245864	51	507	4.03E-102	316.913	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#6029 - 	CGI_10007150	superfamily	245864	36	486	3.27E-91	288.023	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#6030 - 	CGI_10007151	superfamily	241563	18	51	0.00205118	33.0795	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6031 - 	CGI_10007152	superfamily	243072	43	164	4.80E-26	100.921	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6033 - 	CGI_10007154	superfamily	238191	38	157	9.48E-10	55.416	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6034 - 	CGI_10007155	superfamily	238191	30	145	2.57E-05	41.1636	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6035 - 	CGI_10007156	superfamily	238191	31	566	1.63E-94	307.722	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#6036 - 	CGI_10006169	superfamily	241563	70	109	5.02E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6039 - 	CGI_10006172	superfamily	110440	744	770	0.000913662	38.1577	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6041 - 	CGI_10006174	superfamily	245213	531	566	3.84E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6041 - 	CGI_10006174	superfamily	245213	876	907	2.87E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6041 - 	CGI_10006174	superfamily	245213	916	959	6.89E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6041 - 	CGI_10006174	superfamily	245213	834	875	3.82E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6041 - 	CGI_10006174	superfamily	245213	788	824	5.83E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6041 - 	CGI_10006174	superfamily	245213	615	647	0.000393674	39.5422	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6041 - 	CGI_10006174	superfamily	245213	725	770	0.00141553	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6041 - 	CGI_10006174	superfamily	242788	45	203	4.36E-78	253.962	cl01936	Rad52_Rad22 superfamily	 - 	 - 	"Rad52/22 family double-strand break repair protein; The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52. These proteins contain two helix-hairpin-helix motifs."
Q#6041 - 	CGI_10006174	superfamily	221695	597	618	0.000706471	38.9754	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#6041 - 	CGI_10006174	superfamily	245213	960	996	0.0020741	37.6116	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6042 - 	CGI_10006175	superfamily	220647	26	189	8.20E-46	153.252	cl18565	L_HGMIC_fpl superfamily	 - 	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#6044 - 	CGI_10006177	superfamily	243119	26	62	0.00871017	33.1761	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#6045 - 	CGI_10006178	superfamily	248469	90	197	5.20E-09	51.9871	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#6046 - 	CGI_10006179	superfamily	241677	17	163	7.52E-83	243.596	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#6051 - 	CGI_10007502	superfamily	241563	97	129	5.11E-05	41.1188	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6051 - 	CGI_10007502	superfamily	245010	136	230	0.00069483	38.3679	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#6052 - 	CGI_10007503	superfamily	247727	103	207	0.000108446	39.3355	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#6053 - 	CGI_10007504	superfamily	243092	24	112	0.00449546	38.0848	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6054 - 	CGI_10007505	superfamily	110440	396	423	0.00205297	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6056 - 	CGI_10007507	superfamily	243092	27	186	1.02E-05	47.3296	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6057 - 	CGI_10007508	superfamily	241889	144	297	1.94E-61	205.146	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#6057 - 	CGI_10007508	superfamily	222150	599	624	6.48E-06	43.9197	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6057 - 	CGI_10007508	superfamily	222150	628	649	0.000214433	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6058 - 	CGI_10007509	superfamily	215647	97	166	3.22E-05	42.9809	cl18338	7tm_2 superfamily	NC	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#6059 - 	CGI_10007510	superfamily	241874	33	535	0	740.148	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#6060 - 	CGI_10007511	superfamily	215647	74	138	0.00013675	39.1289	cl18338	7tm_2 superfamily	NC	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#6062 - 	CGI_10007513	superfamily	152897	378	685	6.08E-94	297.493	cl13848	DUF3689 superfamily	 - 	 - 	Protein of unknown function (DUF3689); This family of proteins is found in eukaryotes. Proteins in this family are typically between 399 and 797 amino acids in length.
Q#6063 - 	CGI_10007514	superfamily	215686	193	260	0.0015905	36.6265	cl18340	Lipocalin superfamily	N	 - 	"Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel."
Q#6065 - 	CGI_10001203	superfamily	241686	431	493	1.02E-16	77.2609	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#6065 - 	CGI_10001203	superfamily	241686	231	294	3.65E-16	75.7201	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#6065 - 	CGI_10001203	superfamily	241686	62	124	1.80E-15	73.4089	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#6065 - 	CGI_10001203	superfamily	241686	140	200	5.78E-15	72.2533	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#6065 - 	CGI_10001203	superfamily	241686	311	371	6.40E-13	66.0901	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#6065 - 	CGI_10001203	superfamily	241686	506	569	7.87E-13	65.7049	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#6065 - 	CGI_10001203	superfamily	248469	1138	1264	0.00255027	38.5051	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#6065 - 	CGI_10001203	superfamily	215733	730	976	2.24E-60	208.188	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#6066 - 	CGI_10000493	superfamily	214531	7	49	6.06E-07	42.5889	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#6067 - 	CGI_10002974	superfamily	245847	41	187	5.56E-18	76.8265	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6068 - 	CGI_10012519	superfamily	152683	352	447	2.69E-07	48.4381	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#6068 - 	CGI_10012519	superfamily	219525	18	64	4.53E-05	41.2506	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#6069 - 	CGI_10012520	superfamily	246925	394	594	0.000116945	44.2686	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#6069 - 	CGI_10012520	superfamily	210118	801	820	0.00178798	37.6903	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#6070 - 	CGI_10012521	superfamily	241563	40	76	0.000208835	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6070 - 	CGI_10012521	superfamily	110440	462	488	0.000333046	38.5429	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6071 - 	CGI_10012522	superfamily	241623	1825	2144	1.60E-179	550.343	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#6071 - 	CGI_10012522	superfamily	241742	1597	1772	2.51E-75	250.351	cl00271	PI3Ka superfamily	 - 	 - 	"Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture."
Q#6074 - 	CGI_10012525	superfamily	241754	899	1046	3.30E-60	210.17	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#6074 - 	CGI_10012525	superfamily	241754	196	375	9.34E-44	163.175	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#6078 - 	CGI_10012529	superfamily	245101	111	196	0.00625482	36.5221	cl09608	Cas7_I-E superfamily	C	 - 	CRISPR/Cas system-associated RAMP superfamily protein Cas7; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Cse4/CasC family
Q#6080 - 	CGI_10012531	superfamily	219595	563	811	1.34E-66	223.341	cl06723	GLE1 superfamily	 - 	 - 	GLE1-like protein; The members of this family are sequences that are similar to the human protein GLE1. This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm.
Q#6081 - 	CGI_10012532	superfamily	248098	127	159	0.00398577	36.0589	cl17544	U-box superfamily	N	 - 	U-box domain; This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
Q#6083 - 	CGI_10012534	superfamily	220691	66	229	4.95E-06	46.457	cl18569	7TM_GPCR_Srv superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#6084 - 	CGI_10013092	superfamily	243072	159	295	1.69E-12	63.5566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6084 - 	CGI_10013092	superfamily	243072	13	87	0.0040714	35.8223	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6085 - 	CGI_10013093	superfamily	241574	30	165	1.94E-46	151.992	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6088 - 	CGI_10013096	superfamily	217915	255	624	5.68E-79	265.909	cl14957	Spc97_Spc98 superfamily	N	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#6091 - 	CGI_10013099	superfamily	247675	131	467	0	531.529	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#6093 - 	CGI_10013101	superfamily	247725	141	241	7.94E-07	46.4334	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6094 - 	CGI_10013102	superfamily	243091	146	256	3.58E-14	69.6707	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#6094 - 	CGI_10013102	superfamily	222150	442	467	3.08E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6094 - 	CGI_10013102	superfamily	222150	358	383	3.49E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6094 - 	CGI_10013102	superfamily	222150	498	523	3.54E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6094 - 	CGI_10013102	superfamily	222150	386	411	5.42E-06	43.9197	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6094 - 	CGI_10013102	superfamily	222150	470	495	5.53E-06	43.9197	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6094 - 	CGI_10013102	superfamily	222150	414	438	8.11E-06	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6094 - 	CGI_10013102	superfamily	222150	526	551	8.52E-06	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6094 - 	CGI_10013102	superfamily	222150	554	578	3.74E-05	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6095 - 	CGI_10013103	superfamily	243116	2292	2669	5.28E-157	492.897	cl02626	DNA_pol_A superfamily	 - 	 - 	"Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase  beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains."
Q#6095 - 	CGI_10013103	superfamily	247905	528	612	8.63E-10	59.1737	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#6095 - 	CGI_10013103	superfamily	247805	189	343	3.60E-08	54.2656	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6096 - 	CGI_10013104	superfamily	247741	6	269	1.75E-78	242.6	cl17187	Aldolase_Class_I superfamily	 - 	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#6097 - 	CGI_10013105	superfamily	247792	74	111	0.00156089	33.8925	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6098 - 	CGI_10013106	superfamily	247792	37	74	0.00378974	33.5073	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6100 - 	CGI_10013108	superfamily	244913	179	626	0	584.764	cl08327	Glyco_hydro_47 superfamily	 - 	 - 	"Glycosyl hydrolase family 47; Members of this family are alpha-mannosidases that catalyze the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2)."
Q#6101 - 	CGI_10013109	superfamily	218547	14	116	1.34E-34	117.429	cl05054	DUF727 superfamily	 - 	 - 	Protein of unknown function (DUF727); This family consists of several uncharacterized eukaryotic proteins of unknown function.
Q#6103 - 	CGI_10013111	superfamily	243072	48	160	5.80E-30	116.329	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6103 - 	CGI_10013111	superfamily	243072	201	276	4.37E-21	90.9058	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6104 - 	CGI_10013112	superfamily	241599	333	390	7.65E-11	57.6385	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#6107 - 	CGI_10005596	superfamily	242122	1413	1541	5.93E-16	77.0427	cl00824	HEPN superfamily	 - 	 - 	HEPN domain; HEPN domain.  
Q#6108 - 	CGI_10005597	superfamily	241913	195	266	3.06E-06	44.1341	cl00509	hot_dog superfamily	C	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#6109 - 	CGI_10005598	superfamily	241886	13	287	3.46E-86	262.88	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#6110 - 	CGI_10005599	superfamily	243267	26	131	1.58E-33	124.648	cl03000	Innexin superfamily	C	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#6110 - 	CGI_10005599	superfamily	243267	108	209	1.24E-08	53.3864	cl03000	Innexin superfamily	N	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#6112 - 	CGI_10021884	superfamily	247725	400	504	6.26E-41	144.007	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6113 - 	CGI_10021885	superfamily	241782	194	545	3.33E-173	498.624	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#6113 - 	CGI_10021885	superfamily	149929	10	101	8.68E-06	44.4225	cl07589	Preseq_ALAS superfamily	 - 	 - 	"5-aminolevulinate synthase presequence; The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import."
Q#6114 - 	CGI_10021886	superfamily	241563	68	109	1.71E-06	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6114 - 	CGI_10021886	superfamily	241563	28	59	0.00119127	37.0736	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6114 - 	CGI_10021886	superfamily	206779	136	203	0.00898634	36.446	cl16910	MCP_signal superfamily	N	 - 	"Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW."
Q#6115 - 	CGI_10021887	superfamily	241563	227	268	9.57E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6115 - 	CGI_10021887	superfamily	242274	28	110	3.44E-05	43.7935	cl01053	SGNH_hydrolase superfamily	NC	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#6115 - 	CGI_10021887	superfamily	241563	187	218	0.00205471	37.0736	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6117 - 	CGI_10021889	superfamily	247724	169	344	5.33E-17	79.8074	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#6119 - 	CGI_10021891	superfamily	115363	194	255	5.62E-14	65.4709	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#6119 - 	CGI_10021891	superfamily	241578	1	121	0.00186043	37.1602	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#6121 - 	CGI_10021893	superfamily	115363	406	467	2.62E-10	57.3818	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#6121 - 	CGI_10021893	superfamily	115363	605	666	6.14E-10	56.2262	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#6121 - 	CGI_10021893	superfamily	115363	680	715	0.005646	35.8106	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#6123 - 	CGI_10021895	superfamily	247905	54	104	5.13E-15	67.2628	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#6123 - 	CGI_10021895	superfamily	247805	1	76	6.77E-25	95.6293	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6124 - 	CGI_10021896	superfamily	247756	140	237	0.00101948	38.1099	cl17202	HAD superfamily	N	 - 	haloacid dehalogenase-like hydrolase; haloacid dehalogenase-like hydrolase.  
Q#6125 - 	CGI_10021897	superfamily	217473	99	322	3.10E-25	105.91	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#6131 - 	CGI_10021903	superfamily	247769	187	358	1.99E-13	67.7497	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#6131 - 	CGI_10021903	superfamily	203961	42	102	8.50E-13	63.8032	cl07209	PDEase_I_N superfamily	 - 	 - 	3'5'-cyclic nucleotide phosphodiesterase N-terminal; This domain is found to the N-terminus of the calcium/calmodulin-dependent 3'5'-cyclic nucleotide phosphodiesterase domain (pfam00233).
Q#6133 - 	CGI_10021905	superfamily	247856	50	98	0.000747338	33.6753	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#6135 - 	CGI_10021907	superfamily	245874	120	174	0.000178698	38.5614	cl12111	TNFR superfamily	N	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#6136 - 	CGI_10021908	superfamily	247057	25	92	4.61E-15	71.5118	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#6136 - 	CGI_10021908	superfamily	247057	114	181	4.61E-15	71.5118	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#6137 - 	CGI_10021909	superfamily	243175	198	347	8.86E-65	204.763	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#6137 - 	CGI_10021909	superfamily	241832	69	146	1.11E-33	120.591	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#6138 - 	CGI_10021910	superfamily	216554	49	211	5.05E-25	97.9353	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#6139 - 	CGI_10021911	superfamily	216554	80	233	2.43E-20	85.2237	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#6140 - 	CGI_10021912	superfamily	217473	98	289	1.31E-29	118.622	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#6141 - 	CGI_10021913	superfamily	243072	831	956	1.24E-24	101.306	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6141 - 	CGI_10021913	superfamily	243072	900	1023	3.40E-19	85.513	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6143 - 	CGI_10021915	superfamily	199006	43	136	8.45E-29	104.265	cl10918	Cg6151-P superfamily	 - 	 - 	"Uncharacterized conserved protein CG6151-P; This is a family of small, less than 200 residue long, proteins which are named as CG6151-P proteins that are conserved from fungi to humans. The function is unknown. The fungal members have a characteristic ICP sequence motif. Some members are annotated as putative clathrin-coated vesicle protein but this could not be defined."
Q#6144 - 	CGI_10021916	superfamily	217473	711	934	4.83E-27	113.229	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#6144 - 	CGI_10021916	superfamily	217473	96	319	5.25E-26	110.147	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#6148 - 	CGI_10021920	superfamily	243106	332	457	2.95E-47	165.713	cl02608	BAH superfamily	 - 	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#6148 - 	CGI_10021920	superfamily	243106	550	684	3.97E-56	190.786	cl02608	BAH superfamily	 - 	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#6148 - 	CGI_10021920	superfamily	221394	1	131	1.54E-40	147.487	cl13480	DNMT1-RFD superfamily	 - 	 - 	Cytosine specific DNA methyltransferase replication foci domain; This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties.
Q#6148 - 	CGI_10021920	superfamily	238192	724	953	2.30E-34	133.9	cl18939	Cyt_C5_DNA_methylase superfamily	C	 - 	"Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability."
Q#6148 - 	CGI_10021920	superfamily	202085	237	281	1.44E-18	81.2526	cl03401	zf-CXXC superfamily	 - 	 - 	"CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR."
Q#6150 - 	CGI_10021922	superfamily	247805	3	41	0.000504685	34.2352	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6153 - 	CGI_10021925	superfamily	216152	1	198	3.10E-51	171.343	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#6154 - 	CGI_10001660	superfamily	191362	149	202	6.75E-31	109.668	cl05351	zf-nanos superfamily	 - 	 - 	"Nanos RNA binding domain; This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development."
Q#6155 - 	CGI_10001661	superfamily	241563	68	109	6.13E-05	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6158 - 	CGI_10007253	superfamily	199166	657	806	5.46E-17	80.8344	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#6158 - 	CGI_10007253	superfamily	199166	458	645	9.18E-16	76.9824	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#6158 - 	CGI_10007253	superfamily	199166	337	530	5.92E-14	71.2044	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#6158 - 	CGI_10007253	superfamily	243074	292	332	6.52E-11	59.0573	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#6159 - 	CGI_10007254	superfamily	222150	495	520	1.72E-06	45.8457	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6159 - 	CGI_10007254	superfamily	222150	439	464	1.08E-05	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6159 - 	CGI_10007254	superfamily	222150	467	491	0.00451484	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6159 - 	CGI_10007254	superfamily	222150	581	606	0.00770489	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6163 - 	CGI_10007258	superfamily	248458	109	404	3.84E-05	44.2269	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#6164 - 	CGI_10007259	superfamily	241758	8	136	5.27E-24	97.0554	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#6166 - 	CGI_10007261	superfamily	245847	41	159	1.54E-11	57.9517	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6169 - 	CGI_10009877	superfamily	242043	35	73	1.06E-09	50.8036	cl00713	Auto_anti-p27 superfamily	 - 	 - 	Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
Q#6170 - 	CGI_10009878	superfamily	248054	24	218	2.33E-05	44.2155	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#6171 - 	CGI_10009879	superfamily	248054	6	220	1.88E-14	71.5647	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#6172 - 	CGI_10009880	superfamily	245864	42	305	2.78E-44	159.751	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#6172 - 	CGI_10009880	superfamily	245864	313	361	0.000275927	41.1098	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#6174 - 	CGI_10009882	superfamily	218208	632	750	3.17E-36	133.654	cl18447	CwfJ_C_1 superfamily	 - 	 - 	Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.
Q#6174 - 	CGI_10009882	superfamily	218207	759	853	2.37E-29	113.524	cl04666	CwfJ_C_2 superfamily	 - 	 - 	Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.
Q#6176 - 	CGI_10009884	superfamily	241814	47	226	1.77E-27	105.499	cl00360	COG0212 superfamily	 - 	 - 	5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]
Q#6178 - 	CGI_10009886	superfamily	246681	6	206	2.04E-101	295.169	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#6179 - 	CGI_10009887	superfamily	241974	597	728	1.07E-19	85.7562	cl00604	STAS superfamily	 - 	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#6179 - 	CGI_10009887	superfamily	216188	269	537	1.39E-43	158.535	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#6179 - 	CGI_10009887	superfamily	205965	126	209	1.21E-25	101.72	cl18285	Sulfate_tra_GLY superfamily	 - 	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#6180 - 	CGI_10009888	superfamily	247792	410	434	7.27E-05	40.5068	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6180 - 	CGI_10009888	superfamily	245814	241	286	0.000546821	37.8539	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6180 - 	CGI_10009888	superfamily	245814	325	391	2.73E-09	53.5647	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6180 - 	CGI_10009888	superfamily	245814	147	208	0.00334556	35.5589	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6181 - 	CGI_10009889	superfamily	245814	218	285	2.49E-10	55.4907	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6181 - 	CGI_10009889	superfamily	245814	112	182	7.60E-09	51.7373	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6181 - 	CGI_10009889	superfamily	245814	53	84	0.00115648	36.2308	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6182 - 	CGI_10009890	superfamily	245814	82	128	0.00101357	36.6983	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6182 - 	CGI_10009890	superfamily	245814	262	329	1.24E-11	59.3427	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6182 - 	CGI_10009890	superfamily	245814	156	227	6.85E-07	46.3445	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6183 - 	CGI_10009891	superfamily	243034	394	492	3.51E-11	61.6272	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6183 - 	CGI_10009891	superfamily	243034	786	891	1.10E-08	54.3084	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6183 - 	CGI_10009891	superfamily	243034	20	84	1.32E-05	44.6784	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6183 - 	CGI_10009891	superfamily	243072	259	366	0.00133302	38.9039	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6184 - 	CGI_10009892	superfamily	243072	296	410	7.66E-06	46.993	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6184 - 	CGI_10009892	superfamily	243072	5	81	0.00847421	37.3631	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6186 - 	CGI_10000669	superfamily	244895	38	514	4.51E-110	337.982	cl08294	Peptidase_M17 superfamily	 - 	 - 	"Cytosol aminopeptidase family, N-terminal and catalytic domains.  Family M17 contains zinc- and manganese-dependent exopeptidases ( EC  3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants."
Q#6187 - 	CGI_10002040	superfamily	247727	84	194	3.55E-07	47.0395	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#6188 - 	CGI_10002041	superfamily	188051	276	550	4.09E-112	340.213	cl18155	nop2p superfamily	 - 	 - 	"NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base modification]."
Q#6190 - 	CGI_10002043	superfamily	242406	25	67	0.000738169	35.432	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#6192 - 	CGI_10005659	superfamily	242406	1	45	0.00457227	33.7189	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#6194 - 	CGI_10005661	superfamily	243072	70	179	1.27E-29	108.24	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6196 - 	CGI_10005663	superfamily	241585	216	250	1.51E-06	44.8172	cl00066	FU superfamily	C	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#6196 - 	CGI_10005663	superfamily	216254	29	144	1.44E-26	101.941	cl08303	Recep_L_domain superfamily	 - 	 - 	Receptor L domain; The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
Q#6197 - 	CGI_10000878	superfamily	241802	53	168	6.89E-24	94.8612	cl00342	Trp-synth-beta_II superfamily	C	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#6198 - 	CGI_10000879	superfamily	221442	19	85	1.61E-23	91.4565	cl18607	Hydrolase_4 superfamily	 - 	 - 	"Putative lysophospholipase; This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins."
Q#6198 - 	CGI_10000879	superfamily	225375	106	153	0.000262771	40.0821	cl18715	COG2819 superfamily	NC	 - 	Predicted hydrolase of the alpha/beta superfamily [General function prediction only]
Q#6204 - 	CGI_10001100	superfamily	241563	62	97	0.00034947	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6204 - 	CGI_10001100	superfamily	241563	8	53	0.008482	34.6203	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6207 - 	CGI_10006678	superfamily	219619	352	426	1.15E-10	57.6027	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#6207 - 	CGI_10006678	superfamily	243066	10	90	1.02E-07	49.4737	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#6208 - 	CGI_10006679	superfamily	219619	281	356	3.35E-11	58.7583	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#6208 - 	CGI_10006679	superfamily	243066	2	43	0.00508183	34.8361	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#6209 - 	CGI_10006680	superfamily	214531	821	863	4.34E-09	54.1449	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#6209 - 	CGI_10006680	superfamily	214531	164	207	2.77E-05	42.9741	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#6209 - 	CGI_10006680	superfamily	241578	320	353	0.000212199	42.7572	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#6209 - 	CGI_10006680	superfamily	214531	210	249	0.000569119	39.1221	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#6209 - 	CGI_10006680	superfamily	214531	131	159	0.00469864	36.4257	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#6210 - 	CGI_10006681	superfamily	241578	1	130	6.60E-22	89.6582	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#6210 - 	CGI_10006681	superfamily	111397	152	232	1.93E-08	50.0323	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#6212 - 	CGI_10006683	superfamily	111397	17	78	2.80E-06	41.1727	cl03620	HYR superfamily	N	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#6213 - 	CGI_10006684	superfamily	241786	9	264	2.26E-85	262.08	cl00325	Ribosomal_L4 superfamily	 - 	 - 	Ribosomal protein L4/L1 family; This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA.
Q#6213 - 	CGI_10006684	superfamily	222716	274	353	1.02E-27	104.224	cl16836	Ribos_L4_asso_C superfamily	 - 	 - 	60S ribosomal protein L4 C-terminal domain; This family is found at the very C-terminal of 60 ribosomal L4 proteins.
Q#6214 - 	CGI_10006685	superfamily	217915	4	562	1.29E-97	311.748	cl14957	Spc97_Spc98 superfamily	 - 	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#6215 - 	CGI_10006686	superfamily	245814	27	95	4.32E-06	41.7059	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6217 - 	CGI_10010123	superfamily	247677	901	1033	4.18E-40	146.661	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#6217 - 	CGI_10010123	superfamily	247677	1154	1286	1.42E-38	142.038	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#6217 - 	CGI_10010123	superfamily	243128	65	274	1.95E-22	97.4002	cl02652	MIF4G superfamily	N	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#6217 - 	CGI_10010123	superfamily	243129	711	812	1.56E-17	80.7605	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#6217 - 	CGI_10010123	superfamily	243129	483	594	7.53E-15	73.0565	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#6218 - 	CGI_10010124	superfamily	247068	570	661	1.48E-07	50.0046	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6218 - 	CGI_10010124	superfamily	247068	483	560	3.65E-07	48.849	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6219 - 	CGI_10010125	superfamily	247743	153	299	6.43E-13	65.6303	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#6220 - 	CGI_10010126	superfamily	216554	69	248	4.73E-26	104.869	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#6221 - 	CGI_10010127	superfamily	241913	511	621	8.27E-30	114.588	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#6221 - 	CGI_10010127	superfamily	241913	321	440	1.36E-14	71.0609	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#6222 - 	CGI_10010128	superfamily	241644	9	145	5.45E-55	173.157	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#6223 - 	CGI_10010129	superfamily	241644	9	160	8.77E-63	192.417	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#6225 - 	CGI_10010131	superfamily	247095	50	496	8.60E-155	449.799	cl15837	alkPPc superfamily	 - 	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#6226 - 	CGI_10010132	superfamily	247095	85	531	3.71E-171	493.712	cl15837	alkPPc superfamily	 - 	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#6227 - 	CGI_10010133	superfamily	241750	8	447	0	579.245	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#6233 - 	CGI_10010139	superfamily	221049	881	1139	2.95E-73	247.235	cl12807	Tho2 superfamily	 - 	 - 	"Transcription factor/nuclear export subunit protein 2; THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability. Tho2, along with four other subunits forms THO"
Q#6233 - 	CGI_10010139	superfamily	152168	593	668	3.07E-33	125.066	cl13220	Thoc2 superfamily	 - 	 - 	"Transcription- and export-related complex subunit; The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats. In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex."
Q#6234 - 	CGI_10010140	superfamily	243175	339	400	5.59E-25	98.1586	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#6234 - 	CGI_10010140	superfamily	242920	42	91	1.11E-06	46.2679	cl02174	TAF13 superfamily	N	 - 	"The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is  involved  in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID.   Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and are found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF13 interacts with TAF11 and makes a histone-like heterodimer similar to H3/H4-like proteins. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex."
Q#6235 - 	CGI_10010141	superfamily	217474	71	332	9.53E-32	122.461	cl03979	PAE superfamily	 - 	 - 	Pectinacetylesterase; Pectinacetylesterase.  
Q#6236 - 	CGI_10001227	superfamily	222225	8	124	1.11E-05	44.0504	cl18652	DoxX_2 superfamily	 - 	 - 	DoxX-like family; This family of uncharacterized proteins are related to DoxX pfam07681.
Q#6237 - 	CGI_10001228	superfamily	243948	8	328	2.49E-120	353.133	cl04955	LanC_like superfamily	 - 	 - 	"LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans), in addition to  2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition. A related domain is also present in LanM and other pro- and eukaryotic proteins of unknown function."
Q#6239 - 	CGI_10004240	superfamily	247746	251	365	0.00149674	38.0082	cl17192	ATP-synt_B superfamily	 - 	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#6240 - 	CGI_10004241	superfamily	247683	255	328	0.0086401	34.4785	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6245 - 	CGI_10001192	superfamily	247724	40	87	0.00157367	36.8165	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#6248 - 	CGI_10001391	superfamily	248458	50	449	1.04E-17	83.5173	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#6249 - 	CGI_10014087	superfamily	243555	10	202	2.05E-12	62.0234	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#6252 - 	CGI_10014090	superfamily	241766	20	294	5.79E-124	371.06	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#6254 - 	CGI_10014092	superfamily	241782	32	400	1.82E-51	177.533	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#6255 - 	CGI_10014093	superfamily	241596	55	110	1.17E-09	51.4459	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#6256 - 	CGI_10014094	superfamily	248458	39	204	1.48E-11	64.6425	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#6256 - 	CGI_10014094	superfamily	248458	352	534	1.53E-07	52.3161	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#6257 - 	CGI_10014095	superfamily	176599	20	153	1.89E-29	106.4	cl03381	pVHL superfamily	 - 	 - 	"von Hippel-Landau (pVHL) tumor suppressor protein; von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts as the substrate recognition component of an E3 ubiquitin ligase complex.  Several proteins have been identified as pVHL-binding proteins that are subject to ubiquitin-mediated proteolysis; the best characterized putative substrates are the alpha subunits of the hypoxia-inducible factor (HIF1alpha, HIF2alpha, and HIF3alpha). In addition to HIF degradation, pVHL has been implicated to be involved in HIF independent cellular processes. Germline VHL mutations cause renal cell carcinomas, hemangioblastomas and pheochromocytomas in humans. pVHL can bind to and direct the proper deposition of fibronectin and collagen IV within the extracellular matrix. It works to stabilize microtubules and foster the maintenance of primary cilium. It also has been reported to promote the stabilization and activation of p53 in a HIF-independent manner and, in neuronal cells, promote apoptosis by down-regulation of Jun-B."
Q#6260 - 	CGI_10014098	superfamily	245213	182	215	1.75E-05	41.6934	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6260 - 	CGI_10014098	superfamily	245847	225	354	1.40E-16	75.0813	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6261 - 	CGI_10014099	superfamily	245213	177	210	2.00E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6261 - 	CGI_10014099	superfamily	247068	106	162	0.000112515	39.9894	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6261 - 	CGI_10014099	superfamily	245847	228	355	1.06E-08	52.3545	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6262 - 	CGI_10014100	superfamily	245847	177	317	3.62E-28	107.053	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6262 - 	CGI_10014100	superfamily	218564	122	160	0.000803867	36.81	cl18463	He_PIG superfamily	 - 	 - 	Putative Ig domain; This alignment represents the conserved core region of ~90 residue repeat found in several haemagglutinins and other cell surface proteins. Sequence similarities to (pfam02494) and (pfam00801) suggest an Ig-like fold (personal obs:C. Yeats). So this family may be similar in function to the (pfam02639) and (pfam02638) domains. This domain is also found in the WisP family of proteins of Tropheryma whipplei.
Q#6263 - 	CGI_10014101	superfamily	245213	328	362	2.76E-08	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6263 - 	CGI_10014101	superfamily	219635	21	186	1.14E-45	159.734	cl06790	Peptidase_C78 superfamily	 - 	 - 	Peptidase family C78; This family formerly known as DUF1671 has been shown to be a cysteine peptidase called (Ufm1)-specific protease.
Q#6263 - 	CGI_10014101	superfamily	245847	370	515	4.96E-11	60.4437	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6264 - 	CGI_10014102	superfamily	245847	209	352	1.06E-24	97.4228	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6264 - 	CGI_10014102	superfamily	245213	169	203	2.21E-08	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6264 - 	CGI_10014102	superfamily	247068	93	169	1.61E-05	42.3006	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6266 - 	CGI_10014104	superfamily	241563	69	98	0.00228662	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6266 - 	CGI_10014104	superfamily	204194	111	208	0.00907434	34.9353	cl07806	Cortex-I_coil superfamily	 - 	 - 	"Cortexillin I, coiled coil; Members of this family are predominantly found in the actin-bundling protein Cortexillin I from Dictyostelium discoideum. They adopt a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and are a prerequisite for the assembly of Cortexillin I."
Q#6267 - 	CGI_10014105	superfamily	246669	1115	1267	2.08E-67	224.186	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#6267 - 	CGI_10014105	superfamily	243096	768	951	4.17E-47	168.245	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#6267 - 	CGI_10014105	superfamily	247683	582	639	2.46E-31	118.98	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6267 - 	CGI_10014105	superfamily	247683	689	740	6.42E-26	103.264	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6267 - 	CGI_10014105	superfamily	247683	376	425	1.21E-25	102.493	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6267 - 	CGI_10014105	superfamily	247683	283	334	1.92E-25	101.674	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6267 - 	CGI_10014105	superfamily	247725	978	1104	2.08E-44	158.775	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6267 - 	CGI_10014105	superfamily	247683	176	231	9.27E-22	91.2654	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6270 - 	CGI_10001538	superfamily	245201	131	305	6.12E-37	134.184	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6275 - 	CGI_10018561	superfamily	243992	9	72	7.10E-09	47.1834	cl05087	Complex1_LYR_1 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#6276 - 	CGI_10018562	superfamily	215648	1	199	2.74E-15	71.858	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#6277 - 	CGI_10018563	superfamily	245225	28	344	2.65E-27	109.659	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#6278 - 	CGI_10018564	superfamily	247723	46	119	1.66E-39	136.55	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#6279 - 	CGI_10018565	superfamily	247749	11	466	0	546.205	cl17195	LDH_MDH_like superfamily	 - 	 - 	"NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others."
Q#6281 - 	CGI_10018567	superfamily	241555	4	169	5.09E-65	199.317	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#6282 - 	CGI_10018568	superfamily	241866	1	407	0	853.128	cl00445	Iso_dh superfamily	 - 	 - 	Isocitrate/isopropylmalate dehydrogenase; Isocitrate/isopropylmalate dehydrogenase.  
Q#6283 - 	CGI_10018569	superfamily	221051	1	220	2.93E-73	238.217	cl12809	Med25_VWA superfamily	 - 	 - 	"Mediator complex subunit 25 von Willebrand factor type A; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex."
Q#6283 - 	CGI_10018569	superfamily	192726	412	561	5.63E-53	179.956	cl12779	Med25 superfamily	 - 	 - 	"Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear."
Q#6284 - 	CGI_10018570	superfamily	247065	4	112	8.63E-20	79.6962	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#6285 - 	CGI_10018571	superfamily	241581	438	535	8.26E-08	51.233	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#6285 - 	CGI_10018571	superfamily	241754	1	338	1.13E-161	483.352	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#6287 - 	CGI_10018573	superfamily	243072	248	357	5.68E-19	81.661	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6287 - 	CGI_10018573	superfamily	243072	185	299	7.49E-12	61.6306	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6288 - 	CGI_10018574	superfamily	241870	7	164	2.42E-57	189.617	cl00451	MoCF_BD superfamily	 - 	 - 	"MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin."
Q#6288 - 	CGI_10018574	superfamily	241758	300	450	2.30E-36	132.529	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#6289 - 	CGI_10018575	superfamily	245815	5	160	1.07E-80	248.29	cl11961	ALDH-SF superfamily	C	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#6290 - 	CGI_10018576	superfamily	245815	1	251	2.63E-141	407.763	cl11961	ALDH-SF superfamily	N	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#6291 - 	CGI_10018577	superfamily	128937	4	69	2.93E-11	55.3464	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#6291 - 	CGI_10018577	superfamily	128937	79	139	8.95E-11	54.1908	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#6292 - 	CGI_10018579	superfamily	241563	61	97	0.00251107	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6294 - 	CGI_10018581	superfamily	242457	48	133	1.07E-05	43.4667	cl01368	GyrI-like superfamily	C	 - 	"GyrI-like small molecule binding domain; This family contains the small molecule binding domain of a number of different bacterial transcription activators. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira."
Q#6295 - 	CGI_10018582	superfamily	243050	336	393	2.83E-16	73.2226	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#6296 - 	CGI_10018583	superfamily	245814	281	345	1.32E-11	59.8103	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6296 - 	CGI_10018583	superfamily	245814	186	257	2.71E-08	50.1803	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6297 - 	CGI_10018584	superfamily	242043	27	92	0.00602096	31.9134	cl00713	Auto_anti-p27 superfamily	N	 - 	Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
Q#6303 - 	CGI_10001818	superfamily	241766	23	309	6.55E-127	366.778	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#6305 - 	CGI_10002008	superfamily	245660	2	146	0.0024752	37.5866	cl11493	PQQ_DH_like superfamily	C	 - 	"PQQ-dependent dehydrogenases and related proteins; This family is composed of dehydrogenases with pyrroloquinoline quinone (PQQ) as a cofactor, such as ethanol, methanol, and membrane-bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller, and the family also includes distantly related proteins which are not enzymatically active and do not bind PQQ."
Q#6308 - 	CGI_10005698	superfamily	243091	79	175	2.15E-08	53.1071	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#6308 - 	CGI_10005698	superfamily	222150	772	796	1.43E-05	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6308 - 	CGI_10005698	superfamily	246975	760	780	0.0017452	37.3265	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#6308 - 	CGI_10005698	superfamily	222150	800	824	0.00793209	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6309 - 	CGI_10005699	superfamily	241590	497	550	8.07E-19	81.9696	cl00072	GYF superfamily	 - 	 - 	GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
Q#6311 - 	CGI_10005701	superfamily	243555	36	219	6.09E-05	43.1486	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#6312 - 	CGI_10005702	superfamily	247095	41	476	2.54E-173	496.793	cl15837	alkPPc superfamily	 - 	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#6313 - 	CGI_10005703	superfamily	243250	40	349	1.48E-76	245.251	cl02959	Glyco_hydro_9 superfamily	N	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#6314 - 	CGI_10001863	superfamily	245201	641	711	0.00204894	39.2441	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6314 - 	CGI_10001863	superfamily	219677	21	44	0.00864486	35.106	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#6315 - 	CGI_10001434	superfamily	243035	23	147	4.11E-12	61.8669	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6316 - 	CGI_10002660	superfamily	241600	3	117	5.86E-33	115.801	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6317 - 	CGI_10002661	superfamily	247941	434	489	0.000478447	39.6265	cl17387	Methyltransf_21 superfamily	C	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#6318 - 	CGI_10002662	superfamily	247792	6	51	0.000150813	38.1956	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6319 - 	CGI_10002663	superfamily	219619	90	146	7.93E-15	68.0031	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#6319 - 	CGI_10002663	superfamily	219619	185	230	6.14E-09	51.8247	cl18518	Ion_trans_2 superfamily	C	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#6321 - 	CGI_10002665	superfamily	241600	1	117	1.28E-32	115.03	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6322 - 	CGI_10002285	superfamily	193256	46	114	9.96E-07	46.4792	cl18189	AAA_8 superfamily	N	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#6324 - 	CGI_10002860	superfamily	247068	225	319	8.15E-13	65.0273	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6324 - 	CGI_10002860	superfamily	247068	427	507	2.81E-05	42.6858	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6325 - 	CGI_10003103	superfamily	241568	86	143	6.06E-07	45.9168	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#6325 - 	CGI_10003103	superfamily	241568	214	273	0.00801408	34.0393	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#6325 - 	CGI_10003103	superfamily	205157	23	50	0.00951484	33.6651	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#6327 - 	CGI_10002502	superfamily	243073	358	389	0.000158318	39.117	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#6332 - 	CGI_10003149	superfamily	243072	58	115	4.52E-13	64.327	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6333 - 	CGI_10003150	superfamily	217293	28	221	4.00E-50	172.047	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6333 - 	CGI_10003150	superfamily	202474	229	483	5.26E-21	91.176	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#6337 - 	CGI_10003137	superfamily	241563	109	147	1.27E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6337 - 	CGI_10003137	superfamily	241563	53	97	0.00107232	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6340 - 	CGI_10005469	superfamily	241832	60	184	1.57E-43	144.292	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#6341 - 	CGI_10005470	superfamily	241832	116	215	1.11E-53	171.93	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#6342 - 	CGI_10005471	superfamily	242167	137	210	5.79E-41	135.707	cl00883	RNA_pol_Rpb5_C superfamily	 - 	 - 	"RNA polymerase Rpb5, C-terminal domain; The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain."
Q#6342 - 	CGI_10005471	superfamily	217772	1	95	1.62E-39	132.769	cl04305	RNA_pol_Rpb5_N superfamily	 - 	 - 	"RNA polymerase Rpb5, N-terminal domain; Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure. This module is important for positioning the downstream DNA."
Q#6345 - 	CGI_10000536	superfamily	220647	26	103	4.06E-18	76.2123	cl18565	L_HGMIC_fpl superfamily	C	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#6355 - 	CGI_10014372	superfamily	247907	1421	1598	1.36E-25	106.348	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6355 - 	CGI_10014372	superfamily	247068	76	180	2.09E-24	101.236	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	953	1058	8.27E-23	96.6137	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	749	845	2.69E-21	92.3765	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	189	278	1.52E-19	86.9837	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	416	520	5.96E-19	85.4429	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	529	622	2.38E-18	83.5169	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	638	737	1.66E-17	81.2057	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247907	1686	1801	3.84E-13	69.7544	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6355 - 	CGI_10014372	superfamily	247068	853	946	4.89E-11	62.3309	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	294	399	0.000105062	43.071	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	247068	5	64	0.000302346	41.5302	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6355 - 	CGI_10014372	superfamily	245213	1899	1937	0.000303649	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6355 - 	CGI_10014372	superfamily	245213	1634	1663	0.00376467	37.6162	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6355 - 	CGI_10014372	superfamily	245213	1383	1415	0.00949536	36.6858	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6355 - 	CGI_10014372	superfamily	216265	1971	2044	3.00E-15	75.802	cl03079	Cadherin_C superfamily	N	 - 	Cadherin cytoplasmic region; Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
Q#6355 - 	CGI_10014372	superfamily	243179	2245	2318	0.000707178	40.5939	cl02781	tetraspanin_LEL superfamily	C	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#6356 - 	CGI_10014373	superfamily	155088	161	215	7.45E-07	47.2054	cl02758	AMOP superfamily	N	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#6357 - 	CGI_10014374	superfamily	243124	105	191	4.31E-18	75.9167	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#6358 - 	CGI_10014375	superfamily	241984	89	325	1.64E-11	61.5035	cl00615	Membrane-FADS-like superfamily	 - 	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#6359 - 	CGI_10014376	superfamily	247792	324	376	1.33E-15	70.8279	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6359 - 	CGI_10014376	superfamily	214806	213	299	2.06E-13	65.7797	cl15966	CRA superfamily	 - 	 - 	"CT11-RanBPM; protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)"
Q#6359 - 	CGI_10014376	superfamily	128914	154	206	2.30E-08	50.2622	cl15352	CTLH superfamily	 - 	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#6360 - 	CGI_10014377	superfamily	243092	145	321	2.66E-15	73.5232	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6361 - 	CGI_10014378	superfamily	247725	139	238	6.36E-19	82.626	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6362 - 	CGI_10014379	superfamily	247725	514	611	7.30E-18	79.9296	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6362 - 	CGI_10014379	superfamily	243092	270	404	7.07E-05	43.8628	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6364 - 	CGI_10014381	superfamily	247792	335	377	2.15E-08	50.1368	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6365 - 	CGI_10014382	superfamily	243175	94	218	5.25E-40	135.419	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#6365 - 	CGI_10014382	superfamily	241832	3	70	1.70E-31	111.951	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#6366 - 	CGI_10014383	superfamily	241629	17	95	4.32E-21	83.2712	cl00133	SCP superfamily	N	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#6367 - 	CGI_10014384	superfamily	241610	197	249	1.75E-20	82.2978	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#6367 - 	CGI_10014384	superfamily	241610	134	181	1.15E-16	71.5122	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#6369 - 	CGI_10014386	superfamily	241600	10	84	9.66E-33	122.734	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6370 - 	CGI_10014387	superfamily	220635	30	98	0.00215433	35.5878	cl12380	DUF2151 superfamily	C	 - 	"Cell cycle and development regulator; This is a set of proteins conserved from worms to humans. The proteins are a PAN GU kinase substrate, Mat89Bb, essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells."
Q#6372 - 	CGI_10014389	superfamily	243161	3	60	9.30E-05	38.1442	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#6373 - 	CGI_10012103	superfamily	241563	123	163	8.57E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6373 - 	CGI_10012103	superfamily	110440	387	414	0.00165894	37.7725	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6373 - 	CGI_10012103	superfamily	241563	70	115	0.00202948	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6376 - 	CGI_10012106	superfamily	217490	71	194	0.00268778	36.6241	cl09303	ETX_MTX2 superfamily	C	 - 	Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2; This family appears to be distantly related to pfam01117.
Q#6377 - 	CGI_10012107	superfamily	247057	116	183	1.34E-12	66.2053	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#6378 - 	CGI_10012108	superfamily	246908	5	108	1.87E-43	144.924	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#6378 - 	CGI_10012108	superfamily	247683	107	161	1.08E-23	91.2698	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6378 - 	CGI_10012108	superfamily	247683	195	251	1.14E-23	91.0093	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#6380 - 	CGI_10012110	superfamily	215647	223	465	2.77E-28	111.932	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#6380 - 	CGI_10012110	superfamily	243029	146	209	3.54E-17	76.2353	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#6381 - 	CGI_10012111	superfamily	243066	21	109	8.33E-10	57.2421	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#6382 - 	CGI_10012112	superfamily	243066	249	351	2.24E-19	85.7469	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#6382 - 	CGI_10012112	superfamily	222150	735	759	1.55E-05	43.9197	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6383 - 	CGI_10012113	superfamily	241573	415	713	1.29E-106	338.152	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#6383 - 	CGI_10012113	superfamily	245201	3	222	1.08E-97	311.74	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6383 - 	CGI_10012113	superfamily	241653	739	867	4.45E-24	100.518	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#6384 - 	CGI_10012114	superfamily	243179	115	160	5.01E-05	39.3855	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#6385 - 	CGI_10012115	superfamily	220672	17	244	3.70E-36	130.059	cl10957	Frag1 superfamily	 - 	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#6386 - 	CGI_10012116	superfamily	243092	11	292	7.10E-31	118.977	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6387 - 	CGI_10012117	superfamily	247684	13	434	6.25E-121	366.217	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#6388 - 	CGI_10012118	superfamily	241622	231	311	2.50E-08	52.5691	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#6389 - 	CGI_10012119	superfamily	243263	15	380	8.08E-66	225.365	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#6389 - 	CGI_10012119	superfamily	243263	618	665	0.00105891	40.469	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#6390 - 	CGI_10012120	superfamily	243263	8	149	3.42E-22	98.6341	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#6390 - 	CGI_10012120	superfamily	243263	600	657	7.70E-17	82.0706	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#6391 - 	CGI_10003420	superfamily	109874	31	116	8.97E-07	43.437	cl02980	Stathmin superfamily	N	 - 	Stathmin family; The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton. They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerisation of tubulin heterodimers.
Q#6393 - 	CGI_10003422	superfamily	193253	99	171	0.00705669	35.3977	cl15084	MT superfamily	NC	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#6394 - 	CGI_10003423	superfamily	247916	63	172	1.42E-06	47.7806	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#6396 - 	CGI_10003425	superfamily	202894	112	179	6.07E-24	96.1358	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#6397 - 	CGI_10003426	superfamily	247744	7	196	1.54E-77	234.053	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#6399 - 	CGI_10018793	superfamily	246918	65	110	2.08E-09	50.6631	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#6399 - 	CGI_10018793	superfamily	241613	127	161	0.00033636	36.4158	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#6401 - 	CGI_10018795	superfamily	241613	313	347	3.84E-07	47.2014	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#6401 - 	CGI_10018795	superfamily	241613	85	119	6.23E-07	46.8162	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#6401 - 	CGI_10018795	superfamily	241613	352	386	2.69E-05	41.8086	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#6401 - 	CGI_10018795	superfamily	241613	7	41	2.96E-05	41.8086	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#6401 - 	CGI_10018795	superfamily	241613	46	80	9.19E-05	40.2678	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#6401 - 	CGI_10018795	superfamily	241613	273	302	0.00326248	36.0306	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#6404 - 	CGI_10018798	superfamily	241584	134	227	2.55E-14	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#6407 - 	CGI_10018801	superfamily	242683	12	161	1.10E-10	56.1097	cl01747	SMI1_KNR4 superfamily	 - 	 - 	"SMI1 / KNR4 family (SUKH-1); Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems."
Q#6408 - 	CGI_10018802	superfamily	248204	31	96	3.89E-16	68.0263	cl17650	DUF836 superfamily	 - 	 - 	Glutaredoxin-like domain (DUF836); These proteins are related to the pfam00462 family.
Q#6411 - 	CGI_10018805	superfamily	241563	158	197	4.19E-07	46.5115	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6411 - 	CGI_10018805	superfamily	217020	204	303	0.00195391	36.4186	cl03574	Seryl_tRNA_N superfamily	 - 	 - 	Seryl-tRNA synthetase N-terminal domain; This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Q#6412 - 	CGI_10018806	superfamily	247792	84	147	8.47E-06	42.818	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6412 - 	CGI_10018806	superfamily	241563	182	232	4.68E-05	40.7336	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6418 - 	CGI_10018812	superfamily	241763	48	126	0.000330992	39.1759	cl00298	Peptidase_C1 superfamily	C	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#6419 - 	CGI_10018813	superfamily	243035	97	158	9.61E-19	77.3363	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6420 - 	CGI_10010757	superfamily	242443	64	317	2.48E-73	230.692	cl01342	Peptidase_A22B superfamily	 - 	 - 	"Signal peptide peptidase; The members of this family are membrane proteins. In some proteins this region is found associated with pfam02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with pfam01080."
Q#6421 - 	CGI_10010758	superfamily	241570	163	272	6.05E-32	117.427	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#6421 - 	CGI_10010758	superfamily	241570	281	396	2.73E-30	112.805	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#6422 - 	CGI_10010759	superfamily	247724	3253	3286	0.000311827	42.7123	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#6422 - 	CGI_10010759	superfamily	247724	3420	3507	0.00482324	39.8374	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#6423 - 	CGI_10010760	superfamily	243091	534	581	1.30E-08	53.2648	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#6424 - 	CGI_10010761	superfamily	243034	34	121	3.28E-12	63.9384	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6424 - 	CGI_10010761	superfamily	243034	210	300	0.000135863	40.8264	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6424 - 	CGI_10010761	superfamily	243091	623	662	6.89E-07	48.2572	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#6425 - 	CGI_10010762	superfamily	244723	355	479	1.55E-34	130.508	cl07443	Cdt1_m superfamily	C	 - 	"The middle winged helix fold of replication licensing factor Cdt1 binds geminin to inhibit binding of the MCM complex to origins of replication and DNA; Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the origin recognition complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replication origins in the G phase, ORC first binds origin DNA and triggers the binding of Cdc6 and Cdt1. These two factors recruit a putative replicative helicase and the MCM2-7. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication in S-phase. Cdt1 is present during G1 and early S phase of the cell cycle and degraded during the late S, G2, and M phases. The winged helix fold structure of Cdt1_m is similar to the structures of Cdt1_c and other archaeal homologues of the eukaryotic replication initiator, without apparent sequence similarity."
Q#6425 - 	CGI_10010762	superfamily	176572	465	575	6.65E-30	115.457	cl14631	Cdt1_c superfamily	 - 	 - 	"The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase; Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replication origins in the G phase, ORC first binds origin DNA and triggers the binding of Cdc6 and Cdt1. These two factors recruit a putative replicative helicase and the MCM2-7. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication in S-phase. Cdt1 is present during G1 and early S phase of the cell cycle and is degraded during the late S, G2, and M phases. The winged helix fold structure of Cdt1_m is similar to the structures of Cdt1_c and archaeal homologues of the eukaryotic replication initiator, without apparent sequence similarity."
Q#6428 - 	CGI_10010765	superfamily	246680	163	225	1.59E-10	55.0342	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#6428 - 	CGI_10010765	superfamily	205042	83	102	0.00382093	34.2352	cl15053	RHIM superfamily	N	 - 	"RIP homotypic interaction motif; RIP proteins are receptor-interacting serine/threonine-protein kinases or cell death proteins. This interacting domain is involved in virus recognition. The RHIM domain is necessary for the recruitment of RIP and RIP3 by the IFN-inducible protein DNA-dependent activator of IRFs (DAI), also known as DLM-1 or Z-DNA binding protein (ZBP1). Both the RIP kinases contribute to DAI-induced NF-kappaB activation. RIP3 undergoes auto phosphorylation on binding to DAI."
Q#6429 - 	CGI_10010766	superfamily	220692	37	335	2.21E-23	97.6601	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#6430 - 	CGI_10010767	superfamily	220692	35	333	9.95E-25	101.512	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#6431 - 	CGI_10010768	superfamily	243035	19	81	0.000313628	36.0586	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6433 - 	CGI_10010770	superfamily	248264	58	80	0.00318163	32.5942	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#6434 - 	CGI_10010771	superfamily	243072	10	67	1.38E-05	41.6003	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6434 - 	CGI_10010771	superfamily	222209	76	104	0.000989802	36.2249	cl18648	UvrD_C_2 superfamily	N	 - 	Family description; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Q#6435 - 	CGI_10001665	superfamily	245225	1519	1969	2.77E-75	261.409	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#6435 - 	CGI_10001665	superfamily	245225	2016	2462	1.07E-68	242.149	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#6435 - 	CGI_10001665	superfamily	245225	55	506	2.01E-54	200.162	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#6435 - 	CGI_10001665	superfamily	245225	1041	1416	8.73E-35	140.841	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#6435 - 	CGI_10001665	superfamily	245225	560	1002	3.51E-33	135.833	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#6435 - 	CGI_10001665	superfamily	215648	2554	2685	1.16E-19	91.1179	cl02802	7tm_3 superfamily	C	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#6436 - 	CGI_10001666	superfamily	246597	15	153	2.22E-100	293.362	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#6436 - 	CGI_10001666	superfamily	246597	1	23	1.63E-10	56.8498	cl13995	MPP_superfamily superfamily	NC	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#6437 - 	CGI_10003243	superfamily	248213	60	107	0.000388136	36.7841	cl17659	DivIC superfamily	C	 - 	Septum formation initiator; DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil.
Q#6444 - 	CGI_10002890	superfamily	238012	215	263	3.27E-05	40.8006	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#6444 - 	CGI_10002890	superfamily	243198	29	213	1.49E-61	198.738	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#6444 - 	CGI_10002890	superfamily	238012	274	319	0.00312478	35.0226	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#6446 - 	CGI_10002892	superfamily	248458	59	437	1.41E-22	97.3844	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#6447 - 	CGI_10002893	superfamily	243034	35	134	9.89E-17	78.5759	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6447 - 	CGI_10002893	superfamily	243034	421	533	7.95E-07	48.9156	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6447 - 	CGI_10002893	superfamily	243034	246	371	1.13E-05	45.4488	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6447 - 	CGI_10002893	superfamily	243034	168	274	0.0001609	41.982	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6447 - 	CGI_10002893	superfamily	248422	912	1161	6.56E-25	107.022	cl17868	CHAT superfamily	 - 	 - 	CHAT domain; These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins.
Q#6447 - 	CGI_10002893	superfamily	248422	723	788	2.69E-09	58.8717	cl17868	CHAT superfamily	C	 - 	CHAT domain; These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins.
Q#6452 - 	CGI_10006042	superfamily	220609	11	74	2.87E-08	46.126	cl10860	EnY2 superfamily	C	 - 	Transcription factor e(y)2; EnY2 is a small transcription factor which is combined in a complex with the TAFII40 protein. The protein is conserved from paramecium to humans.
Q#6455 - 	CGI_10006045	superfamily	241644	33	169	6.69E-61	187.795	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#6456 - 	CGI_10006046	superfamily	216363	183	325	2.82E-33	126.046	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#6456 - 	CGI_10006046	superfamily	243141	35	125	1.28E-15	75.0863	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#6456 - 	CGI_10006046	superfamily	215647	1008	1185	1.58E-06	49.5293	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#6458 - 	CGI_10009626	superfamily	241575	134	200	1.42E-08	49.5783	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#6458 - 	CGI_10009626	superfamily	241575	46	111	3.09E-07	45.7263	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#6459 - 	CGI_10009627	superfamily	243132	57	353	1.56E-99	304.301	cl02661	A_deamin superfamily	C	 - 	"Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc."
Q#6460 - 	CGI_10009628	superfamily	217293	1	168	2.07E-67	215.575	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6460 - 	CGI_10009628	superfamily	202474	175	402	2.70E-46	160.512	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#6461 - 	CGI_10009629	superfamily	217293	23	62	3.80E-10	51.8647	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6462 - 	CGI_10009630	superfamily	217293	54	271	3.84E-71	228.671	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6462 - 	CGI_10009630	superfamily	202474	278	510	3.56E-26	106.199	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#6464 - 	CGI_10009632	superfamily	218200	32	260	1.47E-69	223.783	cl04660	Glyco_transf_54 superfamily	 - 	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#6467 - 	CGI_10009635	superfamily	241563	61	97	0.00279577	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6468 - 	CGI_10003812	superfamily	243034	191	310	6.71E-05	41.2116	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6468 - 	CGI_10003812	superfamily	243034	321	399	0.00017962	39.6708	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6469 - 	CGI_10003813	superfamily	248099	145	220	2.17E-10	56.9491	cl17545	Bromo_TP superfamily	 - 	 - 	Bromodomain associated; This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold.
Q#6472 - 	CGI_10003816	superfamily	193257	3243	3478	1.03E-38	148.21	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#6472 - 	CGI_10003816	superfamily	193253	2896	3228	1.39E-32	133.238	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#6472 - 	CGI_10003816	superfamily	193256	2615	2834	7.11E-25	108.111	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#6472 - 	CGI_10003816	superfamily	247743	1981	2106	1.31E-19	89.2768	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#6472 - 	CGI_10003816	superfamily	193251	2258	2497	5.79E-12	68.0388	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#6473 - 	CGI_10003817	superfamily	217613	83	197	4.84E-46	150.018	cl04154	Cullin_binding superfamily	 - 	 - 	"Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices."
Q#6474 - 	CGI_10004931	superfamily	247809	122	328	9.12E-93	282.268	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#6474 - 	CGI_10004931	superfamily	244920	343	450	7.23E-47	158.731	cl08365	Biotin_carb_C superfamily	 - 	 - 	"Biotin carboxylase C-terminal domain; Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyzes the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain."
Q#6474 - 	CGI_10004931	superfamily	201133	27	116	2.81E-36	129.91	cl02837	CPSase_L_chain superfamily	 - 	 - 	"Carbamoyl-phosphate synthase L chain, N-terminal domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117."
Q#6475 - 	CGI_10004932	superfamily	243082	1666	1685	1.31E-07	54.1855	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#6476 - 	CGI_10004933	superfamily	243035	814	930	3.56E-30	116.565	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6477 - 	CGI_10004934	superfamily	221177	158	409	1.82E-79	252.352	cl13203	Slu7 superfamily	 - 	 - 	"Pre-mRNA splicing Prp18-interacting factor; The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyzes the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain."
Q#6483 - 	CGI_10015660	superfamily	245847	3	137	0.000534623	36.3264	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6485 - 	CGI_10015662	superfamily	241563	61	97	0.0043574	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6486 - 	CGI_10015663	superfamily	241568	14	68	6.70E-05	35.9016	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#6487 - 	CGI_10015664	superfamily	247068	167	239	0.000398701	39.9894	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6487 - 	CGI_10015664	superfamily	245201	721	996	9.64E-120	372.759	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6488 - 	CGI_10015665	superfamily	215754	119	206	1.27E-21	87.3088	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#6488 - 	CGI_10015665	superfamily	215754	221	313	3.50E-19	80.3752	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#6488 - 	CGI_10015665	superfamily	215754	11	99	2.44E-18	78.064	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#6489 - 	CGI_10015666	superfamily	247068	739	839	8.16E-21	92.7617	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3406	3500	3.37E-19	88.1393	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1392	1484	2.52E-16	79.6649	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4709	4805	3.24E-16	79.2797	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1933	2026	1.62E-15	77.3537	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4060	4154	2.57E-15	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3513	3612	4.52E-15	76.1981	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7170	7263	8.77E-15	75.4277	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1499	1590	9.49E-15	75.0425	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1279	1379	1.42E-14	74.6573	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	849	946	2.42E-14	73.8869	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6454	6544	2.95E-14	73.8869	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	158	249	3.72E-14	73.5017	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1068	1159	4.92E-14	73.1165	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3624	3719	7.03E-14	72.7313	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8900	9001	8.01E-14	72.3461	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	9754	9855	8.01E-14	72.3461	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2688	2782	1.52E-13	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8434	8526	2.05E-13	71.1905	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	9288	9380	2.05E-13	71.1905	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5628	5722	2.65E-13	70.8053	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8325	8413	3.93E-13	70.4201	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5024	5114	4.18E-13	70.4201	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5421	5511	7.03E-13	69.6497	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4491	4583	1.63E-12	68.4941	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7275	7365	2.03E-12	68.4941	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2475	2568	2.12E-12	68.1089	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2149	2242	2.18E-12	68.1089	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2255	2356	2.43E-12	68.1089	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3844	3937	4.51E-12	67.3385	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5523	5615	5.11E-12	67.3385	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6950	7053	6.44E-12	66.9533	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2041	2137	6.68E-12	66.9533	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1603	1700	7.40E-12	66.5681	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	9394	9493	7.69E-12	66.5681	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8540	8639	1.65E-11	65.7977	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6847	6942	1.93E-11	65.4125	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7798	7889	2.17E-11	65.4125	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1715	1812	3.67E-11	64.6421	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8131	8209	4.41E-11	64.2569	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4822	4912	6.35E-11	63.8717	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3300	3394	6.75E-11	63.8717	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4167	4265	7.31E-11	63.8717	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4277	4370	8.94E-11	63.4865	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7587	7680	1.07E-10	63.1013	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2368	2449	1.12E-10	63.1013	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2908	2994	1.42E-10	62.7161	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3952	4045	1.51E-10	62.7161	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6246	6339	2.41E-10	62.3309	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2601	2675	2.52E-10	61.9457	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6145	6234	2.74E-10	61.9457	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4384	4479	4.92E-10	61.1753	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3117	3211	5.86E-10	61.1753	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	958	1055	1.79E-09	59.6345	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7377	7473	1.25E-08	56.9382	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	402	507	1.60E-08	56.9382	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3732	3832	1.66E-08	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6662	6757	1.71E-08	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7065	7157	2.67E-08	56.1678	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8220	8311	3.19E-08	55.7826	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6037	6132	4.11E-08	55.3974	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	2797	2894	4.39E-08	55.3974	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5932	6025	4.74E-08	55.3974	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6353	6441	6.39E-08	55.0122	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1172	1265	8.83E-08	54.627	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	1828	1921	1.20E-07	54.2418	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6557	6649	2.22E-07	53.4714	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5316	5408	3.54E-07	52.701	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7483	7574	4.07E-07	52.701	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7692	7785	4.70E-07	52.3158	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8009	8101	5.00E-07	52.3158	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	7901	7983	5.16E-07	52.3158	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	632	729	7.74E-07	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5740	5830	8.09E-07	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	9202	9267	1.07E-06	51.1602	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4596	4700	2.48E-06	50.0046	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	6767	6836	3.53E-06	49.6194	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8768	8881	6.59E-06	48.849	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	9622	9735	6.94E-06	48.849	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	4924	5016	1.58E-05	47.6934	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	3013	3109	0.000112537	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	8652	8752	0.000122884	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	9506	9606	0.000122884	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5838	5895	0.00050618	43.071	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6489 - 	CGI_10015666	superfamily	247068	5243	5304	0.00347088	40.3746	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6490 - 	CGI_10015667	superfamily	247723	10	81	1.30E-14	71.1821	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#6490 - 	CGI_10015667	superfamily	243098	190	237	8.37E-13	65.3119	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#6490 - 	CGI_10015667	superfamily	245201	898	1017	1.09E-08	55.7057	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6490 - 	CGI_10015667	superfamily	245039	412	515	0.0022921	40.2584	cl09232	YqaJ superfamily	N	 - 	"YqaJ-like viral recombinase domain; This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit."
Q#6491 - 	CGI_10015668	superfamily	241782	222	585	1.97E-156	457.793	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#6495 - 	CGI_10015672	superfamily	110440	314	339	0.000870792	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6496 - 	CGI_10015673	superfamily	241563	68	109	5.14E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6496 - 	CGI_10015673	superfamily	241563	28	59	0.00616994	35.1476	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6497 - 	CGI_10015674	superfamily	241563	68	109	2.04E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6497 - 	CGI_10015674	superfamily	241563	28	59	0.00183013	36.6884	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6498 - 	CGI_10015675	superfamily	241563	68	109	2.41E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6498 - 	CGI_10015675	superfamily	241563	21	59	0.000685314	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6499 - 	CGI_10006466	superfamily	222150	292	317	0.000868479	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6500 - 	CGI_10006467	superfamily	201217	440	486	7.89E-07	46.3648	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6500 - 	CGI_10006467	superfamily	201217	277	326	2.07E-05	42.1276	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6500 - 	CGI_10006467	superfamily	201217	179	238	8.47E-05	40.2016	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6500 - 	CGI_10006467	superfamily	205718	263	289	0.0006446	37.4698	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6500 - 	CGI_10006467	superfamily	205718	422	451	0.000738965	37.4698	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6500 - 	CGI_10006467	superfamily	201217	330	377	0.00160472	36.7348	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6502 - 	CGI_10006469	superfamily	247904	1	74	8.57E-19	76.4403	cl17350	HD_3 superfamily	N	 - 	HD domain; HD domains are metal dependent phosphohydrolases.
Q#6503 - 	CGI_10006470	superfamily	247639	66	323	2.59E-45	156.853	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#6504 - 	CGI_10006471	superfamily	150167	13	451	3.71E-112	340.449	cl09652	DUF2003 superfamily	 - 	 - 	Eukaryotic protein of unknown function (DUF2003); This is a family of proteins of unknown function which adopt an alpha helical and beta sheet structure.
Q#6505 - 	CGI_10006472	superfamily	241874	237	678	2.15E-65	225.005	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#6506 - 	CGI_10012031	superfamily	247805	32	142	2.55E-15	69.6736	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6507 - 	CGI_10012033	superfamily	248264	207	365	2.14E-44	152.391	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#6507 - 	CGI_10012033	superfamily	222263	123	212	0.00671664	34.6009	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#6511 - 	CGI_10012037	superfamily	241607	64	89	4.47E-06	40.7162	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#6511 - 	CGI_10012037	superfamily	241607	24	58	0.000304672	35.7086	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#6512 - 	CGI_10012038	superfamily	222324	129	239	3.50E-22	87.8326	cl16352	zf-3CxxC superfamily	 - 	 - 	Zinc-binding domain; This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue.
Q#6515 - 	CGI_10012041	superfamily	247792	16	66	2.26E-08	50.9072	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6515 - 	CGI_10012041	superfamily	241563	101	130	0.00491239	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6517 - 	CGI_10012043	superfamily	246669	1	110	4.15E-59	191.509	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#6518 - 	CGI_10012044	superfamily	246669	1256	1375	4.24E-80	260.021	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#6518 - 	CGI_10012044	superfamily	246669	357	522	2.85E-77	252.104	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#6518 - 	CGI_10012044	superfamily	241566	235	284	2.85E-16	75.6063	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#6518 - 	CGI_10012044	superfamily	220800	1064	1221	1.38E-39	144.755	cl11172	Membr_traf_MHD superfamily	 - 	 - 	"Munc13 (mammalian uncoordinated) homology domain; Munc13 proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster, mouse, rat and human, some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical."
Q#6518 - 	CGI_10012044	superfamily	218976	714	820	7.64E-33	124.868	cl05671	DUF1041 superfamily	 - 	 - 	"Domain of Unknown Function (DUF1041); This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains."
Q#6521 - 	CGI_10005658	superfamily	248264	1	138	7.36E-10	55.7062	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#6522 - 	CGI_10004116	superfamily	246918	42	93	4.68E-05	36.6146	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#6531 - 	CGI_10005582	superfamily	110440	148	172	0.00187157	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6532 - 	CGI_10005583	superfamily	241563	63	96	0.00655467	34.9556	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6535 - 	CGI_10005586	superfamily	246925	416	661	2.66E-28	115.916	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#6537 - 	CGI_10005588	superfamily	241568	3	43	0.000195538	35.9016	cl00043	CCP superfamily	C	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#6537 - 	CGI_10005588	superfamily	245226	42	114	4.86E-05	39.2055	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#6539 - 	CGI_10010062	superfamily	241574	1	58	6.87E-18	79.5521	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6539 - 	CGI_10010062	superfamily	241574	195	299	9.07E-12	62.2181	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6541 - 	CGI_10010064	superfamily	245234	205	256	2.40E-05	41.1238	cl10022	ABM superfamily	C	 - 	Antibiotic biosynthesis monooxygenase; This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. It's occurrence as a repeat in Streptomyces coelicolor SCO1909 is suggestive that the other proteins function as multimers. There is also a conserved histidine which is likely to be an active site residue.
Q#6541 - 	CGI_10010064	superfamily	247856	10	31	0.0054368	33.7908	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#6543 - 	CGI_10010066	superfamily	241741	1	146	5.80E-76	238.619	cl00270	PEPCK_HprK superfamily	N	 - 	"Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP  or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity.  PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting that these two phosphotransferases have related functions."
Q#6544 - 	CGI_10010068	superfamily	245208	10	241	8.54E-68	230.679	cl09933	ACAD superfamily	C	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#6544 - 	CGI_10010068	superfamily	245208	233	480	9.85E-66	224.901	cl09933	ACAD superfamily	N	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#6547 - 	CGI_10010071	superfamily	243306	203	411	1.71E-99	298.325	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#6548 - 	CGI_10010072	superfamily	245206	40	282	2.26E-128	368.879	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#6550 - 	CGI_10023077	superfamily	217293	33	234	1.07E-41	146.239	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6551 - 	CGI_10023078	superfamily	220393	235	504	1.10E-68	230.725	cl10751	Tmem26 superfamily	 - 	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#6551 - 	CGI_10023078	superfamily	217293	511	640	7.79E-25	104.252	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6551 - 	CGI_10023078	superfamily	217293	640	767	1.08E-24	103.867	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6551 - 	CGI_10023078	superfamily	202474	791	862	4.98E-09	56.5081	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#6552 - 	CGI_10023079	superfamily	245608	2	200	2.09E-64	200.232	cl11421	FAA_hydrolase superfamily	 - 	 - 	"Fumarylacetoacetate (FAA) hydrolase family; This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase, encoded by mhpD in E. coli, is involved in the phenylpropionic acid pathway of E. coli and catalyzes the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli is involved in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida is a 4-Oxalocrotonate decarboxylase."
Q#6556 - 	CGI_10023083	superfamily	244859	62	289	6.45E-16	75.3005	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#6558 - 	CGI_10023085	superfamily	245226	249	439	2.40E-112	343.04	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#6558 - 	CGI_10023085	superfamily	219714	31	122	5.15E-20	86.5253	cl06895	PMC2NT superfamily	 - 	 - 	"PMC2NT (NUC016) domain; This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components."
Q#6558 - 	CGI_10023085	superfamily	207658	468	548	1.85E-15	73.1002	cl02578	HRDC superfamily	 - 	 - 	HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Q#6561 - 	CGI_10023088	superfamily	220691	151	349	0.00316287	37.5974	cl18569	7TM_GPCR_Srv superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#6564 - 	CGI_10023091	superfamily	245201	948	1141	6.07E-19	87.2921	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6564 - 	CGI_10023091	superfamily	244600	43	163	8.23E-48	168.171	cl07066	Mad3_BUB1_I superfamily	 - 	 - 	Mad3/BUB1 homology region 1; Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.
Q#6568 - 	CGI_10023095	superfamily	243060	182	224	0.000131711	40.8252	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#6571 - 	CGI_10023098	superfamily	203472	19	83	1.26E-11	55.3584	cl05835	B12D superfamily	 - 	 - 	"NADH-ubiquinone reductase complex 1 MLRQ subunit; The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear and is found in plants, insects, fungi and higher metazoans. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation."
Q#6572 - 	CGI_10023099	superfamily	241972	1	86	2.15E-56	171.799	cl00600	Ribosomal_L7Ae superfamily	 - 	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#6574 - 	CGI_10023101	superfamily	243146	44	90	1.34E-10	53.049	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#6574 - 	CGI_10023101	superfamily	243146	4	55	1.22E-08	47.5531	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#6575 - 	CGI_10023102	superfamily	241622	141	206	4.41E-17	72.9846	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#6576 - 	CGI_10023103	superfamily	243096	823	1008	1.61E-37	141.281	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#6576 - 	CGI_10023103	superfamily	241566	564	613	1.53E-12	64.8207	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#6576 - 	CGI_10023103	superfamily	243090	353	475	2.43E-33	127.119	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#6576 - 	CGI_10023103	superfamily	247725	1024	1160	2.25E-31	122.393	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6577 - 	CGI_10023104	superfamily	222150	295	319	4.76E-07	47.0013	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6577 - 	CGI_10023104	superfamily	222150	322	346	2.89E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6577 - 	CGI_10023104	superfamily	246975	282	302	0.000565549	38.0969	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#6577 - 	CGI_10023104	superfamily	222150	350	373	0.00141104	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6577 - 	CGI_10023104	superfamily	243091	30	135	0.001413	37.6991	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#6577 - 	CGI_10023104	superfamily	222150	378	402	0.00572542	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6578 - 	CGI_10023105	superfamily	243077	4	56	1.14E-20	86.4453	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#6579 - 	CGI_10023106	superfamily	248012	478	598	2.79E-23	96.5736	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#6580 - 	CGI_10023107	superfamily	248012	457	595	0.00093716	38.4584	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#6581 - 	CGI_10023108	superfamily	247907	1	100	2.58E-13	69.3692	cl17353	LamG superfamily	N	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6581 - 	CGI_10023108	superfamily	241611	1000	1151	2.21E-11	63.5616	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#6581 - 	CGI_10023108	superfamily	241611	180	316	6.61E-09	55.8576	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#6581 - 	CGI_10023108	superfamily	241611	790	929	1.18E-07	52.0056	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#6581 - 	CGI_10023108	superfamily	241611	367	515	5.24E-06	46.998	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#6582 - 	CGI_10023109	superfamily	247907	491	639	2.94E-21	93.6368	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6582 - 	CGI_10023109	superfamily	247907	1110	1265	1.18E-20	92.096	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6582 - 	CGI_10023109	superfamily	247907	280	423	3.09E-20	90.9404	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6582 - 	CGI_10023109	superfamily	247907	1345	1482	5.19E-19	87.0884	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6582 - 	CGI_10023109	superfamily	247907	929	1074	1.26E-18	85.9328	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6582 - 	CGI_10023109	superfamily	247907	46	207	2.61E-16	79.3844	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6582 - 	CGI_10023109	superfamily	247907	714	859	2.57E-09	57.8133	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#6582 - 	CGI_10023109	superfamily	243092	2100	2405	2.70E-30	123.984	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6582 - 	CGI_10023109	superfamily	245213	1291	1314	0.00952456	36.6436	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6584 - 	CGI_10023111	superfamily	243091	673	789	4.38E-43	152.874	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#6586 - 	CGI_10023113	superfamily	243034	21	120	4.20E-10	57.7752	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6586 - 	CGI_10023113	superfamily	243034	326	430	3.90E-07	48.5304	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6586 - 	CGI_10023113	superfamily	243034	404	478	0.00951496	35.0484	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6587 - 	CGI_10023114	superfamily	203913	4	137	3.18E-11	60.6937	cl07084	P4Ha_N superfamily	 - 	 - 	"Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known."
Q#6588 - 	CGI_10023115	superfamily	241578	8	172	1.95E-22	91.199	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#6589 - 	CGI_10023116	superfamily	241578	23	188	1.49E-31	115.467	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#6592 - 	CGI_10023119	superfamily	243146	319	365	6.84E-10	54.5898	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#6592 - 	CGI_10023119	superfamily	243146	281	330	1.30E-06	45.2419	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#6594 - 	CGI_10023121	superfamily	198867	285	384	1.95E-19	84.7004	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#6594 - 	CGI_10023121	superfamily	243066	169	276	4.81E-16	74.9613	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#6594 - 	CGI_10023121	superfamily	243146	616	662	9.17E-10	55.3602	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#6594 - 	CGI_10023121	superfamily	243146	578	627	3.95E-06	44.8567	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#6599 - 	CGI_10023126	superfamily	242209	278	352	6.18E-46	153.152	cl00942	PCD_DCoH superfamily	 - 	 - 	"PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH  (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme.  DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH).  DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carcinomas and in malignant melanomas."
Q#6599 - 	CGI_10023126	superfamily	243035	49	171	4.03E-27	103.854	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6601 - 	CGI_10010566	superfamily	243058	272	307	0.00122199	37.294	cl02500	ARM superfamily	NC	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#6602 - 	CGI_10010567	superfamily	243058	106	227	1.10E-32	122.038	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#6602 - 	CGI_10010567	superfamily	243058	340	451	1.11E-30	116.645	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#6602 - 	CGI_10010567	superfamily	243058	191	325	1.07E-18	82.7475	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#6602 - 	CGI_10010567	superfamily	243058	470	580	4.00E-16	75.4287	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#6602 - 	CGI_10010567	superfamily	201951	5	92	5.17E-14	68.5614	cl03339	IBB superfamily	 - 	 - 	"Importin beta binding domain; This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain."
Q#6603 - 	CGI_10010568	superfamily	247856	144	209	1.35E-07	48.6981	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#6603 - 	CGI_10010568	superfamily	150162	48	123	8.43E-22	89.1248	cl09646	FOP_dimer superfamily	 - 	 - 	FOP N terminal dimerisation domain; Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to subcellular structures. This domain includes a Lis-homology motif. It forms an alpha helical bundle and is involved in dimerisation.
Q#6604 - 	CGI_10010569	superfamily	243128	315	513	8.73E-13	67.3855	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#6604 - 	CGI_10010569	superfamily	243129	609	694	3.93E-12	64.197	cl02653	MA3 superfamily	C	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#6607 - 	CGI_10010572	superfamily	220187	12	92	1.42E-29	102.326	cl07829	NuA4 superfamily	 - 	 - 	"Histone acetyltransferase subunit NuA4; The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control."
Q#6611 - 	CGI_10003687	superfamily	243066	52	105	3.12E-12	58.3333	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#6612 - 	CGI_10003688	superfamily	218440	104	251	8.07E-05	44.1421	cl14936	AF-4 superfamily	NC	 - 	"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila."
Q#6614 - 	CGI_10003690	superfamily	242274	43	140	0.00253483	35.5649	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#6617 - 	CGI_10003511	superfamily	243091	75	170	4.13E-08	52.1092	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#6618 - 	CGI_10003512	superfamily	220722	74	196	1.07E-20	89.0157	cl11040	EST1 superfamily	 - 	 - 	Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerisation.
Q#6620 - 	CGI_10012045	superfamily	248097	78	195	7.98E-22	86.9354	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6621 - 	CGI_10012046	superfamily	248097	46	114	5.32E-16	71.1422	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6622 - 	CGI_10012047	superfamily	248097	15	78	0.00913704	31.0814	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6623 - 	CGI_10012048	superfamily	248458	52	240	2.72E-13	70.0353	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#6623 - 	CGI_10012048	superfamily	248458	306	515	0.000498387	41.1453	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#6625 - 	CGI_10012050	superfamily	247792	33	76	5.16E-10	56.6852	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6626 - 	CGI_10012051	superfamily	213389	192	375	6.46E-40	142.043	cl17092	STING_C superfamily	 - 	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#6626 - 	CGI_10012051	superfamily	248012	50	159	2.26E-15	71.4548	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#6628 - 	CGI_10012053	superfamily	242311	217	260	0.00207611	35.9364	cl01115	BMFP superfamily	N	 - 	"Membrane fusogenic activity; BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro."
Q#6629 - 	CGI_10012054	superfamily	222150	139	162	0.00213089	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6629 - 	CGI_10012054	superfamily	222150	54	76	0.00278755	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6629 - 	CGI_10012054	superfamily	222150	224	248	0.00754503	33.9045	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6630 - 	CGI_10012055	superfamily	244819	6	60	2.98E-07	44.0432	cl07874	zf-AD superfamily	C	 - 	"Zinc-finger associated domain (zf-AD); The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA."
Q#6634 - 	CGI_10012059	superfamily	217473	65	314	1.08E-26	106.68	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#6636 - 	CGI_10012061	superfamily	247805	86	226	9.10E-29	112.816	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6636 - 	CGI_10012061	superfamily	243778	469	559	2.24E-39	140.822	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#6636 - 	CGI_10012061	superfamily	219532	593	696	2.97E-34	127.045	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#6636 - 	CGI_10012061	superfamily	247905	313	372	2.25E-06	46.0509	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#6637 - 	CGI_10012062	superfamily	247805	100	288	2.69E-47	164.195	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6637 - 	CGI_10012062	superfamily	247805	8	105	8.06E-34	126.445	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6637 - 	CGI_10012062	superfamily	247905	299	366	0.00554633	36.0617	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#6639 - 	CGI_10012064	superfamily	192535	75	240	1.71E-06	48.361	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#6640 - 	CGI_10012065	superfamily	192535	53	185	0.000285137	42.1978	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#6641 - 	CGI_10012066	superfamily	216739	450	483	0.00204611	36.6418	cl03383	PC_rep superfamily	 - 	 - 	Proteasome/cyclosome repeat; Proteasome/cyclosome repeat.  
Q#6641 - 	CGI_10012066	superfamily	216739	503	536	0.00232773	36.6418	cl03383	PC_rep superfamily	 - 	 - 	Proteasome/cyclosome repeat; Proteasome/cyclosome repeat.  
Q#6642 - 	CGI_10001682	superfamily	247739	6	167	1.21E-72	219.397	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#6643 - 	CGI_10001685	superfamily	219318	110	280	5.29E-62	204.341	cl06271	PhaC_N superfamily	 - 	 - 	"Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; This family represents the N-terminal region of the bacterial poly-beta-hydroxybutyrate polymerase (PhaC). Polyhydroxyalkanoic acids (PHAs) are carbon and energy reserve polymers produced in some bacteria when carbon sources are plentiful and another nutrient, such as nitrogen, phosphate, oxygen, or sulfur, becomes limiting. PHAs composed of monomeric units ranging from 3 to 14 carbons exist in nature. When the carbon source is exhausted, PHA is utilised by the bacterium. PhaC links D-(-)-3-hydroxybutyrl-CoA to an existing PHA molecule by the formation of an ester bond. This family appears to be a partial segment of an alpha/beta hydrolase domain."
Q#6644 - 	CGI_10001688	superfamily	245815	7	472	0	754.724	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#6645 - 	CGI_10001690	superfamily	208802	1	229	1.14E-113	331.771	cl07974	DRE_TIM_metallolyase superfamily	 - 	 - 	"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM"."
Q#6645 - 	CGI_10001690	superfamily	149094	232	296	8.89E-28	103.41	cl06739	DmpG_comm superfamily	 - 	 - 	"DmpG-like communication domain; This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain. The communication domain is thought to play an important role in the heterodimerisation of the enzyme."
Q#6646 - 	CGI_10001691	superfamily	220165	124	268	4.32E-76	231.279	cl07796	AcetDehyd-dimer superfamily	 - 	 - 	"Prokaryotic acetaldehyde dehydrogenase, dimerisation; Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerisation of the protein."
Q#6646 - 	CGI_10001691	superfamily	214863	3	116	9.44E-13	63.3363	cl18317	Semialdhyde_dh superfamily	 - 	 - 	"Semialdehyde dehydrogenase, NAD binding domain; The semialdehyde dehydrogenase family is found in N-acetyl-glutamine semialdehyde dehydrogenase (AgrC), which is involved in arginine biosynthesis, and aspartate-semialdehyde dehydrogenase, an enzyme involved in the biosynthesis of various amino acids from aspartate. This family is also found in yeast and fungal Arg5,6 protein, which is cleaved into the enzymes N-acety-gamma-glutamyl-phosphate reductase and acetylglutamate kinase. These are also involved in arginine biosynthesis. All proteins in this entry contain a NAD binding region of semialdehyde dehydrogenase."
Q#6647 - 	CGI_10001692	superfamily	245608	3	257	2.89E-101	298.66	cl11421	FAA_hydrolase superfamily	 - 	 - 	"Fumarylacetoacetate (FAA) hydrolase family; This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase, encoded by mhpD in E. coli, is involved in the phenylpropionic acid pathway of E. coli and catalyzes the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli is involved in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida is a 4-Oxalocrotonate decarboxylase."
Q#6648 - 	CGI_10001696	superfamily	216434	19	347	1.84E-116	344.061	cl08318	PPDK_N superfamily	 - 	 - 	"Pyruvate phosphate dikinase, PEP/pyruvate binding domain; This enzyme catalyzes the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP)."
Q#6649 - 	CGI_10003564	superfamily	241763	115	328	3.04E-117	339.985	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#6649 - 	CGI_10003564	superfamily	244586	27	85	2.63E-17	74.5874	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#6650 - 	CGI_10003565	superfamily	241763	75	287	4.28E-99	292.22	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#6650 - 	CGI_10003565	superfamily	244586	3	45	1.84E-13	63.4167	cl07031	Inhibitor_I29 superfamily	N	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#6651 - 	CGI_10003566	superfamily	241763	25	238	3.36E-115	331.126	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#6652 - 	CGI_10003567	superfamily	248012	68	165	2.94E-21	86.1732	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#6653 - 	CGI_10003568	superfamily	241763	11	103	6.09E-15	66.4934	cl00298	Peptidase_C1 superfamily	N	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#6654 - 	CGI_10003569	superfamily	248012	26	169	1.31E-21	86.2232	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#6657 - 	CGI_10001572	superfamily	245213	374	413	2.38E-08	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6657 - 	CGI_10001572	superfamily	245213	290	325	8.99E-06	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6657 - 	CGI_10001572	superfamily	245213	423	458	1.19E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6657 - 	CGI_10001572	superfamily	245213	237	289	0.00107063	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6657 - 	CGI_10001572	superfamily	205157	199	233	1.02E-06	45.9915	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#6657 - 	CGI_10001572	superfamily	245213	332	370	7.24E-05	40.7952	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6658 - 	CGI_10001573	superfamily	243100	301	362	2.75E-07	47.1736	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#6660 - 	CGI_10004791	superfamily	243035	5	70	8.86E-18	71.9435	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6662 - 	CGI_10008563	superfamily	110440	234	260	0.007974	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6662 - 	CGI_10008563	superfamily	110440	542	568	0.007974	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6666 - 	CGI_10008567	superfamily	245230	1	194	4.05E-139	398.958	cl10017	Tubulin_FtsZ superfamily	N	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#6669 - 	CGI_10008570	superfamily	245716	51	72	6.01E-05	42.1603	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#6670 - 	CGI_10008571	superfamily	247856	110	156	0.000182264	38.6829	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#6671 - 	CGI_10008572	superfamily	242370	1	116	1.47E-30	110.475	cl01218	CutC superfamily	N	 - 	"CutC family; Copper transport in Escherichia coli is mediated by the products of at least six genes, cutA, cutB, cutC, cutD, cutE, and cutF. A mutation in one or more of these genes results in an increased copper sensitivity. Members of this family are between 200 and 300 amino acids in length are found in both eukaryotes and bacteria."
Q#6674 - 	CGI_10016469	superfamily	245206	5	245	3.18E-112	328.353	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#6676 - 	CGI_10016471	superfamily	243034	4	103	5.72E-23	91.6727	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6676 - 	CGI_10016471	superfamily	218373	286	367	1.86E-28	106.336	cl04882	SGS superfamily	 - 	 - 	"SGS domain; This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins."
Q#6676 - 	CGI_10016471	superfamily	241659	173	256	3.15E-26	100.145	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#6678 - 	CGI_10016473	superfamily	243212	166	293	6.05E-19	82.0065	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#6678 - 	CGI_10016473	superfamily	215866	22	144	1.64E-16	75.4395	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#6681 - 	CGI_10016476	superfamily	241984	168	404	1.05E-53	179.76	cl00615	Membrane-FADS-like superfamily	 - 	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#6681 - 	CGI_10016476	superfamily	242849	18	91	1.71E-24	96.1188	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#6682 - 	CGI_10016478	superfamily	219525	137	193	3.19E-06	43.947	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#6682 - 	CGI_10016478	superfamily	219525	200	255	0.000443256	37.7838	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#6683 - 	CGI_10016480	superfamily	217293	20	219	4.22E-30	115.423	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6683 - 	CGI_10016480	superfamily	202474	239	309	3.73E-13	67.2937	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#6687 - 	CGI_10016484	superfamily	241592	23	42	1.87E-08	46.1726	cl00074	H2A superfamily	C	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#6688 - 	CGI_10016485	superfamily	241782	92	482	4.54E-53	184.082	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#6689 - 	CGI_10016486	superfamily	241644	95	170	5.67E-11	57.9972	cl00154	UBCc superfamily	C	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#6690 - 	CGI_10016487	superfamily	208843	424	583	7.64E-75	245.885	cl08275	RHD-n superfamily	 - 	 - 	"N-terminal sub-domain of the Rel homology domain (RHD); Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal sub-domain, which may be distantly related to the DNA-binding domain found in P53. The C-terminal sub-domain has an immunoglobulin-like fold and serves as a dimerization module that also binds DNA (see cd00102). The RHD is found in NF-kappa B, nuclear factor of activated T-cells (NFAT), the tonicity-responsive enhancer binding protein (TonEBP), and the arthropod proteins Dorsal and Relish (Rel)."
Q#6690 - 	CGI_10016487	superfamily	247038	588	688	8.62E-29	112.963	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#6691 - 	CGI_10016488	superfamily	241868	42	192	5.79E-50	162.696	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#6692 - 	CGI_10016489	superfamily	245055	47	144	2.11E-18	85.3169	cl09326	MATE_like superfamily	N	 - 	"Multidrug and toxic compound extrusion family and similar proteins; The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria."
Q#6703 - 	CGI_10008051	superfamily	241572	55	144	2.33E-14	66.4932	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#6703 - 	CGI_10008051	superfamily	241572	154	250	1.94E-13	64.5714	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#6705 - 	CGI_10008053	superfamily	222150	873	895	6.48E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#6705 - 	CGI_10008053	superfamily	246975	860	881	0.000635261	38.8673	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#6706 - 	CGI_10008054	superfamily	217293	16	218	1.87E-26	105.022	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6706 - 	CGI_10008054	superfamily	202474	225	310	1.92E-07	49.9597	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#6709 - 	CGI_10010990	superfamily	247725	14	103	2.82E-44	149.241	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6712 - 	CGI_10010993	superfamily	245226	52	202	1.19E-23	94.6748	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#6713 - 	CGI_10010994	superfamily	193256	2883	3150	2.86E-63	220.975	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#6713 - 	CGI_10010994	superfamily	193251	2530	2793	6.02E-47	173.584	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#6713 - 	CGI_10010994	superfamily	193253	3163	3508	4.67E-35	140.557	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#6713 - 	CGI_10010994	superfamily	193257	3522	3641	5.57E-26	110.845	cl15086	AAA_9 superfamily	N	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#6713 - 	CGI_10010994	superfamily	247743	2227	2362	7.69E-07	50.7568	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#6715 - 	CGI_10010996	superfamily	248097	221	347	4.23E-23	92.3282	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6715 - 	CGI_10010996	superfamily	248097	61	183	5.99E-19	80.7722	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6716 - 	CGI_10010998	superfamily	248097	23	126	8.40E-22	84.6242	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6717 - 	CGI_10010999	superfamily	248097	151	275	1.49E-28	106.581	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6719 - 	CGI_10011001	superfamily	128937	4	69	2.93E-11	55.3464	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#6719 - 	CGI_10011001	superfamily	128937	79	139	8.95E-11	54.1908	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#6721 - 	CGI_10001136	superfamily	246748	180	419	4.02E-119	352.665	cl14876	Zinc_peptidase_like superfamily	N	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#6721 - 	CGI_10001136	superfamily	244870	2	163	2.05E-61	201.364	cl08238	PA superfamily	N	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#6723 - 	CGI_10005202	superfamily	247068	2022	2118	3.35E-15	75.0425	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1757	1842	1.23E-13	70.4201	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	949	1036	1.81E-13	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	2874	2959	3.59E-12	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	2129	2214	4.91E-12	65.7977	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1646	1745	3.92E-10	60.0197	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	245213	3311	3348	4.28E-10	58.8022	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6723 - 	CGI_10005202	superfamily	247068	2765	2862	2.40E-09	57.7086	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1327	1412	5.57E-09	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	520	609	2.31E-08	55.0122	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1546	1634	3.14E-08	54.627	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	2653	2754	6.65E-08	53.4714	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	2351	2431	7.01E-07	50.3898	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1277	1315	8.37E-07	50.0046	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1159	1249	9.13E-07	50.0046	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	770	833	2.55E-06	48.849	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1045	1145	3.48E-06	48.0786	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	241568	255	293	6.07E-05	43.9908	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#6723 - 	CGI_10005202	superfamily	245213	3357	3392	0.000146411	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6723 - 	CGI_10005202	superfamily	247068	632	729	0.00017152	43.071	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	1865	1959	0.000587867	41.145	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	845	938	0.000875244	40.7598	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	247068	405	509	0.00129157	40.3746	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6723 - 	CGI_10005202	superfamily	245213	3396	3430	0.00138406	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6723 - 	CGI_10005202	superfamily	246918	76	122	4.42E-07	50.2779	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#6723 - 	CGI_10005202	superfamily	205157	3271	3308	2.27E-05	44.8359	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#6723 - 	CGI_10005202	superfamily	246918	132	173	2.47E-05	44.8851	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#6723 - 	CGI_10005202	superfamily	247068	1970	2027	0.000359169	41.9515	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6726 - 	CGI_10005205	superfamily	216981	364	468	1.49E-15	74.4913	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#6727 - 	CGI_10005206	superfamily	241946	71	174	9.66E-11	55.641	cl00558	Abi superfamily	 - 	 - 	"CAAX protease self-immunity; Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide being removed by one of the CAAX prenyl proteases). The family contains the CAAX prenyl protease. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding. While they are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity."
Q#6729 - 	CGI_10005208	superfamily	219409	6	164	7.82E-14	65.2484	cl06456	Dynactin_p22 superfamily	 - 	 - 	"Dynactin subunit p22; This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localises to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis. Family members are approximately 170 residues long."
Q#6730 - 	CGI_10005209	superfamily	204415	218	532	5.28E-88	284.111	cl16016	TTKRSYEDQ superfamily	C	 - 	Predicted coiled-coil domain-containing protein; This is the C-terminal 500 amino acids of a family of proteins with a predicted coiled-coil domain conserved from nematodes to humans. It carries a characteristic TTKRSYEDQ sequence-motif. The function is not known.
Q#6730 - 	CGI_10005209	superfamily	150821	8	88	6.61E-25	99.4966	cl10895	KLRAQ superfamily	C	 - 	Predicted coiled-coil domain-containing protein; This is the N-terminal 100 amino acid domain of a family of proteins conserved from nematodes to humans. It carries a characteristic KLRAQ sequence-motif. The function is not known.
Q#6730 - 	CGI_10005209	superfamily	243591	72	164	0.000114005	41.2489	cl03951	CDC37_N superfamily	N	 - 	Cdc37 N terminal kinase binding; Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domain corresponds to the N terminal domain which binds predominantly to protein kinases and is found N terminal to the Hsp (Heat shocked protein) 90-binding domain pfam08565. Expression of a construct consisting of only the N-terminal domain of Saccharomyces pombe Cdc37 results in cellular viability. This indicates that interactions with the cochaperone Hsp90 may not be essential for Cdc37 function.
Q#6733 - 	CGI_10001489	superfamily	241680	208	259	0.00017553	40.6998	cl00200	MIP superfamily	N	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#6734 - 	CGI_10001490	superfamily	245815	50	263	5.69E-120	353.918	cl11961	ALDH-SF superfamily	C	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#6735 - 	CGI_10002143	superfamily	216254	11	91	1.89E-16	75.3622	cl08303	Recep_L_domain superfamily	C	 - 	Receptor L domain; The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
Q#6736 - 	CGI_10002778	superfamily	243072	367	492	7.72E-34	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6736 - 	CGI_10002778	superfamily	243072	268	393	6.23E-31	116.714	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6736 - 	CGI_10002778	superfamily	243072	192	327	4.57E-19	83.587	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6739 - 	CGI_10002427	superfamily	241600	2	118	3.04E-35	122.734	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6740 - 	CGI_10002428	superfamily	241600	2	48	6.57E-09	49.1611	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6742 - 	CGI_10003589	superfamily	201217	553	600	5.56E-13	65.2396	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6742 - 	CGI_10003589	superfamily	201217	603	653	1.67E-10	57.9208	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6742 - 	CGI_10003589	superfamily	201217	709	757	3.25E-09	54.0688	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6742 - 	CGI_10003589	superfamily	201217	656	704	1.52E-08	52.1428	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6742 - 	CGI_10003589	superfamily	201217	446	497	5.19E-07	47.9056	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6742 - 	CGI_10003589	superfamily	201217	501	550	1.41E-05	43.6684	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6742 - 	CGI_10003589	superfamily	201217	397	443	0.00616894	35.5792	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6743 - 	CGI_10003590	superfamily	219542	52	162	8.92E-39	138.914	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#6743 - 	CGI_10003590	superfamily	219541	490	619	1.36E-29	114.488	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#6743 - 	CGI_10003590	superfamily	215896	173	359	2.00E-15	73.8684	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#6744 - 	CGI_10003591	superfamily	243109	1111	1267	6.79E-75	246.469	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#6745 - 	CGI_10003592	superfamily	243092	1234	1583	1.18E-21	97.7908	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#6745 - 	CGI_10003592	superfamily	201217	1904	1953	9.95E-14	68.7064	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6745 - 	CGI_10003592	superfamily	201217	1956	2005	4.93E-13	66.7804	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6745 - 	CGI_10003592	superfamily	201217	2008	2058	3.33E-11	61.3876	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6745 - 	CGI_10003592	superfamily	205718	2097	2126	1.58E-08	53.263	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6745 - 	CGI_10003592	superfamily	201217	2113	2154	1.14E-07	50.9872	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6745 - 	CGI_10003592	superfamily	201217	2062	2110	4.31E-05	43.6684	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6745 - 	CGI_10003592	superfamily	201217	1849	1901	0.000118824	42.1276	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6745 - 	CGI_10003592	superfamily	201217	1802	1846	0.00334182	37.8904	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6746 - 	CGI_10003053	superfamily	241563	60	95	2.94E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6748 - 	CGI_10003055	superfamily	110440	160	186	0.00240433	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6749 - 	CGI_10003056	superfamily	241563	60	95	0.000196094	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6749 - 	CGI_10003056	superfamily	110440	482	508	0.000860983	37.3873	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#6750 - 	CGI_10003057	superfamily	247856	292	355	2.07E-06	44.8461	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#6751 - 	CGI_10004229	superfamily	243064	19	111	0.000182887	39.6494	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#6752 - 	CGI_10004230	superfamily	243119	251	295	2.27E-07	46.658	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#6752 - 	CGI_10004230	superfamily	243100	92	142	0.00250561	35.2324	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#6753 - 	CGI_10004231	superfamily	243064	19	98	1.71E-06	43.8866	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#6755 - 	CGI_10002810	superfamily	243072	33	89	0.00436531	33.1259	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6756 - 	CGI_10002811	superfamily	221797	1552	1737	1.48E-42	156.323	cl15115	Nipped-B_C superfamily	 - 	 - 	Sister chromatid cohesion C-terminus; This domain lies towards the C-terminus of nipped-B or sister chromatid cohesion proteins.
Q#6756 - 	CGI_10002811	superfamily	205062	1070	1111	1.31E-11	62.4882	cl15079	Cohesin_HEAT superfamily	 - 	 - 	"HEAT repeat associated with sister chromatid cohesion; This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B. HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble."
Q#6760 - 	CGI_10018191	superfamily	241642	127	186	2.53E-10	56.3498	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#6760 - 	CGI_10018191	superfamily	220133	5	67	6.45E-18	78.8295	cl07702	Syntaxin-6_N superfamily	C	 - 	"Syntaxin 6, N-terminal; Members of this family, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport."
Q#6761 - 	CGI_10018192	superfamily	241862	134	270	7.27E-20	85.4856	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#6762 - 	CGI_10018193	superfamily	243034	100	208	3.80E-11	57.0048	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6763 - 	CGI_10018194	superfamily	246749	8	94	4.37E-21	89.0936	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#6763 - 	CGI_10018194	superfamily	243098	603	649	1.01E-14	69.9343	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#6763 - 	CGI_10018194	superfamily	246749	133	196	7.38E-09	53.3917	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#6763 - 	CGI_10018194	superfamily	246749	313	384	4.80E-16	74.3784	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#6763 - 	CGI_10018194	superfamily	246749	417	490	9.68E-06	44.4104	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#6764 - 	CGI_10018195	superfamily	247792	37	85	6.48E-07	47.4404	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6764 - 	CGI_10018195	superfamily	128778	236	356	0.0023839	37.2443	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#6766 - 	CGI_10018197	superfamily	247918	562	806	4.26E-55	193.313	cl17364	PMT_2 superfamily	 - 	 - 	Dolichyl-phosphate-mannose-protein mannosyltransferase; This family contains members that are not captured by pfam02366.
Q#6766 - 	CGI_10018197	superfamily	241739	256	481	1.50E-13	71.4367	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#6766 - 	CGI_10018197	superfamily	197746	838	897	3.93E-08	51.9583	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#6766 - 	CGI_10018197	superfamily	197746	980	1030	1.46E-06	47.3359	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#6766 - 	CGI_10018197	superfamily	197746	911	968	1.60E-06	47.3359	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#6768 - 	CGI_10018199	superfamily	243072	1	81	1.60E-18	77.0386	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6770 - 	CGI_10018202	superfamily	245847	20	159	1.58E-17	74.9005	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6771 - 	CGI_10018203	superfamily	245847	39	160	1.92E-21	86.4565	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6774 - 	CGI_10018207	superfamily	241600	82	135	3.83E-19	80.3623	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6776 - 	CGI_10018209	superfamily	243035	62	123	0.000206484	37.5794	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6777 - 	CGI_10018210	superfamily	245847	18	141	8.91E-18	74.9005	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6779 - 	CGI_10018212	superfamily	221601	18	134	9.03E-07	47.5504	cl13870	ARA70 superfamily	 - 	 - 	"Nuclear coactivator; This domain family is found in eukaryotes, and is typically between 127 and 138 amino acids in length. This family is ARA70, a nuclear coactivator which interacts with peroxisome proliferator-activated receptor gamma (PPARgamma) to regulate transcription and the addition of the PPARgamma ligand (prostaglandin J2) enhances this interaction."
Q#6780 - 	CGI_10018213	superfamily	246680	212	288	4.66E-15	68.131	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#6781 - 	CGI_10018214	superfamily	248097	201	332	8.21E-15	69.6385	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6781 - 	CGI_10018214	superfamily	248097	84	181	0.000280726	38.7854	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6783 - 	CGI_10018216	superfamily	241733	2	90	9.32E-62	184.714	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#6784 - 	CGI_10018217	superfamily	242877	40	260	1.58E-121	348.835	cl02093	Coq4 superfamily	 - 	 - 	"Coenzyme Q (ubiquinone) biosynthesis protein Coq4; Coq4p was shown to peripherally associate with the matrix face of the mitochondrial inner membrane. The putative mitochondrial- targeting sequence present at the amino-terminus of the polypeptide efficiently imported it to mitochondria. The function of Coq4p is unknown, although its presence is required to maintain a steady-state level of Coq7p, another component of the Q biosynthetic pathway. The overall structure of Coq4 is alpha helical and shows resemblance to haemoglobin/myoglobin (information from TOPSAN)."
Q#6785 - 	CGI_10018218	superfamily	244843	47	578	4.63E-148	440.9	cl08040	Ggt superfamily	 - 	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#6786 - 	CGI_10018219	superfamily	243155	2	105	4.71E-51	160.258	cl02716	RNA_pol_Rpb8 superfamily	C	 - 	"RNA polymerase Rpb8; Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits."
Q#6787 - 	CGI_10018220	superfamily	243155	46	80	1.92E-15	66.343	cl02716	RNA_pol_Rpb8 superfamily	N	 - 	"RNA polymerase Rpb8; Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits."
Q#6792 - 	CGI_10002472	superfamily	247792	17	67	6.31E-06	43.9736	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6792 - 	CGI_10002472	superfamily	241563	164	193	0.00364409	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#6793 - 	CGI_10002473	superfamily	242324	112	196	0.000978724	38.2385	cl01133	Na_H_antiport_1 superfamily	NC	 - 	Na+/H+ antiporter 1; This family contains a number of bacterial Na+/H+ antiporter 1 proteins. These are integral membrane proteins that catalyze the exchange of H+ for Na+ in a manner that is highly dependent on the pH.
Q#6795 - 	CGI_10002475	superfamily	241986	25	96	2.54E-21	81.8264	cl00617	SRP19 superfamily	C	 - 	SRP19 protein; The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and several proteins. One of these proteins is the SRP19 protein (Sec65 in yeast).
Q#6797 - 	CGI_10008304	superfamily	207662	37	109	6.72E-29	109.188	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#6797 - 	CGI_10008304	superfamily	245599	353	526	3.12E-20	88.0486	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#6798 - 	CGI_10008305	superfamily	248013	15	31	0.000351955	36.3972	cl17459	CHROMO superfamily	NC	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#6799 - 	CGI_10008306	superfamily	243058	14	90	8.69E-10	55.3983	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#6799 - 	CGI_10008306	superfamily	248012	110	209	1.08E-19	82.2404	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#6800 - 	CGI_10008307	superfamily	218847	17	186	1.75E-49	166.521	cl18479	CDO_I superfamily	 - 	 - 	Cysteine dioxygenase type I; Cysteine dioxygenase type I (EC:1.13.11.20) converts cysteine to cysteinesulphinic acid and is the rate-limiting step in sulphate production.
Q#6802 - 	CGI_10008310	superfamily	243035	519	586	1.51E-07	49.9258	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6802 - 	CGI_10008310	superfamily	248281	380	421	2.40E-07	48.4303	cl17727	GT1 superfamily	C	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#6803 - 	CGI_10017832	superfamily	246676	60	272	7.86E-87	260.726	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#6804 - 	CGI_10017833	superfamily	241886	96	157	1.18E-16	74.5989	cl00470	Aldo_ket_red superfamily	C	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#6810 - 	CGI_10017839	superfamily	241872	181	462	3.73E-23	99.4667	cl00453	CDP-OH_P_transf superfamily	N	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#6811 - 	CGI_10017840	superfamily	201678	99	128	9.49E-06	43.2576	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#6811 - 	CGI_10017840	superfamily	201678	170	196	2.69E-05	41.7168	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#6811 - 	CGI_10017840	superfamily	201678	135	161	0.000461205	38.25	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#6811 - 	CGI_10017840	superfamily	201678	57	81	0.00140871	36.7092	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#6811 - 	CGI_10017840	superfamily	201678	221	244	0.00154698	36.7092	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#6811 - 	CGI_10017840	superfamily	149008	249	306	0.00496284	35.6037	cl06654	RabGGT_insert superfamily	C	 - 	"Rab geranylgeranyl transferase alpha-subunit, insert domain; Rab geranylgeranyl transferase (RabGGT) catalyzes the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. This domain is inserted between pfam01239 repeats. This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP."
Q#6812 - 	CGI_10017841	superfamily	241958	46	472	8.81E-101	310.987	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#6813 - 	CGI_10017842	superfamily	247057	20	86	5.24E-30	105.095	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#6814 - 	CGI_10017844	superfamily	245596	1	147	2.85E-48	157.05	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#6816 - 	CGI_10017847	superfamily	241583	4	97	1.73E-32	117.475	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#6818 - 	CGI_10017849	superfamily	245847	47	112	0.000193113	37.151	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6819 - 	CGI_10012741	superfamily	243072	186	327	8.41E-07	47.7634	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6819 - 	CGI_10012741	superfamily	243072	66	211	4.52E-05	42.3707	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6819 - 	CGI_10012741	superfamily	243072	10	87	0.000112953	41.2151	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6819 - 	CGI_10012741	superfamily	243072	287	424	0.00131892	38.1335	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6819 - 	CGI_10012741	superfamily	220672	444	643	1.67E-23	99.2434	cl10957	Frag1 superfamily	 - 	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#6820 - 	CGI_10012742	superfamily	213107	21	61	3.94E-06	42.6423	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#6821 - 	CGI_10012743	superfamily	215827	179	357	2.53E-23	99.8503	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#6822 - 	CGI_10012744	superfamily	243072	86	234	7.35E-27	109.01	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6822 - 	CGI_10012744	superfamily	241568	1449	1481	4.01E-05	43.6056	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#6822 - 	CGI_10012744	superfamily	243179	1706	1784	9.22E-09	55.2315	cl02781	tetraspanin_LEL superfamily	C	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#6822 - 	CGI_10012744	superfamily	219521	320	472	0.000204209	43.3807	cl09440	7TMR-DISM_7TM superfamily	C	 - 	7TM diverse intracellular signalling; This entry represents the transmembrane region of the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules).
Q#6823 - 	CGI_10012745	superfamily	243179	294	369	8.00E-07	47.1423	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#6824 - 	CGI_10012746	superfamily	241683	147	530	1.58E-149	450.814	cl00204	PFK superfamily	N	 - 	"Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases. Some members evolved by gene duplication and thus have a large C-terminal/N-terminal extension comprising a second PFK domain. Generally, ATP-PFKs are allosteric homotetramers, and  PPi-PFKs are dimeric and nonallosteric except for plant PPi-PFKs which are allosteric heterotetramers."
Q#6824 - 	CGI_10012746	superfamily	245206	78	140	2.69E-05	45.0336	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#6825 - 	CGI_10012747	superfamily	247775	1	199	1.20E-31	122.308	cl17221	ArsB_NhaD_permease superfamily	C	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#6826 - 	CGI_10012748	superfamily	247875	114	231	5.30E-06	44.9612	cl17321	2OG-FeII_Oxy_2 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; 2OG-Fe(II) oxygenase superfamily.  
Q#6827 - 	CGI_10012749	superfamily	241574	86	289	3.93E-48	171.23	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6827 - 	CGI_10012749	superfamily	217309	346	816	5.51E-173	514.169	cl09289	EMP70 superfamily	 - 	 - 	Endomembrane protein 70; Endomembrane protein 70.  
Q#6829 - 	CGI_10012751	superfamily	241574	295	501	3.76E-80	252.122	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6831 - 	CGI_10005126	superfamily	241754	59	755	0	1201.76	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#6831 - 	CGI_10005126	superfamily	216736	1634	1723	9.48E-31	119.212	cl03379	DIL superfamily	 - 	 - 	DIL domain; The DIL domain has no known function.
Q#6831 - 	CGI_10005126	superfamily	210118	859	876	0.00258434	37.7008	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#6831 - 	CGI_10005126	superfamily	210118	810	827	0.00582265	36.9199	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#6831 - 	CGI_10005126	superfamily	210118	758	780	0.00592841	36.5347	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#6832 - 	CGI_10005127	superfamily	222453	991	1049	4.79E-20	86.5916	cl16474	DUF4210 superfamily	 - 	 - 	"Domain of unknown function (DUF4210); This short domain is found in fungi, plants and animals, and the proteins appear to be necessary for chromosome segregation during meiosis."
Q#6832 - 	CGI_10005127	superfamily	206060	1121	1178	9.25E-20	85.3972	cl16457	Chromosome_seg superfamily	 - 	 - 	"Chromosome segregation during meiosis; The proteins come from eukaryotes, plants and animals, and are necessary for chromosome segregation during meiosis."
Q#6833 - 	CGI_10005128	superfamily	243072	874	995	3.05E-26	107.084	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6833 - 	CGI_10005128	superfamily	243072	1331	1446	6.09E-24	100.151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6833 - 	CGI_10005128	superfamily	243072	1135	1255	1.05E-23	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6833 - 	CGI_10005128	superfamily	243072	1427	1542	5.39E-23	97.4542	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6833 - 	CGI_10005128	superfamily	243072	1523	1638	1.29E-22	96.2986	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6833 - 	CGI_10005128	superfamily	243072	1236	1382	1.95E-21	92.8318	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6833 - 	CGI_10005128	superfamily	243072	944	1052	3.58E-20	89.365	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6833 - 	CGI_10005128	superfamily	247744	229	263	0.00259393	39.5592	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#6838 - 	CGI_10011307	superfamily	114912	40	60	4.41E-05	38.5713	cl17946	zf-U1 superfamily	N	 - 	"U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family."
Q#6839 - 	CGI_10011308	superfamily	247916	716	786	1.34E-13	67.7931	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#6839 - 	CGI_10011308	superfamily	247916	263	313	1.07E-07	50.8443	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#6841 - 	CGI_10011310	superfamily	241600	83	259	7.88E-86	257.554	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6846 - 	CGI_10011315	superfamily	241754	1	191	9.86E-104	306.16	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#6849 - 	CGI_10011318	superfamily	241754	24	147	1.73E-77	244.914	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#6852 - 	CGI_10011321	superfamily	243072	141	261	1.16E-35	134.819	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6852 - 	CGI_10011321	superfamily	243072	47	193	6.73E-26	106.699	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6852 - 	CGI_10011321	superfamily	243072	233	324	3.79E-12	66.253	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#6859 - 	CGI_10021027	superfamily	192060	154	229	4.88E-08	50.8207	cl09599	HbrB superfamily	N	 - 	HbrB-like; HbrB is involved hyphal growth and polarity.
Q#6860 - 	CGI_10021028	superfamily	246723	1	345	1.12E-166	491.308	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#6862 - 	CGI_10021030	superfamily	245201	240	490	3.55E-123	386.469	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6862 - 	CGI_10021030	superfamily	201217	570	616	2.17E-12	64.4692	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6862 - 	CGI_10021030	superfamily	201217	620	669	4.22E-12	63.6988	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6862 - 	CGI_10021030	superfamily	201217	672	721	6.43E-11	60.232	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6862 - 	CGI_10021030	superfamily	201217	793	838	3.86E-08	52.1428	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6862 - 	CGI_10021030	superfamily	205718	552	581	0.00030031	40.1662	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6862 - 	CGI_10021030	superfamily	201217	725	789	0.000672167	39.4312	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#6863 - 	CGI_10021031	superfamily	238211	26	259	9.64E-117	338.096	cl18908	TS_Pyrimidine_HMase superfamily	 - 	 - 	"Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the biosynthesis of DNA precursors and are active as homodimers. However, they exhibit distinct pyrimidine base specificities and differ in the details of their catalyzed reactions. TS is biologically ubiquitous and catalyzes the conversion of dUMP and methylene-tetrahydrofolate (CH2THF) to dTMP and dihydrofolate (DHF). It also acts as a regulator of its own expression by binding and inactivating its own RNA. Due to its key role in the de novo pathway for thymidylate synthesis and, hence, DNA synthesis, it is one of the most conserved enzymes across species and phyla. TS is a well-recognized target for anticancer chemotherapy, as well as a valuable new target against infectious diseases. Interestingly, in several protozoa, a single polypeptide chain codes for both, dihydrofolate reductase (DHFR) and thymidylate synthase (TS), forming a bifunctional enzyme (DHFR-TS), possibly through gene fusion at a single evolutionary point. DHFR-TS is also active as a dimer. Virus encoded dCMP-HMase catalyzes the reversible conversion of dCMP and CH2THF to hydroxymethyl-dCMP and THF. This family also includes dUMP hydroxymethylase, which is encoded by several bacteriophages that infect Bacillus subtilis, for their own protection against the host restriction system,  and contain hydroxymethyl-dUMP instead of dTMP in their DNA."
Q#6865 - 	CGI_10021033	superfamily	243069	104	207	8.37E-20	86.8174	cl02525	Band_7 superfamily	C	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#6865 - 	CGI_10021033	superfamily	242376	307	390	9.29E-13	64.1686	cl01225	SCP2 superfamily	 - 	 - 	"SCP-2 sterol transfer family; This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145."
Q#6868 - 	CGI_10021036	superfamily	243096	53	111	7.64E-08	46.522	cl02571	RhoGEF superfamily	C	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#6869 - 	CGI_10021037	superfamily	243096	16	90	1.64E-06	43.0552	cl02571	RhoGEF superfamily	NC	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#6871 - 	CGI_10021039	superfamily	243095	68	261	1.03E-60	206.381	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#6872 - 	CGI_10021040	superfamily	215647	63	264	9.70E-11	59.5445	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#6873 - 	CGI_10021041	superfamily	243199	5	87	6.52E-09	54.2194	cl02808	RT_like superfamily	N	 - 	"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs."
Q#6874 - 	CGI_10021042	superfamily	245201	32	278	3.45E-67	211.61	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6875 - 	CGI_10021043	superfamily	217473	110	371	2.04E-38	144.43	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#6875 - 	CGI_10021043	superfamily	243034	665	692	0.00367429	36.2416	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6876 - 	CGI_10021044	superfamily	247745	261	512	5.05E-173	509.241	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#6876 - 	CGI_10021044	superfamily	245003	527	610	4.77E-21	89.5634	cl08536	Alpha-mann_mid superfamily	 - 	 - 	"Alpha mannosidase, middle domain; Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase."
Q#6877 - 	CGI_10021045	superfamily	217473	113	354	2.56E-32	126.711	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#6879 - 	CGI_10021047	superfamily	248097	2	103	1.27E-15	67.6754	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6880 - 	CGI_10021048	superfamily	248097	177	303	9.42E-20	82.6982	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6882 - 	CGI_10021050	superfamily	248097	243	348	7.24E-14	68.4458	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6883 - 	CGI_10021051	superfamily	248097	10	84	1.12E-12	59.9714	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6884 - 	CGI_10021052	superfamily	248097	26	114	4.81E-14	64.5938	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#6885 - 	CGI_10021053	superfamily	246918	258	304	1.95E-10	57.2115	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#6885 - 	CGI_10021053	superfamily	246918	308	368	7.65E-09	52.5891	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#6888 - 	CGI_10021056	superfamily	246911	159	262	9.75E-32	116.964	cl15262	PUB superfamily	 - 	 - 	"PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.   The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes (except for fungi) and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97."
Q#6888 - 	CGI_10021056	superfamily	241645	336	407	0.00648506	34.5544	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#6892 - 	CGI_10007180	superfamily	245029	8	126	6.09E-11	55.7316	cl09190	MAPEG superfamily	 - 	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#6893 - 	CGI_10007181	superfamily	218140	335	819	6.68E-132	406.984	cl04579	Anoctamin superfamily	 - 	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#6894 - 	CGI_10007182	superfamily	218140	304	781	4.06E-135	416.614	cl04579	Anoctamin superfamily	 - 	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#6895 - 	CGI_10007183	superfamily	241798	9	327	0	563.141	cl00338	ALAD_PBGS superfamily	 - 	 - 	"Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cysteine-rich zinc binding site appears more common. Most members represented by this model also have a second allosteric magnesium binding site (consensus RX~164DX~65EXXXD, missing in a eukaryotic subfamily with cysteine-rich zinc binding site)."
Q#6896 - 	CGI_10007184	superfamily	247068	473	564	1.57E-07	51.1602	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6896 - 	CGI_10007184	superfamily	247068	1349	1440	3.10E-07	50.3898	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6896 - 	CGI_10007184	superfamily	247068	668	727	4.04E-06	46.923	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6896 - 	CGI_10007184	superfamily	247068	1546	1605	1.41E-05	45.3822	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6896 - 	CGI_10007184	superfamily	247068	382	461	0.00152808	38.8338	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6896 - 	CGI_10007184	superfamily	247068	1250	1337	0.00894543	36.5226	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#6898 - 	CGI_10007186	superfamily	241629	233	367	1.27E-59	191.269	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#6898 - 	CGI_10007186	superfamily	241629	1	76	3.65E-30	113.074	cl00133	SCP superfamily	N	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#6899 - 	CGI_10007187	superfamily	245206	4	259	3.67E-95	283.148	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#6900 - 	CGI_10007188	superfamily	245206	5	139	9.39E-37	136.387	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#6901 - 	CGI_10002908	superfamily	241600	24	93	7.01E-19	77.2807	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6902 - 	CGI_10002909	superfamily	218912	18	150	1.04E-46	162.429	cl18485	COG2 superfamily	 - 	 - 	"COG (conserved oligomeric Golgi) complex component, COG2; The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function. The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficing proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs."
Q#6902 - 	CGI_10002909	superfamily	221383	574	698	1.84E-31	119.69	cl13459	DUF3510 superfamily	 - 	 - 	Domain of unknown function (DUF3510); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 130 amino acids in length. This domain is found associated with pfam06148.
Q#6903 - 	CGI_10002910	superfamily	246680	712	791	0.000153356	40.8364	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#6905 - 	CGI_10024310	superfamily	241574	61	105	3.57E-20	83.0189	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6906 - 	CGI_10024311	superfamily	241574	118	182	0.00127467	37.9506	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6907 - 	CGI_10024312	superfamily	241574	2	97	2.52E-27	107.672	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6907 - 	CGI_10024312	superfamily	241574	188	387	4.65E-24	98.4269	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6910 - 	CGI_10024315	superfamily	247905	93	232	3.32E-18	78.8188	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#6910 - 	CGI_10024315	superfamily	247805	6	62	0.000124287	40.7055	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6911 - 	CGI_10024316	superfamily	247999	496	546	6.84E-07	47.4852	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#6912 - 	CGI_10024317	superfamily	241574	10	177	6.93E-58	191.645	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6912 - 	CGI_10024317	superfamily	241574	207	427	3.40E-26	104.975	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#6913 - 	CGI_10024318	superfamily	245847	11	93	1.11E-06	46.7268	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#6914 - 	CGI_10024319	superfamily	246597	7	287	0	623.864	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#6915 - 	CGI_10024320	superfamily	243069	72	199	1.33E-53	177.363	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#6916 - 	CGI_10024321	superfamily	217867	8	176	1.02E-107	308.405	cl04383	P21-Arc superfamily	 - 	 - 	ARP2/3 complex ARPC3 (21 kDa) subunit; The seven component ARP2/3 actin-organising complex is involved in actin assembly and function.
Q#6917 - 	CGI_10024322	superfamily	247757	7	140	1.82E-06	46.4705	cl17203	Fer4_NifH superfamily	C	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#6918 - 	CGI_10024323	superfamily	243034	207	302	3.39E-19	81.2723	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6918 - 	CGI_10024323	superfamily	243034	61	156	3.40E-10	56.2344	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6919 - 	CGI_10024324	superfamily	243034	472	567	1.97E-19	84.3539	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6919 - 	CGI_10024324	superfamily	243034	326	421	1.30E-10	58.9308	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#6920 - 	CGI_10024325	superfamily	242113	18	251	1.53E-54	177.904	cl00814	Cyclase superfamily	 - 	 - 	Putative cyclase; Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.
Q#6922 - 	CGI_10024327	superfamily	243035	20	89	2.03E-09	49.8401	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#6924 - 	CGI_10024329	superfamily	220692	48	367	5.97E-22	93.8081	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#6925 - 	CGI_10024330	superfamily	192535	88	184	8.09E-05	42.9682	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#6929 - 	CGI_10024334	superfamily	241672	5	294	1.16E-61	199.555	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#6930 - 	CGI_10024335	superfamily	219565	481	549	5.53E-07	50.9521	cl06690	DUF1619 superfamily	N	 - 	Protein of unknown function (DUF1619); This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.
Q#6930 - 	CGI_10024335	superfamily	219565	216	387	0.000629668	41.3221	cl06690	DUF1619 superfamily	C	 - 	Protein of unknown function (DUF1619); This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.
Q#6931 - 	CGI_10024336	superfamily	248145	7	99	7.08E-10	57.2595	cl17591	CAF1 superfamily	C	 - 	CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Q#6931 - 	CGI_10024336	superfamily	248145	171	227	0.00188687	37.6144	cl17591	CAF1 superfamily	NC	 - 	CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Q#6936 - 	CGI_10024341	superfamily	218247	25	257	2.33E-34	126.337	cl04727	Pex2_Pex12 superfamily	 - 	 - 	"Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain."
Q#6936 - 	CGI_10024341	superfamily	247792	288	325	4.92E-05	40.1849	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#6937 - 	CGI_10024342	superfamily	243058	121	231	1.56E-08	53.8575	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#6937 - 	CGI_10024342	superfamily	244760	820	929	3.22E-36	133.588	cl07618	B2-adapt-app_C superfamily	 - 	 - 	"Beta2-adaptin appendage, C-terminal sub-domain; Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15)."
Q#6937 - 	CGI_10024342	superfamily	243521	711	811	1.39E-15	74.2018	cl03759	Alpha_adaptinC2 superfamily	 - 	 - 	"Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins."
Q#6938 - 	CGI_10024343	superfamily	243306	11	237	5.91E-140	394.988	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#6939 - 	CGI_10024344	superfamily	217247	6	66	8.68E-06	42.3802	cl18397	Glyco_hydro_2_C superfamily	NC	 - 	"Glycosyl hydrolases family 2, TIM barrel domain; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities."
Q#6942 - 	CGI_10024347	superfamily	149667	34	219	8.35E-19	81.2627	cl07343	GON superfamily	 - 	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#6943 - 	CGI_10024348	superfamily	241600	1	187	5.36E-63	196.307	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#6944 - 	CGI_10004049	superfamily	115363	201	249	4.38E-08	48.9074	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#6945 - 	CGI_10004050	superfamily	115363	178	228	5.62E-09	52.3742	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#6945 - 	CGI_10004050	superfamily	115363	243	279	8.87E-06	43.1294	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#6945 - 	CGI_10004050	superfamily	207713	364	393	0.00185095	36.5285	cl02729	WWE superfamily	C	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#6946 - 	CGI_10004051	superfamily	207713	4	33	0.000229597	34.2173	cl02729	WWE superfamily	C	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#6948 - 	CGI_10004053	superfamily	247725	29	199	2.08E-99	299.516	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#6948 - 	CGI_10004053	superfamily	246908	414	507	1.88E-44	152.885	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#6949 - 	CGI_10004054	superfamily	247805	472	525	6.57E-06	45.7912	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6949 - 	CGI_10004054	superfamily	192286	104	255	4.52E-97	306.274	cl18178	UPF1_Zn_bind superfamily	 - 	 - 	RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD).
Q#6949 - 	CGI_10004054	superfamily	221913	663	860	5.65E-78	254.772	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#6952 - 	CGI_10004528	superfamily	242372	32	72	2.81E-09	49.6775	cl01221	DTW superfamily	C	 - 	DTW domain; This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after.
Q#6953 - 	CGI_10004529	superfamily	217293	32	230	7.64E-29	115.808	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6953 - 	CGI_10004529	superfamily	220608	424	536	5.44E-25	101.999	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#6953 - 	CGI_10004529	superfamily	202474	237	315	1.20E-10	61.1305	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#6954 - 	CGI_10004530	superfamily	241573	25	244	3.13E-72	232.222	cl00051	CysPc superfamily	N	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#6954 - 	CGI_10004530	superfamily	241653	260	408	2.77E-30	113.955	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#6955 - 	CGI_10004531	superfamily	245213	74	109	6.59E-06	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6955 - 	CGI_10004531	superfamily	245213	37	72	0.000246727	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6955 - 	CGI_10004531	superfamily	245213	111	146	0.000392372	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#6956 - 	CGI_10000862	superfamily	246669	56	188	1.68E-74	227.932	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#6957 - 	CGI_10002928	superfamily	246722	1	163	1.55E-15	74.4549	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#6958 - 	CGI_10002929	superfamily	241867	106	229	9.59E-08	49.818	cl00446	Lactamase_B superfamily	N	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#6958 - 	CGI_10002929	superfamily	241867	75	103	0.000206567	39.4422	cl00446	Lactamase_B superfamily	C	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#6962 - 	CGI_10007093	superfamily	246613	83	314	6.98E-141	403.313	cl14058	lectin_L-type superfamily	 - 	 - 	"legume lectins; The L-type (legume-type) lectins are a highly diverse family of carbohydrate binding proteins that generally display no enzymatic activity toward the sugars they bind.  This family includes arcelin, concanavalinA, the lectin-like receptor kinases, the ERGIC-53/VIP36/EMP46 type1 transmembrane proteins, and an alpha-amylase inhibitor.  L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face".  This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers.  Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely."
Q#6964 - 	CGI_10007095	superfamily	248318	289	349	1.36E-10	56.6753	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#6965 - 	CGI_10007096	superfamily	246669	2400	2515	2.58E-42	154.236	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#6965 - 	CGI_10007096	superfamily	246708	2223	2377	1.37E-41	151.9	cl14781	PI-PLC-Y superfamily	 - 	 - 	"Phosphatidylinositol-specific phospholipase C, Y domain; This associates with pfam00388 to form a single structural unit."
Q#6965 - 	CGI_10007096	superfamily	246675	2055	2131	1.13E-35	139.214	cl14615	PI-PLCc_GDPD_SF superfamily	NC	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#6965 - 	CGI_10007096	superfamily	243053	1364	1592	2.43E-27	114.265	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#6965 - 	CGI_10007096	superfamily	241645	2701	2797	5.60E-24	100.348	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#6965 - 	CGI_10007096	superfamily	241645	2570	2661	3.82E-11	62.5984	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#6968 - 	CGI_10003488	superfamily	247805	1	82	7.46E-09	48.4876	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#6971 - 	CGI_10010929	superfamily	245201	1022	1262	8.87E-57	197.459	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#6971 - 	CGI_10010929	superfamily	243045	352	395	0.00046076	40.3091	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#6972 - 	CGI_10010930	superfamily	247058	11	205	1.05E-59	190.464	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#6973 - 	CGI_10010931	superfamily	244539	1133	1312	2.81E-42	155.926	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#6973 - 	CGI_10010931	superfamily	247856	693	754	1.89E-06	47.1573	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#6973 - 	CGI_10010931	superfamily	246664	9	487	8.33E-166	513.386	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#6973 - 	CGI_10010931	superfamily	203841	1371	1473	1.17E-13	70.4444	cl17716	NAD_binding_6 superfamily	N	 - 	Ferric reductase NAD binding domain; Ferric reductase NAD binding domain.  
Q#6973 - 	CGI_10010931	superfamily	242267	948	1092	1.48E-09	57.6852	cl01043	Ferric_reduct superfamily	 - 	 - 	"Ferric reductase like transmembrane component; This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease."
Q#6974 - 	CGI_10010932	superfamily	150820	15	280	6.85E-51	175.407	cl10894	DuoxA superfamily	 - 	 - 	"Dual oxidase maturation factor; DuoxA (Dual oxidase maturation factor) is the essential protein necessary for the final release of DUOX2 (an NADPH:O2 oxidoreductase flavoprotein) from the endoplasmic reticulum. Dual oxidases (DUOX1 and DUOX2) constitute the catalytic core of the hydrogen peroxide generator, which generates H2O2 at the apical membrane of thyroid follicular cells, essential for iodination of thyroglobulin by thyroid peroxidases. DuoxA carries five membrane-integral regions including a reverse signal-anchor with external N-terminus (type III) and two N-glycosylation sites. It is conserved from nematodes to humans."
Q#6977 - 	CGI_10010935	superfamily	245814	298	371	6.04E-11	59.056	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6977 - 	CGI_10010935	superfamily	245814	393	477	8.75E-11	58.2856	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6977 - 	CGI_10010935	superfamily	245814	182	267	0.000235973	39.6018	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6977 - 	CGI_10010935	superfamily	245814	79	154	0.000685329	37.7713	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6977 - 	CGI_10010935	superfamily	245814	12	45	0.00709076	35.0287	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#6978 - 	CGI_10010936	superfamily	241578	203	343	4.67E-38	139.344	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#6978 - 	CGI_10010936	superfamily	219345	479	567	0.000937407	40.9739	cl06326	Phlebovirus_G1 superfamily	C	 - 	Phlebovirus glycoprotein G1; This family consists of several Phlebovirus glycoprotein G1 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi.
Q#6978 - 	CGI_10010936	superfamily	243119	583	614	0.0013632	37.4234	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#6982 - 	CGI_10010940	superfamily	241615	58	97	1.96E-06	45.9393	cl00107	LysM superfamily	 - 	 - 	"Lysine Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes."
Q#6982 - 	CGI_10010940	superfamily	242902	775	881	2.45E-36	135.527	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#6983 - 	CGI_10010941	superfamily	217293	69	214	3.09E-19	85.7623	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#6985 - 	CGI_10010943	superfamily	248312	12	181	0.00167194	36.5625	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#6986 - 	CGI_10010944	superfamily	248312	21	190	2.34E-05	41.9553	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#6987 - 	CGI_10010945	superfamily	248312	16	191	2.18E-07	47.7333	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#6988 - 	CGI_10010946	superfamily	248312	16	191	2.18E-07	47.7333	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#6991 - 	CGI_10010949	superfamily	247786	1	265	6.53E-110	322.676	cl17232	F420_oxidored superfamily	 - 	 - 	NADP oxidoreductase coenzyme F420-dependent; NADP oxidoreductase coenzyme F420-dependent.  
Q#6992 - 	CGI_10008168	superfamily	247986	3	107	7.53E-11	60.0794	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#6992 - 	CGI_10008168	superfamily	247986	222	357	2.79E-06	46.5974	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#6993 - 	CGI_10008169	superfamily	247986	389	479	6.49E-15	74.3318	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#6993 - 	CGI_10008169	superfamily	247986	634	738	1.41E-06	48.5234	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#6993 - 	CGI_10008169	superfamily	245225	42	368	6.19E-76	253.387	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#6996 - 	CGI_10008172	superfamily	155088	505	658	1.18E-36	136.957	cl02758	AMOP superfamily	 - 	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#6996 - 	CGI_10008172	superfamily	243124	139	265	2.26E-15	75.1561	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#6997 - 	CGI_10008173	superfamily	155088	506	667	3.91E-31	121.164	cl02758	AMOP superfamily	 - 	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#6997 - 	CGI_10008173	superfamily	243124	123	270	1.36E-17	81.7044	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#6997 - 	CGI_10008173	superfamily	243065	662	843	2.06E-06	47.7817	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#6998 - 	CGI_10008174	superfamily	155088	474	617	2.37E-31	120.779	cl02758	AMOP superfamily	 - 	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#7000 - 	CGI_10008176	superfamily	217293	1	181	8.07E-34	125.438	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7000 - 	CGI_10008176	superfamily	202474	190	269	1.51E-29	113.903	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7000 - 	CGI_10008176	superfamily	202474	330	356	0.000593472	39.5593	cl08379	Neur_chan_memb superfamily	N	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7001 - 	CGI_10008177	superfamily	217293	35	246	8.05E-37	134.683	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7001 - 	CGI_10008177	superfamily	202474	253	437	7.07E-33	123.918	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7002 - 	CGI_10008178	superfamily	247068	464	559	1.80E-28	111.251	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7002 - 	CGI_10008178	superfamily	247068	362	456	7.80E-22	92.3765	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7002 - 	CGI_10008178	superfamily	247068	567	664	8.67E-22	92.3765	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7002 - 	CGI_10008178	superfamily	247068	242	341	1.53E-21	91.6061	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7002 - 	CGI_10008178	superfamily	247068	132	234	8.66E-16	75.0425	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7002 - 	CGI_10008178	superfamily	247068	686	772	3.05E-13	67.3385	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7002 - 	CGI_10008178	superfamily	247068	23	101	3.24E-05	43.2503	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7003 - 	CGI_10008179	superfamily	247068	470	565	2.17E-28	111.251	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7003 - 	CGI_10008179	superfamily	247068	573	668	1.96E-23	96.9989	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7003 - 	CGI_10008179	superfamily	247068	249	347	1.73E-21	91.2209	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7003 - 	CGI_10008179	superfamily	247068	139	241	5.43E-18	81.2057	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7003 - 	CGI_10008179	superfamily	247068	368	461	5.14E-17	78.5093	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7003 - 	CGI_10008179	superfamily	247068	688	775	7.58E-12	63.4865	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7003 - 	CGI_10008179	superfamily	247068	23	130	4.59E-08	51.9306	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7005 - 	CGI_10008181	superfamily	247068	417	512	6.05E-25	100.851	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7005 - 	CGI_10008181	superfamily	247068	521	621	9.08E-20	86.2133	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7005 - 	CGI_10008181	superfamily	247068	199	301	2.91E-19	84.6725	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7005 - 	CGI_10008181	superfamily	247068	325	408	1.83E-16	76.5833	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7005 - 	CGI_10008181	superfamily	247068	93	191	5.19E-16	75.0425	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7005 - 	CGI_10008181	superfamily	247068	634	717	3.69E-13	66.9533	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7005 - 	CGI_10008181	superfamily	247068	9	81	5.68E-05	42.3006	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7007 - 	CGI_10008183	superfamily	214781	195	255	4.43E-09	54.6556	cl02747	NRF superfamily	C	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#7008 - 	CGI_10005849	superfamily	245814	3	79	2.24E-06	42.4763	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7010 - 	CGI_10005851	superfamily	241596	36	101	2.28E-12	58.7647	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#7011 - 	CGI_10005852	superfamily	244881	99	397	1.19E-174	494.447	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#7012 - 	CGI_10005853	superfamily	218015	123	206	9.16E-13	63.3035	cl08416	FBA superfamily	N	 - 	"F-box associated region; Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. Human FBXO2 is involved in binding to N-glycosylated proteins."
Q#7012 - 	CGI_10005853	superfamily	243074	8	52	8.25E-11	55.2053	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#7013 - 	CGI_10005854	superfamily	243092	1822	1979	2.00E-15	78.1456	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7014 - 	CGI_10005855	superfamily	245040	24	70	3.36E-05	37.4077	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#7018 - 	CGI_10015706	superfamily	247684	21	238	9.80E-61	199.426	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7019 - 	CGI_10015707	superfamily	247684	3	418	1.15E-89	284.555	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7021 - 	CGI_10015709	superfamily	247684	3	418	1.09E-74	245.265	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7022 - 	CGI_10015710	superfamily	247684	1	412	5.14E-82	264.91	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7023 - 	CGI_10015711	superfamily	202484	23	70	1.09E-13	60.3204	cl03798	zf-Tim10_DDP superfamily	N	 - 	Tim10/DDP family zinc finger; Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein TIMM8A. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localised to the mitochondrial intermembrane space.
Q#7024 - 	CGI_10015712	superfamily	245835	710	910	9.76E-123	373.197	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#7024 - 	CGI_10015712	superfamily	243047	13	129	4.43E-34	127.736	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#7024 - 	CGI_10015712	superfamily	220441	444	545	0.000780191	40.8066	cl18557	DUF2076 superfamily	NC	 - 	"Uncharacterized protein conserved in bacteria (DUF2076); This domain, found in various hypothetical prokaryotic proteins, has no known function. The domain, however, is found in various periplasmic ligand-binding sensor proteins."
Q#7025 - 	CGI_10015713	superfamily	247725	1406	1577	1.84E-48	173.197	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7025 - 	CGI_10015713	superfamily	243052	584	689	2.78E-31	120.901	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#7025 - 	CGI_10015713	superfamily	247725	880	1006	2.90E-30	119.233	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7025 - 	CGI_10015713	superfamily	243052	1142	1253	6.83E-25	102.797	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#7025 - 	CGI_10015713	superfamily	243052	225	333	1.24E-22	97.4311	cl02480	MyTH4 superfamily	C	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#7025 - 	CGI_10015713	superfamily	242889	1856	1969	3.75E-11	62.2354	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#7025 - 	CGI_10015713	superfamily	243052	489	520	0.00605472	38.1104	cl02480	MyTH4 superfamily	C	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#7025 - 	CGI_10015713	superfamily	243052	172	203	0.00605472	38.1104	cl02480	MyTH4 superfamily	C	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#7027 - 	CGI_10015715	superfamily	241790	1	71	6.86E-43	144.091	cl00330	Ribosomal_S8 superfamily	C	 - 	Ribosomal protein S8; Ribosomal protein S8.  
Q#7031 - 	CGI_10015719	superfamily	243062	126	228	2.03E-53	169.379	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#7032 - 	CGI_10015720	superfamily	216062	48	245	5.90E-33	121.776	cl02928	TGFb_propeptide superfamily	 - 	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#7033 - 	CGI_10015721	superfamily	215647	364	575	1.62E-11	63.3964	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#7035 - 	CGI_10015723	superfamily	241600	4	74	2.35E-29	104.63	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7038 - 	CGI_10007550	superfamily	243072	141	275	1.40E-32	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7038 - 	CGI_10007550	superfamily	243072	210	343	2.35E-32	123.648	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7038 - 	CGI_10007550	superfamily	243072	419	545	2.02E-31	120.951	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7038 - 	CGI_10007550	superfamily	243072	486	607	8.79E-31	119.025	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7038 - 	CGI_10007550	superfamily	243072	284	409	4.59E-30	117.099	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7038 - 	CGI_10007550	superfamily	243072	17	167	7.96E-19	84.7426	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7039 - 	CGI_10007551	superfamily	246918	148	196	1.69E-12	61.8339	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7040 - 	CGI_10007552	superfamily	241571	257	321	5.98E-05	40.8587	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#7040 - 	CGI_10007552	superfamily	241571	104	173	0.0014385	36.5182	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#7041 - 	CGI_10007704	superfamily	207662	57	128	9.23E-35	124.982	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7041 - 	CGI_10007704	superfamily	245599	353	516	4.53E-21	90.3598	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7042 - 	CGI_10007705	superfamily	243051	268	411	2.31E-37	139.435	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#7042 - 	CGI_10007705	superfamily	243051	469	639	2.22E-30	119.405	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#7042 - 	CGI_10007705	superfamily	243051	691	814	1.48E-15	75.8773	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#7042 - 	CGI_10007705	superfamily	241571	74	176	1.25E-13	69.3634	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#7042 - 	CGI_10007705	superfamily	245213	645	674	0.000277322	40.3126	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7042 - 	CGI_10007705	superfamily	245213	217	244	0.000765144	38.7718	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7042 - 	CGI_10007705	superfamily	248012	829	928	9.09E-21	89.5592	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#7043 - 	CGI_10007706	superfamily	207662	57	129	1.56E-31	116.122	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7043 - 	CGI_10007706	superfamily	245599	343	507	1.58E-20	88.819	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7044 - 	CGI_10007707	superfamily	207662	61	133	5.78E-31	114.966	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7044 - 	CGI_10007707	superfamily	245599	379	537	2.37E-20	88.4338	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7045 - 	CGI_10007708	superfamily	207662	38	109	1.76E-30	113.426	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7045 - 	CGI_10007708	superfamily	245599	340	495	5.43E-27	106.923	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7046 - 	CGI_10007709	superfamily	207662	100	171	1.52E-31	118.048	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7046 - 	CGI_10007709	superfamily	245599	497	671	7.82E-26	105.383	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7047 - 	CGI_10007710	superfamily	242922	102	184	1.36E-41	137.313	cl02176	TAF11 superfamily	 - 	 - 	"TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity.  TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone. TAF11 also directly interacts with TFIIA, acting as a bridging factor that stabilizes the TFIIA-TBP-DNA complex. Each TAF, with the help of a specific activator, is required only for the expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID.   Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. The TAF11 domain is structurally analogous to histone H3 and interacts with TAF13, making a novel histone-like heterodimer. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex."
Q#7048 - 	CGI_10007711	superfamily	245201	99	469	0	710.289	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7049 - 	CGI_10007712	superfamily	218671	18	193	1.31E-68	214.586	cl05290	NKAIN superfamily	 - 	 - 	"Na,K-Atpase Interacting protein; NKAIN (Na,K-Atpase INteracting) proteins are a family of evolutionary conserved transmembrane proteins that localise to neurons, that are critical for neuronal function, and that interact with the beta subunits, beta1 in vertebrates and beta in Drosophila, of Na,K-ATPase. NKAINs have highly conserved trans-membrane domains but otherwise no other characterized domains. NKAINs may function as subunits of pore or channel structures in neurons or they may affect the function of other membrane proteins. They are likely to function within the membrane bilayer."
Q#7053 - 	CGI_10004688	superfamily	247755	1317	1537	3.55E-113	357.189	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#7053 - 	CGI_10004688	superfamily	247755	671	871	2.75E-110	348.305	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#7053 - 	CGI_10004688	superfamily	216049	366	627	1.18E-34	135.877	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#7053 - 	CGI_10004688	superfamily	216049	999	1270	3.04E-32	128.558	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#7054 - 	CGI_10004689	superfamily	245598	3	196	3.29E-50	170.923	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#7054 - 	CGI_10004689	superfamily	247856	300	360	6.75E-05	40.6089	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#7055 - 	CGI_10004690	superfamily	245598	98	263	6.31E-38	134.714	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#7057 - 	CGI_10007747	superfamily	245847	41	188	3.03E-17	74.9005	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#7061 - 	CGI_10007751	superfamily	245596	93	412	0	530.256	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#7062 - 	CGI_10007752	superfamily	247804	345	391	1.42E-13	64.8959	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#7062 - 	CGI_10007752	superfamily	243177	59	203	8.46E-15	71.7088	cl02779	TRFH superfamily	N	 - 	"Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains."
Q#7063 - 	CGI_10007753	superfamily	215827	174	343	3.06E-19	86.7535	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#7066 - 	CGI_10002719	superfamily	241563	61	99	1.53E-07	48.4375	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7066 - 	CGI_10002719	superfamily	110440	486	510	0.000764974	37.3873	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#7066 - 	CGI_10002719	superfamily	243092	306	439	0.00206062	38.8552	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7067 - 	CGI_10006759	superfamily	207662	125	197	9.33E-35	124.982	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7067 - 	CGI_10006759	superfamily	245599	317	482	2.07E-28	110.775	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7068 - 	CGI_10006760	superfamily	190261	76	151	5.99E-28	108.405	cl03504	RFX_DNA_binding superfamily	 - 	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#7069 - 	CGI_10006761	superfamily	207662	317	393	4.82E-30	114.196	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7069 - 	CGI_10006761	superfamily	245599	501	732	5.45E-14	70.8413	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7070 - 	CGI_10006762	superfamily	242577	12	109	4.79E-19	77.8651	cl01553	GFA superfamily	C	 - 	Glutathione-dependent formaldehyde-activating enzyme; Glutathione-dependent formaldehyde-activating enzyme.  
Q#7071 - 	CGI_10006763	superfamily	247743	316	468	3.40E-09	55.2299	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#7072 - 	CGI_10006764	superfamily	220695	20	139	0.000971035	39.0991	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#7073 - 	CGI_10006765	superfamily	241563	9	40	2.14E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7074 - 	CGI_10006766	superfamily	241584	8	97	0.000320435	37.4759	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7077 - 	CGI_10004170	superfamily	241563	68	109	9.48E-07	46.3184	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7078 - 	CGI_10009893	superfamily	241563	60	97	1.85E-05	43.0447	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7079 - 	CGI_10009894	superfamily	242406	140	177	0.00765803	35.0468	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#7082 - 	CGI_10009897	superfamily	241563	187	223	1.35E-06	46.3184	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7084 - 	CGI_10009899	superfamily	241691	294	349	1.94E-05	43.2696	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#7084 - 	CGI_10009899	superfamily	221377	191	257	0.00295043	37.0631	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#7085 - 	CGI_10009900	superfamily	205062	628	660	0.000746713	38.6058	cl15079	Cohesin_HEAT superfamily	N	 - 	"HEAT repeat associated with sister chromatid cohesion; This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B. HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble."
Q#7086 - 	CGI_10009901	superfamily	245819	654	830	9.65E-62	206.661	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#7086 - 	CGI_10009901	superfamily	245201	359	581	1.82E-32	127.268	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7086 - 	CGI_10009901	superfamily	219526	593	640	2.22E-08	53.7771	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#7088 - 	CGI_10009903	superfamily	241699	6	93	1.34E-35	128.078	cl00221	ACBP superfamily	 - 	 - 	Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Q#7089 - 	CGI_10009904	superfamily	248458	285	477	3.28E-07	50.7753	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7090 - 	CGI_10009905	superfamily	243152	106	233	1.23E-29	112.382	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#7090 - 	CGI_10009905	superfamily	241700	319	483	7.94E-39	139.447	cl00222	lysozyme_like superfamily	 - 	 - 	"lysozyme_like domain.  This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides."
Q#7091 - 	CGI_10009906	superfamily	245596	57	348	1.45E-150	429.962	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#7092 - 	CGI_10009907	superfamily	217293	1	192	1.96E-33	124.667	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7092 - 	CGI_10009907	superfamily	202474	199	275	6.72E-09	54.5821	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7093 - 	CGI_10009908	superfamily	246918	57	104	3.12E-08	47.5815	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7093 - 	CGI_10009908	superfamily	246918	1	50	6.51E-07	44.1147	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7094 - 	CGI_10009909	superfamily	246918	18	66	6.53E-08	44.4999	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7097 - 	CGI_10009912	superfamily	244201	399	524	1.80E-06	46.8403	cl05797	SMC_hinge superfamily	 - 	 - 	SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.
Q#7099 - 	CGI_10009915	superfamily	243175	6	126	1.45E-57	176.671	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#7100 - 	CGI_10002529	superfamily	243035	22	89	1.37E-13	62.3936	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7102 - 	CGI_10002531	superfamily	245841	300	780	1.85E-171	517.637	cl12025	PolY superfamily	 - 	 - 	"Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions.  Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases.  Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria.  In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion.  Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention."
Q#7102 - 	CGI_10002531	superfamily	213388	1201	1294	4.28E-22	93.4908	cl17091	Rev1_C superfamily	 - 	 - 	"C-terminal domain of the Y-family polymerase Rev1; Rev1 is a eukaryotic translesion synthesis (TLS) polymerase; TLS is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. The C-terminal domain modeled here is essential for TLS and has been shown to mediate interactions with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7), as well as with the RIRs (Rev1-interacting regions) of polymerases kappa, iota, and eta. Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment."
Q#7102 - 	CGI_10002531	superfamily	241565	52	120	3.93E-07	49.2423	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#7103 - 	CGI_10002759	superfamily	247724	15	182	1.23E-37	131.114	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#7105 - 	CGI_10002761	superfamily	247724	14	177	7.86E-39	133.035	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#7106 - 	CGI_10002762	superfamily	247911	27	366	3.49E-133	400.946	cl17357	Fumble superfamily	 - 	 - 	"Fumble; Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organisation, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with high similarity to the pantothenate kinases of A. nidulans and mouse. A role of fumble in membrane synthesis has been proposed."
Q#7106 - 	CGI_10002762	superfamily	246946	459	756	5.72E-53	186.344	cl15397	DUF89 superfamily	 - 	 - 	Protein of unknown function DUF89; This family has no known function.
Q#7108 - 	CGI_10000684	superfamily	242889	16	88	3.28E-15	66.8578	cl02111	PCI superfamily	N	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#7110 - 	CGI_10004818	superfamily	241578	553	706	1.53E-18	85.421	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7110 - 	CGI_10004818	superfamily	241578	755	913	1.31E-12	67.7018	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7110 - 	CGI_10004818	superfamily	241578	365	504	1.14E-11	64.6202	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7110 - 	CGI_10004818	superfamily	247068	1124	1213	1.84E-05	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7110 - 	CGI_10004818	superfamily	152683	98	200	6.79E-09	55.3717	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#7111 - 	CGI_10004819	superfamily	247684	27	95	8.72E-15	67.6875	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7112 - 	CGI_10004820	superfamily	247684	3	307	8.90E-76	245.265	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7113 - 	CGI_10004821	superfamily	247684	45	149	6.14E-22	90.4143	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7114 - 	CGI_10004822	superfamily	247684	36	464	1.09E-105	327.697	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7115 - 	CGI_10004823	superfamily	247684	4	331	3.09E-81	259.902	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7116 - 	CGI_10004824	superfamily	247684	4	254	1.72E-54	187.099	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7118 - 	CGI_10019849	superfamily	246975	39	60	0.00488209	33.4745	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#7123 - 	CGI_10019854	superfamily	245201	38	347	0	627.482	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7124 - 	CGI_10019855	superfamily	241675	53	232	4.65E-68	211.68	cl00195	SIR2 superfamily	N	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#7125 - 	CGI_10019856	superfamily	243072	737	775	7.16E-08	51.6154	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7126 - 	CGI_10019857	superfamily	242728	84	112	1.78E-08	46.8906	cl01821	zf-CHCC superfamily	N	 - 	Zinc-finger domain; This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C.
Q#7128 - 	CGI_10019859	superfamily	247068	43	149	4.95E-06	44.2266	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7128 - 	CGI_10019859	superfamily	247068	166	255	0.000250208	39.219	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7131 - 	CGI_10019862	superfamily	220736	188	340	1.79E-29	111.633	cl11068	PTEN_C2 superfamily	 - 	 - 	"C2 domain of PTEN tumour-suppressor protein; This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane."
Q#7131 - 	CGI_10019862	superfamily	241574	88	187	1.51E-11	62.0837	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#7132 - 	CGI_10019863	superfamily	219632	1	72	4.03E-21	82.706	cl06786	Eaf7 superfamily	 - 	 - 	"Chromatin modification-related protein EAF7; The S. cerevisiae member of this family is part of NuA4, the only essential histone acetyltransferase complex in Saccharomyces cerevisiae involved in global histone acetylation."
Q#7133 - 	CGI_10019864	superfamily	247799	82	128	1.89E-10	54.8735	cl17245	KH-I superfamily	N	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#7135 - 	CGI_10019866	superfamily	247727	16	47	6.19E-08	47.6905	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#7136 - 	CGI_10019867	superfamily	247727	36	136	1.97E-08	50.5063	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#7137 - 	CGI_10019868	superfamily	243034	82	172	4.92E-07	47.3748	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#7138 - 	CGI_10019869	superfamily	241564	287	352	2.74E-29	110.433	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#7138 - 	CGI_10019869	superfamily	241564	47	111	1.29E-13	66.5203	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#7138 - 	CGI_10019869	superfamily	247792	512	551	0.000116998	40.1216	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7142 - 	CGI_10019873	superfamily	241574	89	170	4.90E-11	59.989	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#7144 - 	CGI_10019875	superfamily	218406	1	122	5.57E-45	151.043	cl04914	MGAT2 superfamily	N	 - 	"N-acetylglucosaminyltransferase II (MGAT2); UDP-N-acetyl-D-glucosamine:alpha-6-D-mannoside beta-1,2-N- acetylglucosaminyltransferase II (EC 2.4.1.143) (GnT II/MGAT2) is a Golgi resident enzyme that catalyzes an essential step in the biosynthetic pathway leading from high mannose to complex N-linked oligosaccharides. Mutations in the MGAT2 gene lead to congenital disorder of glycosylation (CDG IIa). CDG IIa patients have an increased bleeding tendency, unrelated to coagulation factors."
Q#7145 - 	CGI_10019876	superfamily	218406	74	225	4.76E-68	216.142	cl04914	MGAT2 superfamily	C	 - 	"N-acetylglucosaminyltransferase II (MGAT2); UDP-N-acetyl-D-glucosamine:alpha-6-D-mannoside beta-1,2-N- acetylglucosaminyltransferase II (EC 2.4.1.143) (GnT II/MGAT2) is a Golgi resident enzyme that catalyzes an essential step in the biosynthetic pathway leading from high mannose to complex N-linked oligosaccharides. Mutations in the MGAT2 gene lead to congenital disorder of glycosylation (CDG IIa). CDG IIa patients have an increased bleeding tendency, unrelated to coagulation factors."
Q#7146 - 	CGI_10019877	superfamily	216981	508	651	1.31E-14	71.4098	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#7146 - 	CGI_10019877	superfamily	207690	223	246	1.09E-05	43.4605	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#7146 - 	CGI_10019877	superfamily	207690	131	152	0.000193159	39.9937	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#7148 - 	CGI_10019879	superfamily	243084	134	240	1.14E-31	114.007	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#7149 - 	CGI_10019880	superfamily	112128	1106	1310	4.18E-92	296.319	cl03992	TF_AP-2 superfamily	 - 	 - 	Transcription factor AP-2; Transcription factor AP-2.  
Q#7149 - 	CGI_10019880	superfamily	146396	10	82	4.52E-23	95.7762	cl04239	ENT superfamily	 - 	 - 	ENT domain; This presumed domain is named after Emsy N Terminus (ENT). Emsy is a protein that is amplified in breast cancer and interacts with BRCA2. The N terminus of this protein is found to be similar to other vertebrate and plant proteins of unknown function. This domain has a completely conserved histidine residue that may be functionally important.
Q#7151 - 	CGI_10019882	superfamily	243179	40	118	2.66E-21	84.6625	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#7152 - 	CGI_10010868	superfamily	247866	9	128	6.63E-26	100.22	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#7153 - 	CGI_10010869	superfamily	241592	24	75	4.51E-08	46.8362	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#7155 - 	CGI_10010871	superfamily	217944	40	114	2.13E-24	97.4039	cl04436	RPAP2_Rtr1 superfamily	 - 	 - 	Rtr1/RPAP2 family; This family includes the human RPAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 protein. It has been suggested that this family of proteins are regulators of core RNA polymerase II function.
Q#7156 - 	CGI_10010872	superfamily	220370	25	318	1.61E-61	204.168	cl10719	Tau95 superfamily	 - 	 - 	"RNA polymerase III transcription factor (TF)IIIC subunit; TFIIIC1 is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents the tau 95 subunit which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription."
Q#7160 - 	CGI_10010876	superfamily	247725	3	182	2.20E-99	288.398	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7163 - 	CGI_10010879	superfamily	243092	360	651	1.49E-51	184.846	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7163 - 	CGI_10010879	superfamily	243092	49	392	8.41E-14	71.9824	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7164 - 	CGI_10010880	superfamily	207717	392	465	1.66E-34	128.313	cl02755	LAM superfamily	 - 	 - 	"LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes."
Q#7164 - 	CGI_10010880	superfamily	128927	903	941	5.98E-13	65.4703	cl02733	DM15 superfamily	 - 	 - 	"Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function.  "
Q#7164 - 	CGI_10010880	superfamily	128927	862	901	2.22E-08	52.3735	cl02733	DM15 superfamily	 - 	 - 	"Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function.  "
Q#7165 - 	CGI_10010881	superfamily	245201	1	235	3.07E-133	402.842	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7167 - 	CGI_10010883	superfamily	203768	156	258	6.61E-42	141.485	cl06716	RED_C superfamily	 - 	 - 	"RED-like protein C-terminal region; This family contains sequences that are similar to the C-terminal region of Red protein. This and related proteins are thought to be localised to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated or that the protein self-aggregates extremely efficiently."
Q#7168 - 	CGI_10010884	superfamily	219589	76	236	1.23E-38	136.133	cl06717	RED_N superfamily	 - 	 - 	"RED-like protein N-terminal region; This family contains sequences that are similar to the N-terminal region of Red protein. This and related proteins contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences and a putative trimeric coiled-coil region, suggesting that these proteins are expressed in the nucleus. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated of that the protein self-aggregates extremely efficiently."
Q#7169 - 	CGI_10010885	superfamily	241740	1	127	4.22E-46	149.347	cl00269	cytidine_deaminase-like superfamily	 - 	 - 	"Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes.  All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate."
Q#7170 - 	CGI_10010886	superfamily	247684	12	426	2.84E-100	312.674	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7171 - 	CGI_10018464	superfamily	241577	258	479	6.04E-142	409.937	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#7171 - 	CGI_10018464	superfamily	241576	1	57	9.49E-39	137.969	cl00055	MH1 superfamily	N	 - 	"N-terminal Mad Homology 1 (MH1) domain; The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure.  It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. Receptor-regulated SMAD proteins (R-SMADs, including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by phosphorylation by transforming growth factor (TGF)-beta type I receptors. The active R-SMAD associates with a common mediator SMAD (Co-SMAD or SMAD4) and other cofactors, which together translocate to the nucleus to regulate gene expression. The inhibitory or antagonistic SMADs (I-SMADs, including SMAD6 and SMAD7) negatively regulate TGF-beta signaling by competing with R-SMADs for type I receptor or Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a nuclear localization signal as well as DNA-binding activity. The activated R-SMAD/SMAD4 complex then binds with very low affinity to a DNA sequence CAGAC called SMAD-binding element (SBE) via the MH1 domain."
Q#7172 - 	CGI_10018465	superfamily	246723	156	601	0	601.09	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#7178 - 	CGI_10018471	superfamily	241691	502	618	0.00294818	37.8768	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#7180 - 	CGI_10018473	superfamily	246680	1008	1071	0.000772889	39.241	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#7181 - 	CGI_10018474	superfamily	243146	125	166	5.50E-06	41.493	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#7183 - 	CGI_10018476	superfamily	246680	114	194	4.59E-28	104.014	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#7183 - 	CGI_10018476	superfamily	241640	2	87	6.23E-20	85.0369	cl00149	Tryp_SPc superfamily	N	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#7184 - 	CGI_10018477	superfamily	241640	37	168	1.90E-42	143.186	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#7185 - 	CGI_10018478	superfamily	241578	88	246	8.77E-44	153.986	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7185 - 	CGI_10018478	superfamily	243119	527	568	0.0047028	35.4873	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7185 - 	CGI_10018478	superfamily	243119	573	624	0.00493785	35.4974	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7186 - 	CGI_10018479	superfamily	241578	186	344	3.54E-48	167.083	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7186 - 	CGI_10018479	superfamily	243119	688	721	0.000133518	40.505	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7187 - 	CGI_10018480	superfamily	241578	124	282	2.68E-46	161.69	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7187 - 	CGI_10018480	superfamily	243119	618	669	0.000142108	40.1198	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7187 - 	CGI_10018480	superfamily	243119	571	609	0.00205124	36.653	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7189 - 	CGI_10018482	superfamily	243034	159	259	6.54E-15	69.3311	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#7190 - 	CGI_10018483	superfamily	245010	29	134	8.24E-07	43.3755	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#7191 - 	CGI_10018484	superfamily	243074	63	107	2.33E-14	67.9169	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#7192 - 	CGI_10018485	superfamily	242059	43	465	3.16E-94	294.011	cl00738	MBOAT superfamily	 - 	 - 	"MBOAT, membrane-bound O-acyltransferase family; The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue."
Q#7193 - 	CGI_10018486	superfamily	243056	33	236	3.51E-30	114.764	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#7194 - 	CGI_10018487	superfamily	247750	20	201	1.18E-116	352.837	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#7194 - 	CGI_10018487	superfamily	247750	256	438	4.55E-48	171.408	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#7195 - 	CGI_10018488	superfamily	245876	17	82	8.09E-11	54.8146	cl12113	HSF_DNA-bind superfamily	C	 - 	HSF-type DNA-binding; HSF-type DNA-binding.  
Q#7198 - 	CGI_10018491	superfamily	116798	37	186	6.39E-18	76.1762	cl17955	Lipocalin_2 superfamily	 - 	 - 	"Lipocalin-like domain; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel."
Q#7199 - 	CGI_10018492	superfamily	216686	134	309	1.87E-35	128.98	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#7200 - 	CGI_10003249	superfamily	247725	255	290	1.93E-10	56.4407	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7201 - 	CGI_10001599	superfamily	245819	631	806	1.41E-71	234.396	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#7201 - 	CGI_10001599	superfamily	245201	322	559	4.09E-40	149.609	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7201 - 	CGI_10001599	superfamily	219526	577	618	3.28E-08	53.3919	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#7205 - 	CGI_10014807	superfamily	247724	2	62	4.90E-21	87.5907	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#7206 - 	CGI_10014808	superfamily	243744	38	57	0.00959794	30.7946	cl04410	DFP superfamily	N	 - 	"DNA / pantothenate metabolism flavoprotein; The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism."
Q#7208 - 	CGI_10014812	superfamily	243035	43	85	1.34E-07	45.3034	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7212 - 	CGI_10014816	superfamily	243091	135	235	6.99E-09	52.8796	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#7213 - 	CGI_10014817	superfamily	243035	18	51	0.000138526	37.1942	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7216 - 	CGI_10014820	superfamily	241563	103	138	0.000547638	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7218 - 	CGI_10014635	superfamily	245206	4	302	0	524.569	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#7221 - 	CGI_10014638	superfamily	241802	69	372	6.93E-121	358.338	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#7221 - 	CGI_10014638	superfamily	245020	393	463	5.27E-19	81.4354	cl09141	ACT superfamily	 - 	 - 	"ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but  the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times."
Q#7222 - 	CGI_10014639	superfamily	243095	713	904	1.70E-63	217.29	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#7222 - 	CGI_10014639	superfamily	245835	314	541	7.91E-13	69.2985	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#7223 - 	CGI_10014640	superfamily	241599	73	133	2.28E-14	66.498	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#7224 - 	CGI_10014641	superfamily	241760	274	322	9.31E-23	92.0337	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#7224 - 	CGI_10014641	superfamily	149946	175	265	5.01E-14	68.4499	cl07621	efhand_2 superfamily	 - 	 - 	"EF-hand; Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding."
Q#7224 - 	CGI_10014641	superfamily	165695	431	487	0.00666033	35.8998	cl14550	PLN00126 superfamily	NC	 - 	"succinate dehydrogenase, cytochrome b subunit family; Provisional"
Q#7225 - 	CGI_10014642	superfamily	243146	178	221	4.07E-16	69.5095	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#7225 - 	CGI_10014642	superfamily	243146	84	130	8.85E-15	65.6575	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#7225 - 	CGI_10014642	superfamily	243146	38	82	8.95E-13	60.2647	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#7225 - 	CGI_10014642	superfamily	243146	132	177	6.92E-12	57.9535	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#7225 - 	CGI_10014642	superfamily	243146	1	36	0.00980709	32.5304	cl02701	Kelch_3 superfamily	N	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#7226 - 	CGI_10014643	superfamily	248458	380	531	5.93E-05	44.6121	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7226 - 	CGI_10014643	superfamily	199528	694	827	3.21E-05	45.8572	cl15392	PRK10429 superfamily	N	 - 	melibiose:sodium symporter; Provisional
Q#7227 - 	CGI_10014644	superfamily	245201	1137	1404	9.22E-144	441.609	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7229 - 	CGI_10014646	superfamily	241842	26	128	6.12E-44	141.179	cl00400	Fe-S_biosyn superfamily	 - 	 - 	Iron-sulphur cluster biosynthesis; This family is involved in iron-sulphur cluster biosynthesis. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins.
Q#7230 - 	CGI_10014647	superfamily	245202	64	149	3.09E-47	153.184	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#7231 - 	CGI_10014648	superfamily	247727	156	254	7.12E-14	68.2254	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#7231 - 	CGI_10014648	superfamily	247725	52	107	0.000595978	38.5359	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7233 - 	CGI_10014650	superfamily	247905	1058	1185	3.35E-25	103.857	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#7233 - 	CGI_10014650	superfamily	247805	749	888	2.25E-24	102.03	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#7233 - 	CGI_10014650	superfamily	243084	1402	1487	5.79E-39	142.567	cl02556	Bromodomain superfamily	C	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#7233 - 	CGI_10014650	superfamily	207699	681	719	1.03E-09	56.5335	cl02688	BRK superfamily	 - 	 - 	BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.
Q#7233 - 	CGI_10014650	superfamily	244735	311	344	6.40E-09	53.9756	cl07469	QLQ superfamily	 - 	 - 	"QLQ; The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions."
Q#7233 - 	CGI_10014650	superfamily	243139	553	594	2.25E-06	47.3922	cl02676	HSA superfamily	C	 - 	HSA; This domain is predicted to bind DNA and is often found associated with helicases.
Q#7234 - 	CGI_10014651	superfamily	242203	33	292	9.33E-89	269.181	cl00935	Brix superfamily	 - 	 - 	Brix domain; Brix domain.  
Q#7235 - 	CGI_10014652	superfamily	243128	96	293	7.74E-14	68.8954	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#7236 - 	CGI_10014653	superfamily	214022	14	225	1.18E-108	316.523	cl17166	MMACHC-like superfamily	 - 	 - 	"Methylmalonic aciduria and homocystinuria type C protein and similar proteins; MMACHC, also called CblC, is involved in the intracellular processing of vitamin B12 by catalyzing two reactions: the reductive decyanation of cyanocobalamin in the presence of a flavoprotein oxidoreductase and the dealkylation of alkylcobalamins through the nucleophilic displacement of the alkyl group by glutathione. Mutations in MMACHC cause combined methylmalonic acidemia/aciduria and homocystinuria (CblC type), the most common inherited disorder of cobalamin metabolism. The structure of MMACHC reveals it to be the most divergent member of the NADPH-dependent flavin reductase family that can use FMN or FAD to catalyze reductive decyanation; it is also the first enzyme with glutathione transferase (GST) activity that is unrelated to the GST superfamily in structure and sequence."
Q#7240 - 	CGI_10014657	superfamily	151147	1	63	7.75E-16	68.2689	cl11240	DUF2475 superfamily	 - 	 - 	Protein of unknown function (DUF2475); This family of proteins has no known function.
Q#7241 - 	CGI_10014658	superfamily	217833	38	219	3.11E-87	258.564	cl04364	VPS28 superfamily	 - 	 - 	VPS28 protein; VPS28 protein.  
Q#7243 - 	CGI_10014660	superfamily	151147	18	84	7.12E-18	73.6617	cl11240	DUF2475 superfamily	 - 	 - 	Protein of unknown function (DUF2475); This family of proteins has no known function.
Q#7244 - 	CGI_10014661	superfamily	217833	36	217	1.80E-87	258.949	cl04364	VPS28 superfamily	 - 	 - 	VPS28 protein; VPS28 protein.  
Q#7246 - 	CGI_10014663	superfamily	246751	93	386	8.22E-119	353.472	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#7246 - 	CGI_10014663	superfamily	241546	405	504	0.00104124	37.7482	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#7247 - 	CGI_10014664	superfamily	246751	422	713	7.56E-96	304.551	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#7247 - 	CGI_10014664	superfamily	246751	62	353	2.94E-92	295.306	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#7247 - 	CGI_10014664	superfamily	246751	724	782	2.47E-13	69.9647	cl14883	Lipase superfamily	N	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#7248 - 	CGI_10014665	superfamily	241619	41	99	0.000494029	35.6357	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#7249 - 	CGI_10002273	superfamily	202351	1	129	2.82E-31	120.68	cl03662	Na_Pi_cotrans superfamily	 - 	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#7249 - 	CGI_10002273	superfamily	219963	872	968	1.19E-12	65.707	cl08487	GCV_T_C superfamily	 - 	 - 	"Glycine cleavage T-protein C-terminal barrel domain; This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyzes the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase."
Q#7249 - 	CGI_10002273	superfamily	202351	119	207	1.66E-07	50.5732	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#7249 - 	CGI_10002273	superfamily	183292	258	375	6.37E-06	48.2792	cl18135	PRK11728 superfamily	NC	 - 	hydroxyglutarate oxidase; Provisional
Q#7249 - 	CGI_10002273	superfamily	242769	740	825	2.41E-05	44.6949	cl01893	SoxG superfamily	N	 - 	"Sarcosine oxidase, gamma subunit family; Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+). This enzyme catalyzes the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2."
Q#7250 - 	CGI_10002275	superfamily	245815	15	468	0	746.876	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#7251 - 	CGI_10002277	superfamily	241782	11	377	0	625.785	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#7252 - 	CGI_10004890	superfamily	245814	281	351	2.51E-08	50.5655	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7252 - 	CGI_10004890	superfamily	241578	20	188	3.00E-32	119.867	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7252 - 	CGI_10004890	superfamily	245213	196	231	4.93E-07	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7253 - 	CGI_10004891	superfamily	245814	147	223	3.77E-05	40.9355	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7253 - 	CGI_10004891	superfamily	245814	56	125	2.78E-05	41.525	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7254 - 	CGI_10004892	superfamily	215577	26	161	1.36E-05	42.7331	cl14728	PLN03103 superfamily	N	 - 	GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional
Q#7255 - 	CGI_10004893	superfamily	147983	14	166	1.04E-40	144.471	cl05576	BRE superfamily	C	 - 	"Brain and reproductive organ-expressed protein (BRE); This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities."
Q#7255 - 	CGI_10004893	superfamily	147983	259	305	3.04E-06	46.6303	cl05576	BRE superfamily	N	 - 	"Brain and reproductive organ-expressed protein (BRE); This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities."
Q#7256 - 	CGI_10004894	superfamily	247805	161	242	2.78E-10	56.7241	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#7257 - 	CGI_10004895	superfamily	247905	2	124	3.80E-24	91.9156	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#7258 - 	CGI_10004896	superfamily	246975	289	310	0.00554021	34.6301	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#7258 - 	CGI_10004896	superfamily	243147	365	388	0.00898994	34.1408	cl02703	zf-BED superfamily	N	 - 	BED zinc finger; BED zinc finger.  
Q#7259 - 	CGI_10004897	superfamily	246752	8	63	0.00398592	32.7697	cl14886	UPF0227 superfamily	C	 - 	"Uncharacterized protein family (UPF0227); Despite being classed as uncharacterized proteins, the members of this family are almost certainly enzymes that are distantly related to the pfam00561."
Q#7260 - 	CGI_10000602	superfamily	247684	1	115	6.78E-77	233.824	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7261 - 	CGI_10017571	superfamily	245814	224	284	8.65E-05	41.7059	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7262 - 	CGI_10017572	superfamily	243087	46	119	6.68E-28	108.836	cl02562	PWI superfamily	 - 	 - 	PWI domain; PWI domain.  
Q#7264 - 	CGI_10017574	superfamily	247725	104	229	2.74E-68	226.145	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7264 - 	CGI_10017574	superfamily	243096	690	880	2.44E-47	169.015	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#7264 - 	CGI_10017574	superfamily	241622	492	579	1.18E-10	59.8878	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#7264 - 	CGI_10017574	superfamily	247725	883	1055	1.93E-55	191.826	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7264 - 	CGI_10017574	superfamily	241645	418	490	2.45E-09	55.9799	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#7266 - 	CGI_10017576	superfamily	247725	38	113	1.38E-12	64.6845	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7269 - 	CGI_10017579	superfamily	110440	387	414	0.000339512	38.1577	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#7272 - 	CGI_10017582	superfamily	241659	153	233	3.68E-14	65.2339	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#7272 - 	CGI_10017582	superfamily	241659	47	124	8.06E-14	64.0783	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#7273 - 	CGI_10017583	superfamily	248458	157	472	3.44E-18	84.6729	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7274 - 	CGI_10017584	superfamily	248458	160	422	5.07E-29	116.644	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7275 - 	CGI_10017585	superfamily	248458	135	369	1.72E-10	61.1757	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7276 - 	CGI_10017586	superfamily	248458	150	282	4.05E-15	75.4281	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7276 - 	CGI_10017586	superfamily	248458	339	485	9.04E-09	55.7829	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7278 - 	CGI_10017588	superfamily	216939	708	793	2.64E-10	58.0581	cl03492	PC4 superfamily	 - 	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#7278 - 	CGI_10017588	superfamily	241563	60	102	3.08E-06	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7278 - 	CGI_10017588	superfamily	216939	634	697	3.62E-06	45.7317	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#7279 - 	CGI_10017589	superfamily	241563	568	610	0.000110181	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7279 - 	CGI_10017589	superfamily	241563	19	61	0.00017219	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7279 - 	CGI_10017589	superfamily	191851	97	172	0.000286447	41.4615	cl06708	DUF1640 superfamily	N	 - 	Protein of unknown function (DUF1640); This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Q#7279 - 	CGI_10017589	superfamily	128778	621	723	0.00220974	38.0147	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#7281 - 	CGI_10017591	superfamily	110440	237	263	1.12E-05	41.6245	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#7282 - 	CGI_10017592	superfamily	241564	372	437	1.18E-25	101.188	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#7282 - 	CGI_10017592	superfamily	241564	252	320	5.47E-24	96.1807	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#7282 - 	CGI_10017592	superfamily	241564	30	95	4.00E-17	76.9207	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#7282 - 	CGI_10017592	superfamily	247792	587	626	2.89E-05	42.0476	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7284 - 	CGI_10000905	superfamily	241674	113	146	2.40E-09	50.2876	cl00194	EF1B superfamily	C	 - 	"Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction."
Q#7284 - 	CGI_10000905	superfamily	204519	80	106	1.08E-06	42.2343	cl11209	EF-1_beta_acid superfamily	 - 	 - 	Eukaryotic elongation factor 1 beta central acidic region; Eukaryotic elongation factor 1 beta central acidic region.  
Q#7285 - 	CGI_10004949	superfamily	247684	119	321	6.55E-30	117.378	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7286 - 	CGI_10004950	superfamily	247725	96	197	4.87E-41	137.336	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7286 - 	CGI_10004950	superfamily	247725	10	88	4.79E-38	130.435	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7287 - 	CGI_10004951	superfamily	247684	11	398	1.96E-96	297.652	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7289 - 	CGI_10004953	superfamily	245206	4	290	8.98E-93	279.126	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#7291 - 	CGI_10004955	superfamily	242903	23	158	2.44E-86	252.864	cl02148	APC10-like superfamily	 - 	 - 	"APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An  APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here."
Q#7292 - 	CGI_10004956	superfamily	247692	94	434	1.34E-69	243.89	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#7292 - 	CGI_10004956	superfamily	219000	1266	1459	9.92E-62	212.121	cl05717	Drf_FH3 superfamily	 - 	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#7292 - 	CGI_10004956	superfamily	219001	1089	1262	2.00E-29	118.565	cl05720	Drf_GBD superfamily	 - 	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#7292 - 	CGI_10004956	superfamily	245660	677	949	4.72E-21	96.2469	cl11493	PQQ_DH_like superfamily	 - 	 - 	"PQQ-dependent dehydrogenases and related proteins; This family is composed of dehydrogenases with pyrroloquinoline quinone (PQQ) as a cofactor, such as ethanol, methanol, and membrane-bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller, and the family also includes distantly related proteins which are not enzymatically active and do not bind PQQ."
Q#7292 - 	CGI_10004956	superfamily	245209	489	552	0.00364517	37.9194	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#7293 - 	CGI_10004957	superfamily	243098	656	704	6.83E-14	67.6231	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#7293 - 	CGI_10004957	superfamily	219918	6	86	9.39E-17	76.9588	cl07265	DUF1767 superfamily	 - 	 - 	Domain of unknown function (DUF1767); Eukaryotic domain of unknown function. This domain is found to the N-terminus of the nucleic acid binding domain.
Q#7295 - 	CGI_10006736	superfamily	241675	88	318	5.83E-116	351.548	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#7296 - 	CGI_10006737	superfamily	242206	61	141	1.70E-23	89.2018	cl00938	Rieske superfamily	N	 - 	"Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis."
Q#7298 - 	CGI_10006739	superfamily	217380	29	332	5.25E-112	331.982	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#7299 - 	CGI_10006740	superfamily	246940	77	251	8.91E-07	47.7134	cl15377	Radical_SAM superfamily	C	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#7299 - 	CGI_10006740	superfamily	203999	259	323	1.36E-22	89.9645	cl15482	Wyosine_form superfamily	 - 	 - 	Wyosine base formation; Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Q#7300 - 	CGI_10006741	superfamily	241858	96	215	2.35E-14	66.9252	cl00429	SNARE_assoc superfamily	 - 	 - 	SNARE associated Golgi protein; This is a family of SNARE associated Golgi proteins. The yeast member of this family localises with the t-SNARE Tlg2.
Q#7302 - 	CGI_10006743	superfamily	245864	75	215	9.46E-17	78.4742	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#7305 - 	CGI_10002252	superfamily	220653	133	185	7.67E-16	70.4783	cl10936	PP28 superfamily	C	 - 	"Casein kinase substrate phosphoprotein PP28; This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II."
Q#7305 - 	CGI_10002252	superfamily	222070	229	283	3.80E-09	53.0652	cl18634	DDE_3 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#7306 - 	CGI_10002253	superfamily	242901	1	144	2.17E-86	251.434	cl02138	G10 superfamily	 - 	 - 	G10 protein; G10 protein.  
Q#7307 - 	CGI_10024807	superfamily	220692	27	151	0.000375663	40.2653	cl18570	7TM_GPCR_Srw superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#7309 - 	CGI_10024809	superfamily	245206	35	196	4.83E-68	211.753	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#7311 - 	CGI_10024811	superfamily	243092	121	339	4.36E-25	107.036	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7311 - 	CGI_10024811	superfamily	246721	587	781	6.68E-07	51.4897	cl14807	ACE1-Sec16-like superfamily	N	 - 	"Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16; COPII coat complex plays an important role in vesicular traffic of newly synthezised proteins from the endoplasmatic reticulum (ER) to the Golgi apparatus by mediating the formation of transport vesicles. COPII consists of an outer coat, made up of the scaffold proteins Sec31 and Sec13, and the cargo adaptor complex, Sec23 and Sec24, which are recruited by the small GTPase Sar1. Sec16 is involved in the early steps of the assembly process. Sec16 forms elongated heterotetramers with Sec13, Sec13-(Sec16)2-Sec13. It interacts with Sec13 by insertion of a single beta-blade to close the six-bladded beta propeller of Sec13. In the same way Sec13 interacts with Sec31 and Nup145C, a nuclear pore protein, all of these contain a structurally related ancestral coatomer element 1 (ACE1). Sec16 is believed to be a key component in maintaining the integrity of the ER exit site."
Q#7311 - 	CGI_10024811	superfamily	217249	1134	1178	0.000684051	39.9119	cl03742	Prp18 superfamily	NC	 - 	"Prp18 domain; The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles."
Q#7311 - 	CGI_10024811	superfamily	221501	863	972	0.00573053	37.0746	cl13679	RCR superfamily	N	 - 	"Chitin synthesis regulation, resistance to Congo red; RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5."
Q#7313 - 	CGI_10024813	superfamily	243109	759	937	5.14E-77	254.43	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7313 - 	CGI_10024813	superfamily	218425	4	517	0	721.406	cl04931	eIF-3_zeta superfamily	 - 	 - 	"Eukaryotic translation initiation factor 3 subunit 7 (eIF-3); This family is made up of eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is a multi-subunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. These functions and the complex nature of eIF3 suggest multiple interactions with many components of the translational machinery. The gene coding for the protein has been implicated in cancer in mammals."
Q#7313 - 	CGI_10024813	superfamily	247807	972	1097	0.000516934	40.3562	cl17253	AAA_17 superfamily	 - 	 - 	AAA domain; AAA domain.  
Q#7314 - 	CGI_10024814	superfamily	243051	446	600	4.18E-40	145.213	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#7314 - 	CGI_10024814	superfamily	243051	269	429	9.89E-39	141.361	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#7314 - 	CGI_10024814	superfamily	243051	606	736	2.71E-37	137.509	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#7314 - 	CGI_10024814	superfamily	241568	200	258	1.05E-07	49.7688	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#7314 - 	CGI_10024814	superfamily	241583	82	194	4.48E-44	156.963	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#7315 - 	CGI_10024815	superfamily	244704	3	90	6.41E-44	143.776	cl07364	Nfu_N superfamily	 - 	 - 	"Scaffold protein Nfu/NifU N terminal; This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters."
Q#7315 - 	CGI_10024815	superfamily	241897	106	186	9.02E-27	99.294	cl00484	NifU superfamily	 - 	 - 	NifU-like domain; This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
Q#7316 - 	CGI_10024816	superfamily	244704	3	90	6.41E-44	143.776	cl07364	Nfu_N superfamily	 - 	 - 	"Scaffold protein Nfu/NifU N terminal; This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters."
Q#7316 - 	CGI_10024816	superfamily	241897	106	186	9.02E-27	99.294	cl00484	NifU superfamily	 - 	 - 	NifU-like domain; This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
Q#7317 - 	CGI_10024817	superfamily	248054	27	238	2.00E-27	109.699	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#7318 - 	CGI_10024818	superfamily	244509	369	500	1.82E-16	76.7971	cl06793	PRKCSH superfamily	 - 	 - 	"Glucosidase II beta subunit-like protein; The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain."
Q#7318 - 	CGI_10024818	superfamily	247856	211	266	0.0029515	35.9865	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#7324 - 	CGI_10024825	superfamily	216971	200	369	9.01E-47	158.938	cl03532	Octopine_DH superfamily	 - 	 - 	"NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids."
Q#7324 - 	CGI_10024825	superfamily	201664	8	126	1.24E-08	52.616	cl18216	NAD_Gly3P_dh_N superfamily	C	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
Q#7325 - 	CGI_10024826	superfamily	216971	216	384	1.45E-45	156.241	cl03532	Octopine_DH superfamily	 - 	 - 	"NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids."
Q#7325 - 	CGI_10024826	superfamily	201664	20	139	6.07E-09	53.7716	cl18216	NAD_Gly3P_dh_N superfamily	C	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
Q#7326 - 	CGI_10024827	superfamily	216971	197	368	3.77E-42	146.611	cl03532	Octopine_DH superfamily	 - 	 - 	"NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids."
Q#7326 - 	CGI_10024827	superfamily	201664	4	123	2.96E-06	45.6824	cl18216	NAD_Gly3P_dh_N superfamily	C	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
Q#7328 - 	CGI_10024829	superfamily	216971	91	261	5.63E-42	143.53	cl03532	Octopine_DH superfamily	 - 	 - 	"NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids."
Q#7329 - 	CGI_10024830	superfamily	216971	197	344	4.79E-34	123.885	cl03532	Octopine_DH superfamily	 - 	 - 	"NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids."
Q#7329 - 	CGI_10024830	superfamily	201664	4	123	2.04E-08	51.8456	cl18216	NAD_Gly3P_dh_N superfamily	C	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
Q#7330 - 	CGI_10024831	superfamily	206051	616	685	6.34E-34	126.879	cl16450	Acetyltransf_13 superfamily	 - 	 - 	ESCO1/2 acetyl-transferase; ESCO1/2 acetyl-transferase.  
Q#7330 - 	CGI_10024831	superfamily	206051	1279	1348	8.18E-34	126.494	cl16450	Acetyltransf_13 superfamily	 - 	 - 	ESCO1/2 acetyl-transferase; ESCO1/2 acetyl-transferase.  
Q#7330 - 	CGI_10024831	superfamily	206049	465	504	9.82E-15	70.8172	cl16448	zf-C2H2_3 superfamily	 - 	 - 	zinc-finger of acetyl-transferase ESCO; zinc-finger of acetyl-transferase ESCO.  
Q#7330 - 	CGI_10024831	superfamily	206049	1128	1167	9.82E-15	70.8172	cl16448	zf-C2H2_3 superfamily	 - 	 - 	zinc-finger of acetyl-transferase ESCO; zinc-finger of acetyl-transferase ESCO.  
Q#7331 - 	CGI_10024832	superfamily	246671	113	235	8.69E-08	48.9585	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#7333 - 	CGI_10024834	superfamily	243068	811	901	5.42E-07	50.8482	cl02523	Zona_pellucida superfamily	N	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#7333 - 	CGI_10024834	superfamily	246671	50	172	1.38E-05	44.6323	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#7335 - 	CGI_10024836	superfamily	243091	350	398	0.000528413	39.6251	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#7335 - 	CGI_10024836	superfamily	246975	656	677	0.000780196	38.4821	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#7335 - 	CGI_10024836	superfamily	222150	642	666	0.00280144	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7335 - 	CGI_10024836	superfamily	222150	764	789	0.00577305	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7336 - 	CGI_10024837	superfamily	245206	1	184	2.89E-81	244.344	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#7337 - 	CGI_10024838	superfamily	245201	137	460	0	619.113	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7337 - 	CGI_10024838	superfamily	243088	33	92	1.58E-24	97.4785	cl02563	PX_domain superfamily	N	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#7339 - 	CGI_10024840	superfamily	246676	339	501	3.96E-36	133.624	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#7339 - 	CGI_10024840	superfamily	246710	171	338	2.03E-33	125.233	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#7339 - 	CGI_10024840	superfamily	246671	1	128	3.06E-25	101.731	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#7341 - 	CGI_10024842	superfamily	245835	145	380	3.25E-75	235.737	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#7341 - 	CGI_10024842	superfamily	243088	8	122	5.24E-66	209.115	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#7342 - 	CGI_10024843	superfamily	202715	72	172	5.11E-40	132.702	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#7343 - 	CGI_10024844	superfamily	219284	708	964	2.89E-89	290.41	cl06206	RIC1 superfamily	 - 	 - 	RIC1; RIC1 has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor.
Q#7344 - 	CGI_10024845	superfamily	245201	54	314	0	535.748	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7344 - 	CGI_10024845	superfamily	246908	1	39	1.63E-12	62.5998	cl15255	SH2 superfamily	N	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#7345 - 	CGI_10024846	superfamily	241622	114	193	5.15E-15	67.977	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#7345 - 	CGI_10024846	superfamily	241622	198	271	1.90E-10	55.6507	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#7346 - 	CGI_10024847	superfamily	210068	467	492	1.22E-05	42.8491	cl15286	RPEL superfamily	 - 	 - 	RPEL repeat; The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that the Drosophila myocardin-related transcription factor contains a pfam02037 domain that is also implicated in DNA binding.
Q#7346 - 	CGI_10024847	superfamily	210068	505	530	1.86E-05	42.4639	cl15286	RPEL superfamily	 - 	 - 	RPEL repeat; The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that the Drosophila myocardin-related transcription factor contains a pfam02037 domain that is also implicated in DNA binding.
Q#7346 - 	CGI_10024847	superfamily	210068	429	454	0.00219564	36.3007	cl15286	RPEL superfamily	 - 	 - 	RPEL repeat; The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that the Drosophila myocardin-related transcription factor contains a pfam02037 domain that is also implicated in DNA binding.
Q#7347 - 	CGI_10024848	superfamily	248279	133	246	1.58E-39	138.624	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#7347 - 	CGI_10024848	superfamily	247999	94	126	4.56E-07	46.4847	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#7347 - 	CGI_10024848	superfamily	243098	319	372	8.26E-05	40.3349	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#7347 - 	CGI_10024848	superfamily	243098	261	310	0.000310442	38.4089	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#7349 - 	CGI_10024850	superfamily	245201	1012	1268	2.36E-70	237.435	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7351 - 	CGI_10024852	superfamily	246925	120	323	6.35E-09	56.595	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#7352 - 	CGI_10024853	superfamily	241591	30	101	2.01E-19	79.2023	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#7353 - 	CGI_10024854	superfamily	241584	1227	1311	8.06E-17	78.3071	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7353 - 	CGI_10024854	superfamily	241584	438	527	9.05E-16	75.2255	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7353 - 	CGI_10024854	superfamily	241584	726	816	2.61E-13	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7353 - 	CGI_10024854	superfamily	241584	1132	1214	3.18E-12	64.8251	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7353 - 	CGI_10024854	superfamily	241584	229	316	1.01E-05	45.5651	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7353 - 	CGI_10024854	superfamily	245814	841	901	0.00929044	36.3131	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7353 - 	CGI_10024854	superfamily	216647	338	431	8.84E-14	69.5029	cl03309	DB superfamily	 - 	 - 	"DB module; This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657."
Q#7353 - 	CGI_10024854	superfamily	216647	634	718	3.02E-13	67.9621	cl03309	DB superfamily	 - 	 - 	"DB module; This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657."
Q#7353 - 	CGI_10024854	superfamily	216647	131	222	2.25E-10	59.4877	cl03309	DB superfamily	 - 	 - 	"DB module; This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657."
Q#7353 - 	CGI_10024854	superfamily	216647	1029	1123	5.40E-07	49.4725	cl03309	DB superfamily	 - 	 - 	"DB module; This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657."
Q#7353 - 	CGI_10024854	superfamily	216647	1	47	3.61E-05	43.6945	cl03309	DB superfamily	N	 - 	"DB module; This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657."
Q#7354 - 	CGI_10024855	superfamily	247068	239	334	1.20E-05	43.4562	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7354 - 	CGI_10024855	superfamily	247068	156	232	0.000543453	38.4847	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#7356 - 	CGI_10024857	superfamily	241578	37	189	1.36E-37	130.971	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7357 - 	CGI_10024858	superfamily	192535	30	209	7.57E-07	48.7462	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#7360 - 	CGI_10024861	superfamily	190534	22	114	1.81E-27	99.4047	cl18165	bZIP_Maf superfamily	 - 	 - 	"bZIP Maf transcription factor; Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerisation and DNA binding property. Thus, this family is probably related to pfam00170."
Q#7361 - 	CGI_10024862	superfamily	243072	78	209	4.68E-17	78.5794	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7361 - 	CGI_10024862	superfamily	243072	519	611	1.38E-10	59.3194	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7364 - 	CGI_10024865	superfamily	248264	91	250	7.41E-59	186.289	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#7364 - 	CGI_10024865	superfamily	222263	13	102	8.56E-09	51.1645	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#7365 - 	CGI_10024866	superfamily	220393	27	318	9.48E-95	287.735	cl10751	Tmem26 superfamily	 - 	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#7366 - 	CGI_10024867	superfamily	245303	137	503	0	552.55	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#7366 - 	CGI_10024867	superfamily	241613	94	127	6.95E-15	70.3133	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#7367 - 	CGI_10024868	superfamily	245303	24	160	1.99E-74	228.983	cl10447	GH18_chitinase-like superfamily	C	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#7368 - 	CGI_10024869	superfamily	245303	24	386	0	561.795	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#7368 - 	CGI_10024869	superfamily	243119	445	496	2.95E-13	64.7624	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7369 - 	CGI_10024870	superfamily	245303	26	394	0	540.224	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#7369 - 	CGI_10024870	superfamily	243119	442	491	1.90E-11	60.5353	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7369 - 	CGI_10024870	superfamily	243119	591	633	2.87E-07	48.2089	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7369 - 	CGI_10024870	superfamily	243119	636	677	4.65E-06	44.732	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7369 - 	CGI_10024870	superfamily	243119	563	597	0.00069953	38.1938	cl02629	CBM_14 superfamily	C	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7370 - 	CGI_10024871	superfamily	241884	47	116	2.37E-32	113.819	cl00467	Ntn_hydrolase superfamily	C	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#7373 - 	CGI_10024874	superfamily	241640	2	267	1.54E-78	239.871	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#7375 - 	CGI_10024876	superfamily	243035	15	83	5.63E-07	47.2294	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7377 - 	CGI_10010415	superfamily	241782	68	467	0	734.441	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#7378 - 	CGI_10010416	superfamily	241624	103	414	1.34E-42	152.866	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#7379 - 	CGI_10010417	superfamily	247723	262	334	2.69E-44	152.027	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7379 - 	CGI_10010417	superfamily	247723	431	515	1.22E-42	147.691	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7379 - 	CGI_10010417	superfamily	247723	164	236	5.16E-42	145.441	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7383 - 	CGI_10010421	superfamily	247676	56	173	3.06E-53	167.787	cl17012	GINS_A superfamily	 - 	 - 	"Alpha-helical domain of GINS complex proteins; Sld5, Psf1, Psf2 and Psf3; The GINS complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In eukaryotes, GINS is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has been found in eukaryotes and archaea, but not in bacteria. The four subunits of the complex are homologous and consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3."
Q#7384 - 	CGI_10010422	superfamily	221645	217	325	1.19E-10	59.2854	cl13951	DUF3754 superfamily	 - 	 - 	"Protein of unknown function (DUF3754); This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important."
Q#7385 - 	CGI_10010423	superfamily	247678	196	318	5.87E-61	193.308	cl17014	eIF-5_eIF-2B superfamily	 - 	 - 	"Domain found in IF2B/IF5; This family includes the N terminus of eIF-5, and the C terminus of eIF-2 beta. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger."
Q#7387 - 	CGI_10010425	superfamily	247916	339	404	4.41E-07	48.9183	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#7387 - 	CGI_10010425	superfamily	247916	289	370	0.00260378	37.7654	cl17362	Transglut_core superfamily	C	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#7388 - 	CGI_10010426	superfamily	247778	16	175	4.30E-20	84.2309	cl17224	MenA superfamily	N	 - 	"1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]"
Q#7389 - 	CGI_10010427	superfamily	241623	2001	2279	0	561.381	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#7389 - 	CGI_10010427	superfamily	149738	1863	1962	6.46E-41	148.907	cl07398	Rapamycin_bind superfamily	 - 	 - 	Rapamycin binding domain; This domain forms an alpha helical structure and binds to rapamycin.
Q#7389 - 	CGI_10010427	superfamily	202180	2360	2392	1.10E-13	68.6444	cl03505	FATC superfamily	 - 	 - 	"FATC domain; The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability."
Q#7392 - 	CGI_10010430	superfamily	242917	177	292	1.29E-45	158.035	cl02170	Sec62 superfamily	N	 - 	Translocation protein Sec62; Translocation protein Sec62.  
Q#7394 - 	CGI_10010432	superfamily	243077	18	64	1.71E-10	57.1701	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#7394 - 	CGI_10010432	superfamily	221283	402	541	1.82E-42	149.409	cl13336	DUF3395 superfamily	 - 	 - 	Domain of unknown function (DUF3395); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 147 to 176 amino acids in length. This domain is found associated with pfam00226.
Q#7397 - 	CGI_10010435	superfamily	241764	286	348	1.40E-31	118.522	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#7397 - 	CGI_10010435	superfamily	247743	416	579	1.19E-20	89.5127	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#7397 - 	CGI_10010435	superfamily	204202	659	720	8.97E-30	112.734	cl07827	Vps4_C superfamily	 - 	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#7398 - 	CGI_10010436	superfamily	247743	31	131	2.17E-11	56.7707	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#7399 - 	CGI_10010437	superfamily	248097	279	409	2.32E-15	71.9126	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7400 - 	CGI_10010438	superfamily	191973	279	362	0.00676977	35.0315	cl07022	Striatin superfamily	C	 - 	"Striatin family; Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (pfam00400) repeat domain. It acts as a scaffold protein and is involved in signalling pathways."
Q#7401 - 	CGI_10005743	superfamily	202203	33	98	2.65E-31	113.817	cl03534	E2F_TDP superfamily	 - 	 - 	"E2F/DP family winged-helix DNA-binding domain; This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins."
Q#7402 - 	CGI_10005744	superfamily	242748	311	362	0.00230741	35.99	cl01853	COG4467 superfamily	C	 - 	"Regulator of replication initiation timing [Replication,    recombination, and repair]"
Q#7407 - 	CGI_10012864	superfamily	246669	348	540	2.79E-58	199.529	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#7408 - 	CGI_10012865	superfamily	244307	77	318	3.90E-73	240.278	cl06123	DHR2_DOCK superfamily	N	 - 	"Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins; DOCK proteins comprise a family of atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. They are also called the CZH (CED-5, Dock180, and MBC-zizimin homology) family, after the first family members identified. Dock180 was first isolated as a binding partner for the adaptor protein Crk. The Caenorhabditis elegans protein, Ced-5, is essential for cell migration and phagocytosis, while the Drosophila ortholog, Myoblast city (MBC), is necessary for myoblast fusion and dorsal closure. DOCKs are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1 (or Dock180), 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1, and DHR-2 (also called CZH2 or Docker). This alignment model represents the DHR-2 domain of DOCK proteins, which contains the catalytic GEF activity for Rac and/or Cdc42."
Q#7409 - 	CGI_10012866	superfamily	220184	565	869	1.64E-44	164.684	cl18549	Mcm10 superfamily	 - 	 - 	Mcm10 replication factor; Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha.
Q#7409 - 	CGI_10012866	superfamily	192253	428	473	1.91E-12	63.4641	cl07823	zf-primase superfamily	 - 	 - 	Primase zinc finger; This zinc finger is found in yeast Mcm10 proteins and DnaG-type primases.
Q#7410 - 	CGI_10012867	superfamily	241640	114	212	4.80E-08	51.6711	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#7411 - 	CGI_10012868	superfamily	247948	62	111	9.24E-12	58.0742	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#7412 - 	CGI_10012869	superfamily	241594	25	309	2.23E-09	56.1595	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#7414 - 	CGI_10012871	superfamily	215754	202	291	2.22E-17	77.6788	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#7414 - 	CGI_10012871	superfamily	215754	306	389	2.22E-17	77.6788	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#7414 - 	CGI_10012871	superfamily	215754	406	482	1.47E-10	58.0336	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#7414 - 	CGI_10012871	superfamily	245814	33	124	1.20E-09	55.5113	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7414 - 	CGI_10012871	superfamily	245814	130	150	0.00635822	34.9139	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7415 - 	CGI_10012872	superfamily	247792	250	297	0.000163182	40.1216	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7415 - 	CGI_10012872	superfamily	128778	471	561	0.000186795	40.7111	cl17972	BBC superfamily	N	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#7416 - 	CGI_10012873	superfamily	147626	77	116	1.64E-06	43.7831	cl05227	DUF1519 superfamily	N	 - 	Protein of unknown function (DUF1519); This family consists of several putative homing endonuclease proteins of around 245 residues in length which appear to be found exclusively in Naegleria species. The function of this family is unclear.
Q#7421 - 	CGI_10012878	superfamily	222296	125	375	3.66E-84	265.849	cl16339	DUF4147 superfamily	 - 	 - 	"Domain of unknown function (DUF4147); This domain is frequently found at the N-terminus of proteins carrying the glycerate kinase-like domain MOFRL, pfam05161."
Q#7421 - 	CGI_10012878	superfamily	203185	527	624	1.50E-26	104.657	cl15995	MOFRL superfamily	 - 	 - 	"MOFRL family; MOFRL(multi-organism fragment with rich Leucine) family exists in bacteria and eukaryotes. The function of this domain is not clear, although it exists in some putative enzymes such as reductases and kinases."
Q#7422 - 	CGI_10012879	superfamily	247725	376	484	5.89E-15	72.5961	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7422 - 	CGI_10012879	superfamily	243096	230	360	8.03E-12	63.0034	cl02571	RhoGEF superfamily	C	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#7424 - 	CGI_10012881	superfamily	243072	174	296	1.53E-28	111.707	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7424 - 	CGI_10012881	superfamily	243072	73	230	5.29E-28	110.166	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7424 - 	CGI_10012881	superfamily	245847	417	527	9.23E-05	41.7192	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#7429 - 	CGI_10019821	superfamily	203913	432	574	2.40E-10	58.7677	cl07084	P4Ha_N superfamily	 - 	 - 	"Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known."
Q#7430 - 	CGI_10019822	superfamily	245201	635	933	8.94E-173	507.27	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7430 - 	CGI_10019822	superfamily	245847	18	171	4.55E-25	102.816	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#7435 - 	CGI_10019827	superfamily	248192	17	336	1.58E-89	283.006	cl17638	PLN02808 superfamily	 - 	 - 	alpha-galactosidase
Q#7435 - 	CGI_10019827	superfamily	243030	406	431	0.000174131	39.5379	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#7437 - 	CGI_10019829	superfamily	241913	45	150	2.33E-14	65.7053	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#7438 - 	CGI_10019830	superfamily	202484	1	42	5.71E-08	43.7569	cl03798	zf-Tim10_DDP superfamily	N	 - 	Tim10/DDP family zinc finger; Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein TIMM8A. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localised to the mitochondrial intermembrane space.
Q#7439 - 	CGI_10019831	superfamily	241570	444	555	1.79E-17	79.6774	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#7440 - 	CGI_10019832	superfamily	216966	405	571	2.54E-29	114.729	cl03523	HORMA superfamily	 - 	 - 	"HORMA domain; The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity."
Q#7440 - 	CGI_10019832	superfamily	241621	104	220	5.56E-07	48.4636	cl00116	PDGF superfamily	 - 	 - 	"Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain"
Q#7443 - 	CGI_10019835	superfamily	245230	2	426	0	945.942	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#7445 - 	CGI_10019837	superfamily	241900	385	683	5.46E-119	361.741	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#7450 - 	CGI_10019842	superfamily	247792	44	82	0.00127606	37.4252	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7450 - 	CGI_10019842	superfamily	245716	450	476	1.16E-06	46.3975	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#7451 - 	CGI_10019843	superfamily	245847	654	793	1.18E-07	51.7344	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#7451 - 	CGI_10019843	superfamily	243035	971	1076	1.10E-06	48.365	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7451 - 	CGI_10019843	superfamily	243035	1194	1220	0.000870821	39.3301	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7451 - 	CGI_10019843	superfamily	238012	902	931	0.00279069	37.3338	cl11390	EGF_Lam superfamily	N	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#7454 - 	CGI_10019846	superfamily	192107	503	696	1.05E-68	232.108	cl07312	Med14 superfamily	 - 	 - 	"Mediator complex subunit MED14; Saccharomyces cerevisiae RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes and sporulation, required for glucose repression, HO repression, RME1 repression and sporulation. This subunit is also found in higher eukaryotes and Med14 is the agreed unified nomenclature for this subunit. Med14 is found in the tail region of Mediator."
Q#7454 - 	CGI_10019846	superfamily	218108	1504	1644	0.0049268	39.1037	cl04540	CITED superfamily	C	 - 	"CITED; CITED, CBP/p300-interacting transactivator with ED-rich tail, are characterized by a conserved 32-amino acid sequence at the C-terminus. CITED proteins do not bind DNA directly and are thought to function as transcriptional co-activators."
Q#7455 - 	CGI_10019847	superfamily	205450	50	136	1.02E-26	97.0784	cl16202	DUF4061 superfamily	 - 	 - 	"Domain of unknown function (DUF4061); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 90 amino acids in length. There is a conserved AFG sequence motif."
Q#7456 - 	CGI_10019848	superfamily	215647	7	128	4.78E-26	101.916	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#7457 - 	CGI_10009475	superfamily	220669	20	362	3.34E-160	456.486	cl10954	Tmpp129 superfamily	 - 	 - 	Putative transmembrane protein precursor; This is a family of proteins conserved from worms to humans. The proteins are purported to be transmembrane protein-precursors but the function is unknown.
Q#7458 - 	CGI_10009476	superfamily	243091	258	343	6.24E-08	50.1832	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#7459 - 	CGI_10009477	superfamily	219225	32	112	0.000263363	37.0575	cl06114	FAIM1 superfamily	N	 - 	"Fas apoptotic inhibitory molecule (FAIM1); This family consists of several fas apoptotic inhibitory molecule (FAIM1) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM1 is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology."
Q#7460 - 	CGI_10009478	superfamily	243179	114	216	1.03E-23	92.4245	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#7461 - 	CGI_10009479	superfamily	192194	7	43	4.32E-08	44.8811	cl07556	DUF1903 superfamily	C	 - 	"Domain of unknown function (DUF1903); Members of this family adopt a coiled coil structure, with two antiparallel alpha-helices that are tightly strapped together by two disulfide bridges at each end. The protein sequence shows a cysteine motif, required for the stabilisation of the coiled-coil-like structure. Additional inter-helix hydrophobic contacts impart stability to this scaffold. The precise function of this eukaryotic domain is, as yet, unknown."
Q#7462 - 	CGI_10009480	superfamily	218789	5	169	2.22E-27	104.255	cl05447	Ceramidase superfamily	C	 - 	"Ceramidase; This family consists of several ceramidases. Ceramidases are enzymes involved in regulating cellular levels of ceramides, sphingoid bases, and their phosphates, EC:3.5.1.23."
Q#7463 - 	CGI_10009481	superfamily	241563	18	50	8.11E-05	40.3983	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7464 - 	CGI_10009482	superfamily	247684	1	404	5.57E-80	258.747	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7465 - 	CGI_10009483	superfamily	247684	1	268	2.62E-61	202.122	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7466 - 	CGI_10009484	superfamily	244558	225	306	3.32E-26	104.175	cl06950	AARP2CN superfamily	 - 	 - 	AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU.
Q#7467 - 	CGI_10009485	superfamily	243084	704	803	6.22E-52	176.206	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#7467 - 	CGI_10009485	superfamily	247736	522	577	0.000113731	41.1073	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#7467 - 	CGI_10009485	superfamily	148209	37	288	1.31E-128	387.368	cl05793	PCAF_N superfamily	 - 	 - 	PCAF (P300/CBP-associated factor) N-terminal domain; This region is spliced out of human histone acetyltranfersase KAT2A isoform 2. It is predicted to be of a mixed alpha/beta fold - though predominantly helical.
Q#7469 - 	CGI_10009487	superfamily	241563	60	102	3.97E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7469 - 	CGI_10009487	superfamily	110440	485	509	0.00238181	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#7469 - 	CGI_10009487	superfamily	241563	8	53	0.00428729	35.3907	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7469 - 	CGI_10009487	superfamily	128778	98	230	0.00651088	35.7035	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#7471 - 	CGI_10009489	superfamily	241554	106	232	3.01E-29	109.282	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7472 - 	CGI_10009490	superfamily	241554	2	123	6.24E-26	98.1115	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7473 - 	CGI_10009491	superfamily	241554	118	248	7.20E-08	49.5764	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7473 - 	CGI_10009491	superfamily	241554	9	61	5.16E-06	44.5688	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7474 - 	CGI_10000279	superfamily	247684	1	78	5.68E-15	71.9948	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7475 - 	CGI_10014865	superfamily	248264	163	206	0.000317131	39.5278	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#7476 - 	CGI_10014866	superfamily	217293	37	246	1.15E-41	148.165	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7476 - 	CGI_10014866	superfamily	202474	253	306	1.85E-07	50.3449	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7477 - 	CGI_10014867	superfamily	247692	42	385	1.41E-155	450.919	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#7478 - 	CGI_10014868	superfamily	247723	207	283	3.12E-25	96.9558	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7478 - 	CGI_10014868	superfamily	243077	51	102	8.58E-18	76.0449	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#7479 - 	CGI_10014869	superfamily	243029	28	101	3.18E-13	64.6793	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#7479 - 	CGI_10014869	superfamily	215647	172	298	5.91E-05	42.9809	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#7484 - 	CGI_10014874	superfamily	243107	453	493	0.000575656	37.9098	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#7487 - 	CGI_10014877	superfamily	243045	291	390	4.24E-15	72.6659	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#7487 - 	CGI_10014877	superfamily	243045	117	169	1.55E-09	56.4875	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#7487 - 	CGI_10014877	superfamily	241596	13	65	5.48E-09	53.7571	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#7490 - 	CGI_10014880	superfamily	246946	21	411	1.96E-92	284.57	cl15397	DUF89 superfamily	 - 	 - 	Protein of unknown function DUF89; This family has no known function.
Q#7491 - 	CGI_10014881	superfamily	247065	3	105	3.64E-12	58.8954	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#7492 - 	CGI_10014882	superfamily	216554	107	248	5.09E-22	90.2313	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#7493 - 	CGI_10014883	superfamily	247723	13	87	1.10E-25	98.0762	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7494 - 	CGI_10014884	superfamily	248281	136	204	3.38E-06	42.6427	cl17727	GT1 superfamily	C	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#7495 - 	CGI_10014885	superfamily	194336	183	278	1.02E-19	84.9901	cl02517	ZU5 superfamily	 - 	 - 	ZU5 domain; Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
Q#7495 - 	CGI_10014885	superfamily	246680	532	599	2.73E-10	57.3289	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#7497 - 	CGI_10014887	superfamily	220692	86	371	8.26E-15	73.3925	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#7498 - 	CGI_10014888	superfamily	241599	148	206	9.25E-26	96.5436	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#7499 - 	CGI_10014890	superfamily	247740	12	182	1.69E-74	225.822	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#7501 - 	CGI_10014892	superfamily	247769	166	213	5.63E-06	43.4821	cl17215	HDc superfamily	C	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#7501 - 	CGI_10014892	superfamily	247057	61	112	4.88E-05	39.6054	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#7502 - 	CGI_10014893	superfamily	245814	29	76	0.000395909	37.7089	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7506 - 	CGI_10016706	superfamily	241581	4	70	0.000900831	38.9066	cl00062	FHA superfamily	C	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#7507 - 	CGI_10016707	superfamily	219936	251	349	5.07E-14	68.8165	cl18534	SPA superfamily	 - 	 - 	Stabilisation of polarity axis; Yeast AFI1 (ARF3-interaction protein 1) has been shown to interact with the outer plaque of the spindle pole body. In Aspergillus nidulans the protein member is necessary for stabilisation of the polarity axes during septation. and in S. cerevisiae it functions as a polarisation-specific docking factor.
Q#7507 - 	CGI_10016707	superfamily	219579	36	95	8.53E-13	64.127	cl16001	Afi1 superfamily	 - 	 - 	"Docking domain of Afi1 for Arf3 in vesicle trafficking; This domain occurs at the N-terminal of Afi1, a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3. Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalisation. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth."
Q#7508 - 	CGI_10016708	superfamily	245213	703	737	5.44E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	740	775	1.05E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	625	661	2.51E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	473	509	4.90E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	284	319	4.90E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	511	547	5.52E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	435	471	1.05E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	663	698	2.10E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	360	395	2.74E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	209	244	5.06E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	246	281	6.34E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	549	585	6.49E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	815	850	0.000128982	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	587	622	0.000192379	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	322	357	0.000665766	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	778	812	0.00622585	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7508 - 	CGI_10016708	superfamily	245213	398	432	0.00805851	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7509 - 	CGI_10016709	superfamily	215754	177	270	1.18E-19	81.1456	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#7509 - 	CGI_10016709	superfamily	215754	91	173	6.41E-15	68.0488	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#7509 - 	CGI_10016709	superfamily	215754	16	78	4.45E-12	60.3448	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#7513 - 	CGI_10016713	superfamily	248097	464	586	6.00E-08	51.1118	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7513 - 	CGI_10016713	superfamily	248097	206	259	0.000133243	40.7114	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7514 - 	CGI_10016714	superfamily	243035	64	121	1.08E-16	71.8621	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7516 - 	CGI_10016716	superfamily	241644	31	135	5.18E-41	136.948	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#7517 - 	CGI_10016717	superfamily	217020	2	76	5.06E-18	75.3238	cl03574	Seryl_tRNA_N superfamily	C	 - 	Seryl-tRNA synthetase N-terminal domain; This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Q#7518 - 	CGI_10016718	superfamily	241763	164	258	1.94E-51	168.956	cl00298	Peptidase_C1 superfamily	C	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#7518 - 	CGI_10016718	superfamily	244586	78	135	2.22E-16	70.7354	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#7519 - 	CGI_10016719	superfamily	241763	118	299	1.69E-81	247.922	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#7519 - 	CGI_10016719	superfamily	244586	28	88	1.23E-20	83.0619	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#7520 - 	CGI_10016720	superfamily	241763	115	328	4.27E-117	339.6	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#7520 - 	CGI_10016720	superfamily	244586	27	85	1.89E-17	74.9726	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#7521 - 	CGI_10016721	superfamily	241763	116	329	2.75E-117	340.37	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#7521 - 	CGI_10016721	superfamily	244586	28	83	1.40E-14	67.2686	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#7522 - 	CGI_10016722	superfamily	241763	56	269	8.39E-119	341.911	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#7524 - 	CGI_10016724	superfamily	247908	224	379	4.61E-76	235.651	cl17354	NIF superfamily	 - 	 - 	NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.
Q#7525 - 	CGI_10016725	superfamily	116798	16	104	2.06E-16	70.7834	cl17955	Lipocalin_2 superfamily	C	 - 	"Lipocalin-like domain; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel."
Q#7531 - 	CGI_10010007	superfamily	241584	530	622	0.000280103	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7531 - 	CGI_10010007	superfamily	245814	178	250	2.18E-07	49.0409	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7531 - 	CGI_10010007	superfamily	245814	83	149	7.53E-06	44.32	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7531 - 	CGI_10010007	superfamily	245814	271	328	4.01E-05	42.0088	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7534 - 	CGI_10010010	superfamily	246925	2	293	9.40E-65	214.912	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#7534 - 	CGI_10010010	superfamily	203777	347	515	1.94E-32	121.601	cl06737	RanGAP1_C superfamily	 - 	 - 	"RanGAP1 C-terminal domain; Ran-GTPase activating protein 1 (RanGAP1) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localisation at the vertebrate nuclear pore complex, and is sumoylated by the small ubiquitin-related modifier protein (SUMO-1). This domain is composed almost entirely of helical substructures that are organised into an alpha-alpha superhelix fold, with the exception of the peptide containing the lysine residue required for SUMO-1 conjugation."
Q#7536 - 	CGI_10010012	superfamily	222604	127	636	2.84E-161	511.418	cl16723	MOR2-PAG1_N superfamily	 - 	 - 	Cell morphogenesis N-terminal; This family is the conserved N-terminal region of proteins that are involved in cell morphogenesis.
Q#7536 - 	CGI_10010012	superfamily	222607	1975	2228	2.39E-63	219.729	cl16725	MOR2-PAG1_C superfamily	 - 	 - 	Cell morphogenesis C-terminal; This family is the conserved C-terminal region of proteins that are involved in cell morphogenesis.
Q#7538 - 	CGI_10010014	superfamily	243092	3	295	9.66E-94	292.317	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7538 - 	CGI_10010014	superfamily	243092	298	338	0.000379987	38.8326	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7538 - 	CGI_10010014	superfamily	243092	341	383	0.00147001	36.9066	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7539 - 	CGI_10010015	superfamily	244843	211	574	6.07E-109	339.592	cl08040	Ggt superfamily	C	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#7539 - 	CGI_10010015	superfamily	216363	103	186	2.64E-19	84.059	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#7542 - 	CGI_10010018	superfamily	241600	79	262	2.28E-78	238.679	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7543 - 	CGI_10005454	superfamily	247724	23	146	1.26E-39	136.896	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#7546 - 	CGI_10005457	superfamily	243058	238	351	7.86E-33	121.267	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7546 - 	CGI_10005457	superfamily	243058	104	225	5.43E-31	116.26	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7546 - 	CGI_10005457	superfamily	243058	316	434	4.38E-20	86.2143	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7546 - 	CGI_10005457	superfamily	201951	9	90	2.78E-13	66.2502	cl03339	IBB superfamily	 - 	 - 	"Importin beta binding domain; This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain."
Q#7549 - 	CGI_10008610	superfamily	246597	106	422	1.54E-94	293.796	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#7550 - 	CGI_10008611	superfamily	217293	34	227	9.10E-35	128.519	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7550 - 	CGI_10008611	superfamily	202474	235	330	8.06E-15	72.3013	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7551 - 	CGI_10008612	superfamily	217293	180	380	4.88E-40	145.083	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7551 - 	CGI_10008612	superfamily	202474	388	484	1.00E-13	69.6049	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7552 - 	CGI_10008613	superfamily	247044	120	254	3.20E-49	161.245	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#7552 - 	CGI_10008613	superfamily	247044	2	85	3.75E-40	138.149	cl15697	ADF_gelsolin superfamily	N	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#7553 - 	CGI_10008614	superfamily	247905	196	310	2.41E-19	85.7524	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#7553 - 	CGI_10008614	superfamily	247805	16	178	1.89E-51	179.218	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#7553 - 	CGI_10008614	superfamily	243199	826	872	2.01E-12	66.5458	cl02808	RT_like superfamily	C	 - 	"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs."
Q#7554 - 	CGI_10008615	superfamily	207685	101	171	2.69E-36	123.053	cl02642	PABP superfamily	 - 	 - 	"Poly-adenylate binding protein, unique domain; The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family."
Q#7555 - 	CGI_10008616	superfamily	241571	142	228	3.48E-15	70.1338	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#7556 - 	CGI_10000847	superfamily	241559	29	58	7.97E-05	36.4884	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#7559 - 	CGI_10023171	superfamily	241743	229	343	3.35E-27	104.313	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#7559 - 	CGI_10023171	superfamily	246918	49	101	1.98E-15	69.9231	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7559 - 	CGI_10023171	superfamily	246918	106	158	1.40E-13	64.9155	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7562 - 	CGI_10023174	superfamily	241554	164	209	1.37E-10	58.6724	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7562 - 	CGI_10023174	superfamily	245226	11	59	0.00059847	38.8209	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#7565 - 	CGI_10023177	superfamily	247745	113	453	0	539.545	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#7565 - 	CGI_10023177	superfamily	245003	447	533	1.34E-19	85.7114	cl08536	Alpha-mann_mid superfamily	 - 	 - 	"Alpha mannosidase, middle domain; Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase."
Q#7566 - 	CGI_10023178	superfamily	243072	69	195	1.08E-30	112.862	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7567 - 	CGI_10023179	superfamily	241578	44	208	1.55E-49	169.331	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7569 - 	CGI_10023181	superfamily	207662	13	84	5.19E-34	124.982	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#7569 - 	CGI_10023181	superfamily	245599	540	656	1.92E-07	50.4257	cl11397	NR_LBD superfamily	C	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#7571 - 	CGI_10023183	superfamily	218219	15	199	1.58E-35	125.51	cl04693	PRELI superfamily	 - 	 - 	"PRELI-like family; This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins."
Q#7574 - 	CGI_10023186	superfamily	247792	441	479	0.0086164	34.7288	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7574 - 	CGI_10023186	superfamily	243109	264	392	4.06E-53	177.509	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7577 - 	CGI_10023189	superfamily	216944	55	128	6.03E-12	57.5923	cl03496	Propep_M14 superfamily	 - 	 - 	"Carboxypeptidase activation peptide; Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme."
Q#7578 - 	CGI_10023190	superfamily	245595	5	276	3.58E-143	407.677	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#7579 - 	CGI_10023191	superfamily	110440	334	358	0.00301411	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#7580 - 	CGI_10023192	superfamily	243066	59	172	2.03E-14	70.3389	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#7580 - 	CGI_10023192	superfamily	222150	511	535	0.003698	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7581 - 	CGI_10023193	superfamily	243088	77	184	3.87E-38	132.837	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#7584 - 	CGI_10023196	superfamily	245213	284	317	0.000509306	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7584 - 	CGI_10023196	superfamily	243061	346	445	2.09E-34	125.532	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#7584 - 	CGI_10023196	superfamily	243061	64	163	2.54E-33	122.451	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#7584 - 	CGI_10023196	superfamily	243061	171	269	1.51E-30	115.132	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#7585 - 	CGI_10023197	superfamily	248264	67	113	1.00E-05	42.2242	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#7586 - 	CGI_10023199	superfamily	246664	173	653	2.00E-144	434.045	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#7587 - 	CGI_10023200	superfamily	246664	331	710	4.59E-141	424.68	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#7587 - 	CGI_10023200	superfamily	246664	222	269	2.17E-05	46.1494	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#7588 - 	CGI_10023201	superfamily	220672	18	111	3.70E-15	68.0422	cl10957	Frag1 superfamily	N	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#7589 - 	CGI_10023202	superfamily	245213	1458	1490	7.16E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7589 - 	CGI_10023202	superfamily	245213	1375	1408	3.37E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7589 - 	CGI_10023202	superfamily	245213	1498	1531	6.40E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7589 - 	CGI_10023202	superfamily	245213	1120	1152	0.000133628	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7589 - 	CGI_10023202	superfamily	245213	1576	1612	0.000135648	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7589 - 	CGI_10023202	superfamily	245213	993	1027	0.00159919	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7589 - 	CGI_10023202	superfamily	245213	1204	1244	0.00646413	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7589 - 	CGI_10023202	superfamily	248097	1921	2052	6.56E-26	106.195	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7589 - 	CGI_10023202	superfamily	241578	1270	1323	1.84E-05	46.6092	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7589 - 	CGI_10023202	superfamily	243124	565	642	9.94E-05	42.7896	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#7589 - 	CGI_10023202	superfamily	241578	1034	1074	0.000106186	44.6832	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7589 - 	CGI_10023202	superfamily	241584	307	378	0.000750155	40.0999	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7589 - 	CGI_10023202	superfamily	221695	1358	1378	0.00076541	39.3606	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#7589 - 	CGI_10023202	superfamily	245674	40	113	0.00103555	39.5654	cl11531	DUF904 superfamily	 - 	 - 	Protein of unknown function (DUF904); This family consists of several bacterial and archaeal hypothetical proteins of unknown function.
Q#7589 - 	CGI_10023202	superfamily	241578	1653	1701	0.00884891	38.52	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7590 - 	CGI_10023203	superfamily	246722	1	195	7.10E-74	243.818	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#7590 - 	CGI_10023203	superfamily	246724	196	242	1.43E-15	74.3113	cl14815	H3TH_StructSpec-5'-nucleases superfamily	C	 - 	"H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases."
Q#7590 - 	CGI_10023203	superfamily	246722	262	315	0.0089284	37.3512	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#7591 - 	CGI_10023204	superfamily	243084	1215	1298	5.56E-17	79.3614	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#7591 - 	CGI_10023204	superfamily	247999	1058	1100	3.09E-09	55.1892	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#7596 - 	CGI_10000785	superfamily	247085	84	191	5.92E-27	100.658	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#7596 - 	CGI_10000785	superfamily	245596	1	36	6.01E-20	84.5633	cl11394	Glyco_tranf_GTA_type superfamily	NC	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#7596 - 	CGI_10000785	superfamily	245596	38	65	1.63E-09	54.903	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#7598 - 	CGI_10009080	superfamily	241600	52	217	1.48E-29	117.341	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7598 - 	CGI_10009080	superfamily	241600	281	388	3.16E-18	83.8291	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7598 - 	CGI_10009080	superfamily	241600	549	627	6.25E-06	46.4647	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7600 - 	CGI_10009082	superfamily	241600	12	78	1.82E-17	78.8215	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7600 - 	CGI_10009082	superfamily	241600	274	356	8.91E-06	44.9239	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7601 - 	CGI_10009083	superfamily	241600	125	310	9.78E-53	175.121	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7605 - 	CGI_10009087	superfamily	243269	401	784	9.57E-52	186.32	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#7605 - 	CGI_10009087	superfamily	243269	49	337	8.98E-44	163.593	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#7606 - 	CGI_10009088	superfamily	243269	9	390	1.17E-61	214.824	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#7606 - 	CGI_10009088	superfamily	243269	555	843	1.34E-32	130.851	cl03012	Ammonium_transp superfamily	N	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#7607 - 	CGI_10009089	superfamily	243269	26	436	8.81E-107	327.303	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#7608 - 	CGI_10002458	superfamily	247805	204	262	6.33E-06	45.7912	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#7608 - 	CGI_10002458	superfamily	221913	414	603	2.32E-64	215.867	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#7608 - 	CGI_10002458	superfamily	241762	701	759	1.06E-16	76.2366	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#7608 - 	CGI_10002458	superfamily	207411	903	946	1.81E-09	55.1433	cl01438	zf-AN1 superfamily	 - 	 - 	"AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues."
Q#7609 - 	CGI_10002459	superfamily	247684	174	578	2.31E-64	222.538	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7609 - 	CGI_10002459	superfamily	247684	721	890	7.75E-26	110.515	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7611 - 	CGI_10009747	superfamily	245201	17	291	3.11E-153	433.627	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7614 - 	CGI_10009750	superfamily	241609	55	138	6.81E-22	84.3519	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#7614 - 	CGI_10009750	superfamily	241609	1	52	1.03E-11	56.9306	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#7615 - 	CGI_10009751	superfamily	241589	109	197	4.96E-18	77.3211	cl00071	GLECT superfamily	C	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#7615 - 	CGI_10009751	superfamily	241589	2	93	2.86E-14	66.5036	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#7617 - 	CGI_10009753	superfamily	248097	131	257	2.26E-27	103.114	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7618 - 	CGI_10009754	superfamily	243072	43	166	3.48E-24	93.217	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7621 - 	CGI_10002534	superfamily	248264	31	72	0.00505911	34.135	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#7625 - 	CGI_10002538	superfamily	241619	34	80	4.12E-05	39.8729	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#7625 - 	CGI_10002538	superfamily	245847	136	189	0.00161609	36.3806	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#7626 - 	CGI_10002539	superfamily	199156	101	116	0.000529104	35.4968	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#7630 - 	CGI_10002615	superfamily	248097	13	133	3.42E-19	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7630 - 	CGI_10002615	superfamily	248097	215	334	1.94E-17	76.9202	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7630 - 	CGI_10002615	superfamily	248097	135	202	7.03E-09	52.6526	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#7631 - 	CGI_10002388	superfamily	245213	100	136	1.49E-08	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7633 - 	CGI_10002410	superfamily	248338	183	284	0.000348933	40.6625	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#7634 - 	CGI_10003031	superfamily	243082	32	243	5.36E-21	90.235	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#7634 - 	CGI_10003031	superfamily	243082	263	386	3.90E-14	70.2046	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#7635 - 	CGI_10003032	superfamily	245819	817	995	3.09E-56	193.565	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#7635 - 	CGI_10003032	superfamily	245201	497	744	1.90E-37	143.061	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7635 - 	CGI_10003032	superfamily	245225	25	373	3.07E-33	133.591	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#7635 - 	CGI_10003032	superfamily	219526	763	804	2.85E-07	51.0807	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#7642 - 	CGI_10000979	superfamily	243091	39	150	2.45E-16	71.2115	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#7643 - 	CGI_10027495	superfamily	241563	72	110	0.000130209	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7643 - 	CGI_10027495	superfamily	217579	105	172	0.0057649	35.8725	cl04094	XH superfamily	C	 - 	XH domain; The XH (rice gene X Homology) domain is found in a family of plant proteins including gene X. The molecular function of these proteins is unknown. However these proteins usually contain an XS domain that is also found in the PTGS protein SGS3. This domain contains a conserved glutamate residue that may be functionally important.
Q#7644 - 	CGI_10027496	superfamily	245027	106	217	0.00147681	37.758	cl09176	FlgN superfamily	 - 	 - 	FlgN protein; This family includes the FlgN protein and export chaperone involved in flagellar synthesis.
Q#7644 - 	CGI_10027496	superfamily	241563	72	110	0.00173119	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7646 - 	CGI_10027498	superfamily	246751	72	367	5.75E-119	348.849	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#7647 - 	CGI_10027499	superfamily	246751	57	352	1.11E-113	334.597	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#7648 - 	CGI_10027500	superfamily	243096	68	248	1.26E-32	126.258	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#7649 - 	CGI_10027501	superfamily	241782	21	382	5.21E-150	431.714	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#7652 - 	CGI_10027504	superfamily	247792	234	278	3.60E-06	43.2032	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7652 - 	CGI_10027504	superfamily	218247	22	214	1.07E-33	123.641	cl04727	Pex2_Pex12 superfamily	 - 	 - 	"Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain."
Q#7658 - 	CGI_10027511	superfamily	216363	92	197	2.16E-26	98.6965	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#7659 - 	CGI_10027512	superfamily	248012	22	158	3.41E-10	53.8165	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#7660 - 	CGI_10027513	superfamily	248012	516	657	1.44E-07	50.3497	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#7660 - 	CGI_10027513	superfamily	214507	399	450	3.24E-07	48.1952	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#7661 - 	CGI_10027514	superfamily	245201	639	955	2.39E-49	176.75	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7662 - 	CGI_10027515	superfamily	241645	5	116	1.22E-64	193.991	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#7663 - 	CGI_10027516	superfamily	243132	7	141	2.82E-47	170.637	cl02661	A_deamin superfamily	C	 - 	"Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc."
Q#7663 - 	CGI_10027516	superfamily	243132	321	543	4.53E-45	163.284	cl02661	A_deamin superfamily	N	 - 	"Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc."
Q#7666 - 	CGI_10027519	superfamily	216316	20	234	2.96E-72	230.594	cl10574	CD36 superfamily	N	 - 	CD36 family; The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion.
Q#7667 - 	CGI_10027520	superfamily	217380	39	316	4.60E-88	271.12	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#7668 - 	CGI_10027521	superfamily	216456	569	721	1.03E-15	78.5194	cl03182	RYDR_ITPR superfamily	 - 	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#7668 - 	CGI_10027521	superfamily	219849	1884	1975	6.43E-12	65.2835	cl09597	RIH_assoc superfamily	 - 	 - 	"RyR and IP3R Homology associated; This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815."
Q#7675 - 	CGI_10027528	superfamily	247755	578	813	2.76E-150	443.595	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#7675 - 	CGI_10027528	superfamily	216049	247	420	9.45E-06	46.8954	cl18356	ABC_membrane superfamily	C	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#7676 - 	CGI_10027529	superfamily	241867	26	283	7.50E-119	344.052	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#7677 - 	CGI_10027530	superfamily	245601	2685	2982	1.82E-37	144.439	cl11399	HP superfamily	 - 	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#7677 - 	CGI_10027530	superfamily	245213	2250	2282	1.64E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1266	1298	9.89E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	2334	2377	1.10E-05	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	2067	2101	8.04E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1095	1129	8.04E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	2505	2545	9.83E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	2291	2328	0.000311897	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1307	1343	0.000846663	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1390	1433	0.00390203	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1475	1515	0.00497783	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	2195	2228	0.00661794	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	241578	1511	1553	6.64E-08	54.6983	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7677 - 	CGI_10027530	superfamily	246918	1646	1692	4.51E-07	49.8927	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7677 - 	CGI_10027530	superfamily	241578	2590	2630	1.10E-06	50.8464	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7677 - 	CGI_10027530	superfamily	243124	295	437	1.33E-05	46.6513	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#7677 - 	CGI_10027530	superfamily	245213	166	209	1.60E-05	45.0324	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	241578	1130	1169	2.87E-05	46.6092	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7677 - 	CGI_10027530	superfamily	241578	2102	2141	7.30E-05	45.4536	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7677 - 	CGI_10027530	superfamily	245213	2546	2590	0.000360051	41.1804	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1223	1261	0.000476573	40.7952	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	246918	1822	1871	0.000489004	41.0331	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7677 - 	CGI_10027530	superfamily	246918	13	62	0.000626463	40.6479	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#7677 - 	CGI_10027530	superfamily	221695	1370	1393	0.00185162	38.9754	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#7677 - 	CGI_10027530	superfamily	245213	1052	1086	0.00307216	38.484	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1436	1470	0.0038134	38.0988	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1350	1381	0.00424043	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	2024	2057	0.0044608	38.0988	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	1599	1635	0.00683887	37.2264	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7677 - 	CGI_10027530	superfamily	245213	2464	2497	0.00849291	36.9432	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#7678 - 	CGI_10027531	superfamily	217945	172	247	5.55E-14	69.5625	cl18435	B-block_TFIIIC superfamily	 - 	 - 	B-block binding subunit of TFIIIC; Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding.
Q#7679 - 	CGI_10027532	superfamily	220692	61	355	3.78E-21	92.6525	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#7680 - 	CGI_10027533	superfamily	245870	503	623	2.40E-13	67.7291	cl12097	DUF1772 superfamily	 - 	 - 	Domain of unknown function (DUF1772); This domain is of unknown function.
Q#7681 - 	CGI_10027534	superfamily	245870	23	156	2.24E-12	60.0251	cl12097	DUF1772 superfamily	 - 	 - 	Domain of unknown function (DUF1772); This domain is of unknown function.
Q#7682 - 	CGI_10027535	superfamily	245870	23	156	1.79E-13	63.1067	cl12097	DUF1772 superfamily	 - 	 - 	Domain of unknown function (DUF1772); This domain is of unknown function.
Q#7687 - 	CGI_10027540	superfamily	193687	39	118	8.88E-35	117.639	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#7687 - 	CGI_10027540	superfamily	245596	1	17	4.17E-06	43.3533	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#7688 - 	CGI_10027541	superfamily	241782	64	482	3.70E-85	270.594	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#7689 - 	CGI_10027542	superfamily	245814	450	519	1.55E-12	65.2031	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7689 - 	CGI_10027542	superfamily	245814	344	415	2.22E-11	62.1376	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7689 - 	CGI_10027542	superfamily	245814	232	304	1.02E-06	48.2705	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7689 - 	CGI_10027542	superfamily	245814	11	55	0.00304093	37.4849	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#7690 - 	CGI_10027543	superfamily	247723	274	357	1.76E-32	121.893	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7690 - 	CGI_10027543	superfamily	247723	144	224	2.03E-28	110.161	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7690 - 	CGI_10027543	superfamily	243107	759	803	1.81E-15	72.1925	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#7691 - 	CGI_10027544	superfamily	220771	1	33	3.12E-07	42.8057	cl11113	APC_CDC26 superfamily	C	 - 	"Anaphase-promoting complex APC subunit 1; The anaphase-promoting complex (APC) or cyclosome is a cell cycle-regulated ubiquitin-protein ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins thereby targeting them for proteolysis by the 26S proteasome. CDC26 is one of the nine or so subunits identified within APC but its exact function is not known. The APC/C becomes active at the metaphase/anaphase transition and remains active during G1 phase. One mechanism linked to activation of the APC/C is phosphorylation. The yeast APC/C is composed of at least 13 subunits, but the function of many of the subunits is unknown. Hcn1 is the smallest subunit of the S. pombe APC/C, and is found to be essential for cell viability, APC/C integrity, and proper APC/C regulation. In addition, Hcn1 phosphorylation indicates a specific role for the phosphorylation of this subunit late in the cell cycle."
Q#7692 - 	CGI_10027545	superfamily	241600	307	384	1.41E-27	113.104	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7693 - 	CGI_10027546	superfamily	247684	38	418	7.31E-61	214.449	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7693 - 	CGI_10027546	superfamily	247684	677	964	1.21E-56	202.507	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7694 - 	CGI_10027547	superfamily	243124	99	217	4.67E-29	109.054	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#7700 - 	CGI_10004285	superfamily	241559	172	228	3.18E-05	41.1471	cl00030	CH superfamily	N	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#7701 - 	CGI_10004286	superfamily	198867	14	50	5.21E-06	41.9433	cl06652	BACK superfamily	N	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#7704 - 	CGI_10005988	superfamily	246671	162	259	4.55E-15	73.6112	cl14606	Reeler_cohesin_like superfamily	N	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#7704 - 	CGI_10005988	superfamily	241563	498	532	0.000697306	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7704 - 	CGI_10005988	superfamily	242530	536	600	0.00187283	37.866	cl01483	DUF964 superfamily	C	 - 	Protein of unknown function (DUF964); This family consists of several relatively short bacterial and archaeal hypothetical sequences. The function of this family is unknown.
Q#7707 - 	CGI_10005991	superfamily	220691	86	263	0.00624391	36.4418	cl18569	7TM_GPCR_Srv superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#7708 - 	CGI_10005993	superfamily	110440	523	550	0.00154667	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#7711 - 	CGI_10005996	superfamily	247725	1132	1259	3.10E-56	192.122	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7711 - 	CGI_10005996	superfamily	219738	965	1054	1.55E-06	48.1899	cl06980	Anillin superfamily	C	 - 	"Cell division protein anillin; Anillin is a protein involved in septin organisation during cell division. It is an actin binding protein that is localised to the cleavage furrow, and it maintains the localisation of active myosin, which ensures the spatial control of concerted contraction during cytokinesis."
Q#7716 - 	CGI_10024455	superfamily	218609	21	83	1.16E-22	85.1179	cl05189	Destabilase superfamily	N	 - 	"Destabilase; Destabilase is an endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves isopeptide bonds formed by transglutaminase (Factor XIIIa) between glutamine gamma-carboxamide and the epsilon-amino group of lysine."
Q#7717 - 	CGI_10024456	superfamily	217293	33	232	1.08E-35	131.216	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7717 - 	CGI_10024456	superfamily	202474	239	335	8.65E-14	69.2197	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7718 - 	CGI_10024457	superfamily	218609	1	94	1.43E-36	121.327	cl05189	Destabilase superfamily	 - 	 - 	"Destabilase; Destabilase is an endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves isopeptide bonds formed by transglutaminase (Factor XIIIa) between glutamine gamma-carboxamide and the epsilon-amino group of lysine."
Q#7719 - 	CGI_10024458	superfamily	243035	7	68	5.13E-20	77.7215	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7722 - 	CGI_10024461	superfamily	245864	2	421	1.23E-105	323.846	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#7723 - 	CGI_10024462	superfamily	245864	11	403	1.13E-105	323.076	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#7724 - 	CGI_10024463	superfamily	241816	1	93	4.83E-19	76.4253	cl00364	Ribosomal_L7_L12 superfamily	N	 - 	"Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises L7/L12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that L7/L12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors. In eukaryotes, the proteins that perform the equivalent function to L7/L12 are called P1 and P2, which do not share sequence similarity with L7/L12. However, a bacterial L7/L12 homolog is found in some eukaryotes, in mitochondria and chloroplasts. In archaea, the protein equivalent to L7/L12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to L7/L12."
Q#7725 - 	CGI_10024464	superfamily	241565	329	402	6.26E-05	41.5383	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#7725 - 	CGI_10024464	superfamily	115393	6	274	3.16E-135	398.288	cl05998	Pescadillo_N superfamily	 - 	 - 	"Pescadillo N-terminus; This family represents the N-terminal region of Pescadillo. Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest. This family is often found in conjunction with a pfam00533 domain."
Q#7726 - 	CGI_10024465	superfamily	177822	38	140	9.71E-09	52.6149	cl18088	PLN02164 superfamily	C	 - 	sulfotransferase
Q#7727 - 	CGI_10024466	superfamily	241578	27	193	4.40E-13	65.7758	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#7727 - 	CGI_10024466	superfamily	243119	303	353	5.60E-13	62.8364	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7727 - 	CGI_10024466	superfamily	243119	247	295	1.08E-06	45.1172	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#7729 - 	CGI_10024468	superfamily	191120	26	273	2.17E-113	336.169	cl04821	DUF647 superfamily	 - 	 - 	"Protein of unknown function (DUF647); In plants, this domain plays a role in auxin-transport, plant growth and development."
Q#7730 - 	CGI_10024469	superfamily	245201	492	752	6.52E-44	159.239	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7730 - 	CGI_10024469	superfamily	205721	22	147	5.45E-33	124.386	cl16297	KSR1-SAM superfamily	 - 	 - 	SAM like domain present in kinase suppressor RAS 1; SAM like domain present in kinase suppressor RAS 1.  
Q#7731 - 	CGI_10024470	superfamily	247743	31	172	7.30E-25	97.9871	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#7731 - 	CGI_10024470	superfamily	203973	236	325	1.88E-24	95.266	cl16006	Rep_fac_C superfamily	 - 	 - 	"Replication factor C C-terminal domain; This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A."
Q#7733 - 	CGI_10024472	superfamily	241626	11	86	3.36E-19	76.5041	cl00125	RHOD superfamily	N	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#7734 - 	CGI_10024473	superfamily	241626	6	110	1.20E-28	105.009	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#7734 - 	CGI_10024473	superfamily	241626	157	204	4.05E-10	54.1762	cl00125	RHOD superfamily	N	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#7736 - 	CGI_10024475	superfamily	204801	517	635	3.48E-67	219.849	cl13421	MVP_shoulder superfamily	 - 	 - 	Shoulder domain; This domain is found in the Major Vault Protein and has been called the shoulder domain. This family includes two bacterial proteins. This suggests that some bacteria may possess vault particles.
Q#7736 - 	CGI_10024475	superfamily	201831	114	155	2.43E-15	71.8116	cl03238	Vault superfamily	 - 	 - 	Major Vault Protein repeat; The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeat found in the amino terminal half of the major vault protein.
Q#7736 - 	CGI_10024475	superfamily	201831	167	209	5.91E-11	59.1	cl03238	Vault superfamily	 - 	 - 	Major Vault Protein repeat; The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeat found in the amino terminal half of the major vault protein.
Q#7736 - 	CGI_10024475	superfamily	201831	220	264	2.17E-09	54.4776	cl03238	Vault superfamily	 - 	 - 	Major Vault Protein repeat; The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeat found in the amino terminal half of the major vault protein.
Q#7736 - 	CGI_10024475	superfamily	201831	325	365	1.12E-08	52.5516	cl03238	Vault superfamily	 - 	 - 	Major Vault Protein repeat; The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeat found in the amino terminal half of the major vault protein.
Q#7737 - 	CGI_10024476	superfamily	217539	131	341	4.88E-14	69.274	cl18414	Nucleotid_trans superfamily	 - 	 - 	Nucleotide-diphospho-sugar transferase; Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases.
Q#7738 - 	CGI_10024477	superfamily	221887	5	107	1.62E-38	131.483	cl15229	ING superfamily	 - 	 - 	"Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterized C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail."
Q#7738 - 	CGI_10024477	superfamily	247999	192	239	1.64E-09	52.1076	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#7739 - 	CGI_10024478	superfamily	243109	4	166	3.16E-82	266.291	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7739 - 	CGI_10024478	superfamily	243109	224	392	2.11E-71	236.245	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7739 - 	CGI_10024478	superfamily	243109	437	598	1.45E-69	231.237	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7739 - 	CGI_10024478	superfamily	243109	627	791	6.96E-63	212.363	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7739 - 	CGI_10024478	superfamily	243109	831	989	5.16E-58	198.495	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7740 - 	CGI_10024479	superfamily	241656	8	185	7.83E-43	142.975	cl00169	Mog1 superfamily	 - 	 - 	"homolog to Ran-Binding Protein Mog1p; binds to the small GTPase Ran, which plays an important role in nuclear import. Binding is independent of Ran's nucleotide state (RanGTP/RanGDP)"
Q#7741 - 	CGI_10024480	superfamily	241567	137	196	7.33E-21	87.6559	cl00042	CASc superfamily	NC	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#7741 - 	CGI_10024480	superfamily	246680	2	31	3.24E-06	43.3444	cl14633	DD_superfamily superfamily	N	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#7747 - 	CGI_10024486	superfamily	243110	119	205	8.64E-05	43.1869	cl02616	MACPF superfamily	C	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#7748 - 	CGI_10024487	superfamily	243110	18	66	1.76E-07	50.1205	cl02616	MACPF superfamily	C	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#7751 - 	CGI_10024490	superfamily	199166	136	244	5.36E-07	48.4776	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#7751 - 	CGI_10024490	superfamily	224772	6	50	0.00132467	38.0825	cl15312	KptA superfamily	C	 - 	"RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]"
Q#7752 - 	CGI_10024491	superfamily	242156	58	171	1.41E-52	165.389	cl00869	PTH2_family superfamily	 - 	 - 	"Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes."
Q#7753 - 	CGI_10024492	superfamily	241752	1866	1985	2.17E-46	165.185	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#7753 - 	CGI_10024492	superfamily	247723	351	426	3.21E-16	76.572	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7753 - 	CGI_10024492	superfamily	247723	541	612	5.24E-15	73.1053	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7753 - 	CGI_10024492	superfamily	241554	1387	1496	1.06E-18	85.3899	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7753 - 	CGI_10024492	superfamily	247723	441	519	3.67E-11	61.9345	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7753 - 	CGI_10024492	superfamily	247723	633	684	2.80E-05	44.1804	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7753 - 	CGI_10024492	superfamily	241554	1257	1278	0.000439287	41.7236	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7753 - 	CGI_10024492	superfamily	247723	699	747	0.000756333	39.9781	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7754 - 	CGI_10024493	superfamily	247794	68	386	4.08E-133	390.337	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#7755 - 	CGI_10024494	superfamily	247792	319	373	4.99E-13	63.5091	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7755 - 	CGI_10024494	superfamily	214806	204	295	2.11E-09	54.2238	cl15966	CRA superfamily	 - 	 - 	"CT11-RanBPM; protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)"
Q#7755 - 	CGI_10024494	superfamily	199226	112	145	0.00170685	35.8732	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#7755 - 	CGI_10024494	superfamily	128914	169	208	0.00179976	36.0098	cl15352	CTLH superfamily	N	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#7760 - 	CGI_10024500	superfamily	192467	45	160	3.08E-40	134.877	cl10863	NEP superfamily	 - 	 - 	Uncharacterized conserved protein; This is the N-terminal 80 residues of a family of proteins conserved from plants to humans. It contains a characteristic NEP sequence motif. The function is not known.
Q#7761 - 	CGI_10024501	superfamily	247787	138	419	0	590.003	cl17233	RecA-like_NTPases superfamily	 - 	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#7761 - 	CGI_10024501	superfamily	215848	428	529	3.71E-24	97.3505	cl08258	ATP-synt_ab_C superfamily	 - 	 - 	"ATP synthase alpha/beta chain, C terminal domain; ATP synthase alpha/beta chain, C terminal domain.  "
Q#7761 - 	CGI_10024501	superfamily	217261	69	136	2.17E-16	74.484	cl18399	ATP-synt_ab_N superfamily	 - 	 - 	"ATP synthase alpha/beta family, beta-barrel domain; This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella."
Q#7762 - 	CGI_10024502	superfamily	207794	1	332	1.69E-159	456.754	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#7763 - 	CGI_10024504	superfamily	241563	72	109	4.68E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7763 - 	CGI_10024504	superfamily	241563	28	59	0.00117454	37.0736	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7763 - 	CGI_10024504	superfamily	246954	122	207	0.00212056	39.3238	cl15415	Sec1 superfamily	NC	 - 	Sec1 family; Sec1 family.  
Q#7764 - 	CGI_10010094	superfamily	247692	1	171	8.34E-24	95.4357	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#7765 - 	CGI_10010095	superfamily	245201	48	291	3.81E-86	261.685	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7767 - 	CGI_10010097	superfamily	241563	383	419	0.00338166	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7769 - 	CGI_10016037	superfamily	243134	41	137	5.20E-15	66.904	cl02663	Fasciclin superfamily	C	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#7770 - 	CGI_10016038	superfamily	243134	43	161	3.70E-18	75.7636	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#7770 - 	CGI_10016038	superfamily	243134	1	28	3.44E-05	39.94	cl02663	Fasciclin superfamily	N	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#7772 - 	CGI_10016040	superfamily	243082	1	232	5.53E-135	390.141	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#7779 - 	CGI_10016047	superfamily	192535	59	253	0.00518642	36.805	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#7780 - 	CGI_10016048	superfamily	221340	169	360	6.82E-19	82.4464	cl13405	DUF3472 superfamily	 - 	 - 	"Domain of unknown function (DUF3472); This presumed domain is functionally uncharacterized. This domain is found in bacteria, eukaryotes and viruses. This domain is typically between 174 to 190 amino acids in length. This domain has a single completely conserved residue G that may be functionally important."
Q#7784 - 	CGI_10016052	superfamily	243035	154	229	0.000470121	37.9846	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7786 - 	CGI_10016054	superfamily	207713	140	197	8.73E-05	39.6101	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#7787 - 	CGI_10016055	superfamily	241554	1	158	1.44E-37	135.861	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7787 - 	CGI_10016055	superfamily	241554	210	348	1.34E-27	106.961	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7787 - 	CGI_10016055	superfamily	241554	415	464	3.28E-13	66.5151	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7788 - 	CGI_10016056	superfamily	207713	284	341	1.97E-05	43.0769	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#7788 - 	CGI_10016056	superfamily	241554	56	86	0.000205766	40.3215	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#7789 - 	CGI_10016057	superfamily	247723	7	78	1.87E-12	62.3197	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7790 - 	CGI_10016058	superfamily	247723	82	156	1.31E-09	52.2696	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7791 - 	CGI_10016060	superfamily	241752	44	159	5.82E-37	125.124	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#7793 - 	CGI_10016518	superfamily	242220	28	234	7.09E-58	185.105	cl00957	Translin superfamily	 - 	 - 	"Translin family; Members of this family include Translin that interacts with DNA and forms a ring around the DNA. This family also includes human translin-associated protein X, which was found to interact with translin with yeast two-hybrid screen."
Q#7794 - 	CGI_10016519	superfamily	241754	1	334	3.23E-171	515.709	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#7794 - 	CGI_10016519	superfamily	243088	1180	1305	2.20E-48	169.869	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#7794 - 	CGI_10016519	superfamily	241581	442	508	7.93E-06	45.2799	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#7794 - 	CGI_10016519	superfamily	243082	932	1040	0.00443959	39.3969	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#7795 - 	CGI_10016520	superfamily	219143	2	118	6.18E-37	126.284	cl05971	PIG-F superfamily	N	 - 	GPI biosynthesis protein family Pig-F; PIG-F is involved in glycosylphosphatidylinositol (GPI) anchor biosynthesis.
Q#7796 - 	CGI_10016521	superfamily	243074	12	57	1.74E-09	49.8125	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#7797 - 	CGI_10016522	superfamily	245660	224	416	0.00437287	38.467	cl11493	PQQ_DH_like superfamily	C	 - 	"PQQ-dependent dehydrogenases and related proteins; This family is composed of dehydrogenases with pyrroloquinoline quinone (PQQ) as a cofactor, such as ethanol, methanol, and membrane-bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller, and the family also includes distantly related proteins which are not enzymatically active and do not bind PQQ."
Q#7798 - 	CGI_10016523	superfamily	243054	119	332	7.78E-10	58.9964	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#7799 - 	CGI_10016524	superfamily	219078	179	310	1.52E-05	43.2687	cl12333	DUF1113 superfamily	 - 	 - 	Protein of unknown function (DUF1113); This family consists of several bacterial proteins of unknown function.
Q#7800 - 	CGI_10016525	superfamily	241900	137	461	9.92E-29	114.708	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#7802 - 	CGI_10016527	superfamily	247755	805	1024	9.03E-114	352.952	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#7802 - 	CGI_10016527	superfamily	247755	182	406	8.07E-86	276.658	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#7802 - 	CGI_10016527	superfamily	216049	517	760	2.56E-28	116.231	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#7802 - 	CGI_10016527	superfamily	216049	19	135	2.83E-12	66.9258	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#7803 - 	CGI_10016528	superfamily	245201	36	324	2.15E-176	514.724	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7803 - 	CGI_10016528	superfamily	245201	418	671	7.13E-57	196.202	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7803 - 	CGI_10016528	superfamily	245597	306	366	3.79E-15	72.0079	cl11395	Pkinase_C superfamily	 - 	 - 	Protein kinase C terminal domain; Protein kinase C terminal domain.  
Q#7804 - 	CGI_10016529	superfamily	241557	27	185	1.18E-64	198.511	cl00022	YbaK_like superfamily	 - 	 - 	"YbaK-like.  The YbaK family of deacylase domains includes the INS amino acid-editing domain of  the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX.  The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation.  Organisms whose ProRS lacks the INS domain express an INS homolog in trans (e.g. YbaK, ProX, or PrdX)."
Q#7805 - 	CGI_10016530	superfamily	245227	31	875	0	1485.4	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#7808 - 	CGI_10016533	superfamily	247875	81	287	1.12E-40	143.572	cl17321	2OG-FeII_Oxy_2 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; 2OG-Fe(II) oxygenase superfamily.  
Q#7809 - 	CGI_10016534	superfamily	244824	102	536	3.72E-121	369.766	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#7811 - 	CGI_10016536	superfamily	191210	48	294	1.58E-137	392.056	cl04959	DUF706 superfamily	 - 	 - 	"Family of unknown function (DUF706); Family of uncharacterized eukaryotic function. Some members have a described putative function, but a common theme is not evident."
Q#7812 - 	CGI_10016537	superfamily	247683	235	289	1.30E-26	102.659	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#7812 - 	CGI_10016537	superfamily	241622	140	220	3.59E-13	65.6658	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#7812 - 	CGI_10016537	superfamily	247744	349	527	1.51E-27	108.919	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#7814 - 	CGI_10016539	superfamily	216709	254	402	7.70E-73	230.241	cl03357	Nop superfamily	 - 	 - 	Putative snoRNA binding domain; This family consists of various Pre RNA processing ribonucleoproteins. The function of the aligned region is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Nop5p (Nop58p) from yeast is the protein component of a ribonucleoprotein protein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex. Nop56p and Nop5p interact with Nop1p and are required for ribosome biogenesis. Prp31p is required for pre-mRNA splicing in S. cerevisiae.
Q#7814 - 	CGI_10016539	superfamily	208568	163	213	4.56E-24	95.2664	cl06890	NOSIC superfamily	 - 	 - 	NOSIC (NUC001) domain; This is the central domain in Nop56/SIK1-like proteins.
Q#7814 - 	CGI_10016539	superfamily	219731	1	66	6.90E-10	55.6508	cl06964	NOP5NT superfamily	 - 	 - 	NOP5NT (NUC127) domain; This N terminal domain is found in RNA-binding proteins of the NOP5 family.
Q#7815 - 	CGI_10016540	superfamily	245819	423	557	2.49E-35	132.318	cl11967	Nucleotidyl_cyc_III superfamily	C	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#7815 - 	CGI_10016540	superfamily	219812	87	304	9.68E-13	67.3312	cl07121	NIT superfamily	 - 	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#7815 - 	CGI_10016540	superfamily	219526	383	409	4.10E-07	49.9251	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#7816 - 	CGI_10016541	superfamily	245819	407	583	1.92E-56	190.868	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#7816 - 	CGI_10016541	superfamily	219812	69	223	5.32E-13	68.1016	cl07121	NIT superfamily	C	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#7816 - 	CGI_10016541	superfamily	219526	321	393	5.75E-06	46.4583	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#7817 - 	CGI_10016542	superfamily	243303	5	74	8.01E-43	135.825	cl03104	CKS superfamily	 - 	 - 	Cyclin-dependent kinase regulatory subunit; Cyclin-dependent kinase regulatory subunit.  
Q#7818 - 	CGI_10016543	superfamily	242166	61	177	3.50E-35	121.103	cl00881	SQR_QFR_TM superfamily	 - 	 - 	"Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQRs may reduce either high or low potential quinones while QFRs oxidize only low potential quinols. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit(s) containing the electron donor/acceptor (quinol or quinone). The reversible reduction of quinone is an essential feature of respiration, allowing the transfer of electrons between respiratory complexes. SQRs and QFRs can be classified into five types (A-E) according to the number of their hydrophobic subunits and heme groups. This classification is consistent with the characteristics and phylogeny of the catalytic and iron-sulfur subunits. Type E proteins, e.g. non-classical archael SQRs, contain atypical transmembrane subunits and are not included in this hierarchy. The heme and quinone binding sites reside in the transmembrane subunits. Although succinate oxidation and fumarate reduction are carried out by separate enzymes in most organisms, some bifunctional enzymes that exhibit both SQR and QFR activities exist."
Q#7819 - 	CGI_10016544	superfamily	222150	495	518	5.76E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7819 - 	CGI_10016544	superfamily	222150	691	714	0.0055524	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7819 - 	CGI_10016544	superfamily	222150	775	798	0.00854976	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7820 - 	CGI_10016545	superfamily	246748	138	433	4.85E-86	274.67	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#7821 - 	CGI_10016546	superfamily	241619	8	58	0.000210296	39.4844	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#7821 - 	CGI_10016546	superfamily	219525	210	256	0.00032888	38.5542	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7821 - 	CGI_10016546	superfamily	219525	352	391	0.000563738	37.7838	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7821 - 	CGI_10016546	superfamily	219525	176	222	0.000575661	37.7838	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7821 - 	CGI_10016546	superfamily	219525	318	364	0.00062967	37.7838	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7822 - 	CGI_10016547	superfamily	219525	302	348	0.000677902	37.7838	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7822 - 	CGI_10016547	superfamily	219525	251	285	0.0012864	37.0134	cl06646	GCC2_GCC3 superfamily	C	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7822 - 	CGI_10016547	superfamily	219525	387	433	0.00413851	35.4726	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7822 - 	CGI_10016547	superfamily	219525	200	239	0.00796748	34.7022	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7822 - 	CGI_10016547	superfamily	219525	337	377	0.00806189	34.7022	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7823 - 	CGI_10016548	superfamily	219525	128	167	0.00680749	32.7762	cl06646	GCC2_GCC3 superfamily	N	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#7824 - 	CGI_10003493	superfamily	244880	2	161	1.16E-18	78.7421	cl08263	TBP_TLF superfamily	 - 	 - 	"TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many equivalent positions, suggesting similar structure. However, TLFs contain distinct, conserved amino acids at several positions that distinguish them from TBP."
Q#7827 - 	CGI_10003497	superfamily	216939	9	55	5.92E-05	38.0277	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#7828 - 	CGI_10003498	superfamily	241564	30	99	7.98E-20	77.3059	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#7829 - 	CGI_10009367	superfamily	247725	1	48	1.44E-16	70.7275	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7836 - 	CGI_10009374	superfamily	241645	132	194	0.000493991	38.7874	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#7836 - 	CGI_10009374	superfamily	241645	524	603	1.36E-27	106.745	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#7836 - 	CGI_10009374	superfamily	241832	380	441	2.63E-07	49.4121	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#7837 - 	CGI_10009375	superfamily	243034	709	801	0.00152554	38.5152	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#7837 - 	CGI_10009375	superfamily	247743	265	411	0.00114792	39.4904	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#7838 - 	CGI_10009376	superfamily	247727	632	709	8.42E-05	41.6467	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#7839 - 	CGI_10009377	superfamily	243045	42	143	0.00238477	36.4572	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#7840 - 	CGI_10009378	superfamily	248458	51	207	4.17E-08	53.8569	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7840 - 	CGI_10009378	superfamily	248458	429	525	6.57E-08	53.0865	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#7841 - 	CGI_10009379	superfamily	244824	68	521	0	584.579	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#7842 - 	CGI_10009380	superfamily	246597	3	287	0	546.824	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#7843 - 	CGI_10021654	superfamily	222150	45	70	0.000236644	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7843 - 	CGI_10021654	superfamily	222150	130	154	0.00094706	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7843 - 	CGI_10021654	superfamily	222150	17	40	0.00165046	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7843 - 	CGI_10021654	superfamily	222150	101	126	0.00460294	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7843 - 	CGI_10021654	superfamily	222150	157	182	0.00956112	33.9045	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#7844 - 	CGI_10021655	superfamily	247639	98	343	2.17E-47	163.016	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#7846 - 	CGI_10021657	superfamily	241610	1	47	1.34E-12	58.0302	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#7847 - 	CGI_10021658	superfamily	243035	43	86	1.76E-12	58.4615	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7848 - 	CGI_10021659	superfamily	241584	44	113	8.94E-05	40.9427	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7848 - 	CGI_10021659	superfamily	241584	167	202	0.00487319	35.5499	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7849 - 	CGI_10021660	superfamily	241737	11	167	1.85E-91	266.332	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#7852 - 	CGI_10021663	superfamily	247757	19	233	3.82E-99	290.135	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#7853 - 	CGI_10021664	superfamily	247755	514	735	4.67E-107	341.407	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#7853 - 	CGI_10021664	superfamily	247755	1392	1610	6.15E-103	329.851	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#7854 - 	CGI_10021665	superfamily	243109	75	257	1.12E-98	291.813	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#7856 - 	CGI_10021668	superfamily	243066	28	137	2.42E-13	65.7165	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#7856 - 	CGI_10021668	superfamily	198867	170	253	2.65E-07	48.1064	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#7858 - 	CGI_10021670	superfamily	241563	72	113	0.000207369	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7860 - 	CGI_10021672	superfamily	144065	88	154	2.56E-29	106.986	cl02842	Ribosomal_S5 superfamily	 - 	 - 	"Ribosomal protein S5, N-terminal domain; Ribosomal protein S5, N-terminal domain.  "
Q#7860 - 	CGI_10021672	superfamily	190724	171	244	6.24E-23	89.7838	cl04231	Ribosomal_S5_C superfamily	 - 	 - 	"Ribosomal protein S5, C-terminal domain; Ribosomal protein S5, C-terminal domain.  "
Q#7861 - 	CGI_10021673	superfamily	247684	10	183	2.41E-18	81.0959	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7862 - 	CGI_10021674	superfamily	247684	8	181	6.73E-19	82.6367	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7863 - 	CGI_10021675	superfamily	247723	81	146	4.46E-24	97.2608	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7864 - 	CGI_10021676	superfamily	247723	170	245	2.04E-46	155.643	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#7866 - 	CGI_10021678	superfamily	243058	298	407	1.62E-12	64.6431	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7866 - 	CGI_10021678	superfamily	243058	416	520	0.000901558	38.0644	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7866 - 	CGI_10021678	superfamily	243058	101	208	0.00133556	37.6792	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7867 - 	CGI_10021679	superfamily	247683	2042	2096	5.10E-30	115.862	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#7867 - 	CGI_10021679	superfamily	247683	1830	1882	2.48E-26	105.125	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#7867 - 	CGI_10021679	superfamily	247683	1761	1813	7.87E-24	98.1808	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#7867 - 	CGI_10021679	superfamily	241622	5	80	1.16E-15	75.2958	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#7867 - 	CGI_10021679	superfamily	207673	1198	1244	2.72E-07	49.9273	cl02617	Sorb superfamily	 - 	 - 	Sorbin homologous domain; Sorbin homologous domain.  
Q#7869 - 	CGI_10021681	superfamily	241832	17	99	6.88E-19	75.2688	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#7870 - 	CGI_10021682	superfamily	241622	98	172	4.26E-16	74.9106	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#7874 - 	CGI_10021686	superfamily	247639	2	251	1.25E-39	139.904	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#7875 - 	CGI_10021687	superfamily	243058	197	294	2.37E-06	45.7684	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7875 - 	CGI_10021687	superfamily	248012	318	404	2.16E-19	83.396	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#7876 - 	CGI_10021688	superfamily	245815	3	198	1.40E-121	356.658	cl11961	ALDH-SF superfamily	N	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#7877 - 	CGI_10021689	superfamily	247684	11	381	3.67E-77	251.043	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#7878 - 	CGI_10021690	superfamily	247856	202	266	0.0053819	34.0605	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#7879 - 	CGI_10021691	superfamily	241832	1	69	5.04E-38	125.329	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#7880 - 	CGI_10021692	superfamily	241806	21	163	7.02E-85	248.4	cl00350	Ribosomal_S19 superfamily	 - 	 - 	Ribosomal protein S19; Ribosomal protein S19.  
Q#7881 - 	CGI_10021693	superfamily	247748	104	283	9.64E-93	275.704	cl17194	Oxidored_q6 superfamily	 - 	 - 	"NADH ubiquinone oxidoreductase, 20 Kd subunit; NADH ubiquinone oxidoreductase, 20 Kd subunit.  "
Q#7882 - 	CGI_10021694	superfamily	222681	117	273	3.83E-51	172.786	cl16800	PINIT superfamily	 - 	 - 	PINIT domain; The PINIT domain is a protein domain that is found in PIAS proteins. The PINIT domain is about 180 amino acids in length.
Q#7882 - 	CGI_10021694	superfamily	111745	318	367	1.99E-21	87.7433	cl17930	zf-MIZ superfamily	 - 	 - 	MIZ/SP-RING zinc finger; This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation.
Q#7882 - 	CGI_10021694	superfamily	207684	11	45	0.000109293	40.1624	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#7884 - 	CGI_10021696	superfamily	241616	2	78	1.13E-38	126.513	cl00109	MADS superfamily	 - 	 - 	"MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers.  Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals.  Also found in fungi."
Q#7886 - 	CGI_10021698	superfamily	241715	57	167	3.38E-37	125.841	cl00238	Frataxin superfamily	 - 	 - 	"Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet."
Q#7888 - 	CGI_10021700	superfamily	220372	155	557	0	533.953	cl12369	Det1 superfamily	 - 	 - 	"De-etiolated protein 1 Det1; This is the C-terminal conserved 400 residues of Det1 proteins of approximately 550 amino acids. Det1 (de-etiolated-1) is an essential negative regulator of plant light responses, and it is a component of the Arabidopsis CDD complex containing DDB1 and COP10 ubiquitin E2 variant. Mammalian Det1 forms stable DDD-E2 complexes, consisting of DDB1, DDA1 (DET1, DDB1 Associated 1), and a member of the UBE2E group of canonical ubiquitin conjugating enzymes and modulates Cul4A function."
Q#7889 - 	CGI_10021701	superfamily	241616	2	74	5.23E-37	129.594	cl00109	MADS superfamily	 - 	 - 	"MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers.  Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals.  Also found in fungi."
Q#7890 - 	CGI_10021702	superfamily	217293	8	218	4.65E-67	216.73	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#7890 - 	CGI_10021702	superfamily	202474	226	329	1.45E-06	48.0337	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#7891 - 	CGI_10021703	superfamily	243179	98	202	1.00E-19	81.3163	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#7894 - 	CGI_10005252	superfamily	243092	477	798	1.49E-69	232.225	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7894 - 	CGI_10005252	superfamily	191973	40	174	5.08E-56	188.726	cl07022	Striatin superfamily	 - 	 - 	"Striatin family; Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (pfam00400) repeat domain. It acts as a scaffold protein and is involved in signalling pathways."
Q#7895 - 	CGI_10005253	superfamily	192478	244	473	1.16E-123	378.654	cl10883	DUF2356 superfamily	 - 	 - 	Conserved protein (DUF2356); This is a 200 amino acid region of a family of proteins conserved from plants to humans. Some members have been putatively annotated as being integrator complex subunit 3 but this could not be confirmed. The function is unknown.
Q#7896 - 	CGI_10005254	superfamily	241739	233	552	1.30E-140	412.73	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#7896 - 	CGI_10005254	superfamily	245205	137	220	2.16E-37	133.128	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#7897 - 	CGI_10005255	superfamily	243083	502	587	6.28E-06	45.8472	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#7898 - 	CGI_10005256	superfamily	219924	103	150	0.000116039	40.4123	cl07276	eIF3_subunit superfamily	NC	 - 	Translation initiation factor eIF3 subunit; This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Q#7899 - 	CGI_10000309	superfamily	248100	47	105	7.33E-07	42.1412	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#7900 - 	CGI_10003551	superfamily	203101	95	246	6.90E-41	141.726	cl04785	Popeye superfamily	 - 	 - 	Popeye protein conserved region; The function of Popeye proteins is not well understood. They are predominantly expressed in cardiac and skeletal muscle. This family represents a conserved region which includes three potential transmembrane domains.
Q#7901 - 	CGI_10003553	superfamily	247097	196	232	0.00260149	35.8898	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#7902 - 	CGI_10003554	superfamily	247724	442	593	4.56E-57	191.251	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#7905 - 	CGI_10013565	superfamily	245055	14	512	1.41E-83	280.182	cl09326	MATE_like superfamily	 - 	 - 	"Multidrug and toxic compound extrusion family and similar proteins; The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria."
Q#7906 - 	CGI_10013566	superfamily	192033	443	677	2.93E-91	286.213	cl07158	DUF1741 superfamily	 - 	 - 	Domain of unknown function (DUF1741); This is a eukaryotic domain of unknown function.
Q#7907 - 	CGI_10013567	superfamily	243176	5	400	0	737.56	cl02777	chaperonin_like superfamily	C	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#7908 - 	CGI_10013568	superfamily	243176	1	218	6.17E-151	433.637	cl02777	chaperonin_like superfamily	N	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#7909 - 	CGI_10013569	superfamily	220364	65	180	8.93E-65	201.452	cl10716	Fra10Ac1 superfamily	 - 	 - 	"Folate-sensitive fragile site protein Fra10Ac1; This entry represents the full-length proteins in which, in higher eukaryotes, the nested domain EDSLL lies. Fra10Ac1 is a highly conserved protein, of unknown function that is nuclear and highly expressed in brain."
Q#7911 - 	CGI_10013571	superfamily	241574	792	978	1.93E-68	230.936	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#7911 - 	CGI_10013571	superfamily	241574	312	475	2.84E-33	130.013	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#7911 - 	CGI_10013571	superfamily	243066	1095	1188	1.36E-17	80.7393	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#7912 - 	CGI_10013572	superfamily	241574	96	170	1.28E-17	76.8557	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#7913 - 	CGI_10013573	superfamily	241574	54	270	3.99E-24	97.2713	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#7914 - 	CGI_10013574	superfamily	150445	17	133	1.19E-15	68.945	cl10753	Cid2 superfamily	 - 	 - 	Caffeine-induced death protein 2; Members of this family of proteins mediate the disruption of the DNA replication checkpoint (S-M checkpoint) mechanism caused by caffeine.
Q#7915 - 	CGI_10013575	superfamily	243058	253	364	3.64E-31	117.03	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7915 - 	CGI_10013575	superfamily	243058	116	238	1.38E-28	109.711	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7915 - 	CGI_10013575	superfamily	243058	329	447	1.06E-22	93.5331	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#7915 - 	CGI_10013575	superfamily	201951	4	102	3.32E-26	102.844	cl03339	IBB superfamily	 - 	 - 	"Importin beta binding domain; This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain."
Q#7916 - 	CGI_10013576	superfamily	217895	52	169	0.00650401	34.9263	cl04401	CD20 superfamily	 - 	 - 	"CD20-like family; This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton."
Q#7918 - 	CGI_10013578	superfamily	245040	4	61	5.62E-06	39.7648	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#7921 - 	CGI_10013581	superfamily	246680	749	827	0.000135758	41.2267	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#7921 - 	CGI_10013581	superfamily	248012	16	107	0.000628891	39.0981	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#7921 - 	CGI_10013581	superfamily	246680	300	378	0.00125006	38.1451	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#7923 - 	CGI_10000750	superfamily	241563	59	99	8.57E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7923 - 	CGI_10000750	superfamily	243092	306	406	0.000391374	41.1664	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7924 - 	CGI_10005358	superfamily	247058	70	263	1.02E-52	178.523	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#7924 - 	CGI_10005358	superfamily	205939	293	383	3.20E-43	149.933	cl18284	ECH_C superfamily	C	 - 	2-enoyl-CoA Hydratase C-terminal region; This is the C-terminal region of enoyl-CoA hydratase.
Q#7925 - 	CGI_10005359	superfamily	245206	11	199	2.69E-78	238.256	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#7928 - 	CGI_10005362	superfamily	193607	8	139	4.90E-72	214.358	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#7929 - 	CGI_10005363	superfamily	243161	3	60	1.08E-05	40.8406	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#7931 - 	CGI_10007727	superfamily	241818	103	238	4.83E-49	161.987	cl00366	PMSR superfamily	 - 	 - 	Peptide methionine sulfoxide reductase; This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine.
Q#7931 - 	CGI_10007727	superfamily	245009	4	117	3.04E-06	44.5809	cl09109	NTF2_like superfamily	 - 	 - 	"Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example,  nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and  binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea and eukaryotes."
Q#7932 - 	CGI_10007728	superfamily	218201	434	559	3.97E-40	143.014	cl07855	Tsg superfamily	 - 	 - 	"Twisted gastrulation (Tsg) protein conserved region; Tsg was identified in Drosophila as being required to specify the dorsal-most structures in the embryo, for example amnioserosa. Biochemical experiments have revealed three key properties of Tsg: it can synergistically inhibit Dpp/BMP action in both Drosophila and vertebrates by forming a tripartite complete between itself, SOG/chordin and a BMP ligand; Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilisation; Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling."
Q#7932 - 	CGI_10007728	superfamily	201778	8	114	1.86E-13	67.619	cl18219	GFO_IDH_MocA superfamily	 - 	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#7936 - 	CGI_10007732	superfamily	241833	130	273	4.88E-52	172.71	cl00389	SIS superfamily	 - 	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#7936 - 	CGI_10007732	superfamily	241833	300	383	4.84E-37	133.108	cl00389	SIS superfamily	C	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#7937 - 	CGI_10007733	superfamily	241833	338	529	5.92E-86	266.002	cl00389	SIS superfamily	 - 	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#7937 - 	CGI_10007733	superfamily	241833	130	291	9.38E-69	220.86	cl00389	SIS superfamily	 - 	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#7939 - 	CGI_10007735	superfamily	217905	125	657	8.56E-96	306.418	cl04405	Gaa1 superfamily	 - 	 - 	"Gaa1-like, GPI transamidase component; GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to newly synthesised proteins."
Q#7940 - 	CGI_10007736	superfamily	245836	222	395	3.98E-69	220.901	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#7940 - 	CGI_10007736	superfamily	244947	397	473	1.61E-36	129.946	cl08424	OBF_DNA_ligase_family superfamily	 - 	 - 	"The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain."
Q#7940 - 	CGI_10007736	superfamily	204434	104	128	2.71E-06	44.4929	cl10963	zf-CCHH superfamily	 - 	 - 	"Zinc-finger (CX5CX6HX5H) motif; This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism."
Q#7940 - 	CGI_10007736	superfamily	204434	5	27	0.000101166	39.8705	cl10963	zf-CCHH superfamily	 - 	 - 	"Zinc-finger (CX5CX6HX5H) motif; This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism."
Q#7941 - 	CGI_10007737	superfamily	220624	25	114	3.04E-09	51.9965	cl10881	Nefa_Nip30_N superfamily	 - 	 - 	"N-terminal domain of NEFA-interacting nuclear protein NIP30; This is a the N-terminal 100 amino acids of a family of proteins conserved from plants to humans. The full-length protein has putatively been called NEFA-interacting nuclear protein NIP30, however no reference could be found to confirm this."
Q#7942 - 	CGI_10007738	superfamily	241662	13	113	6.10E-30	104.95	cl00180	RabGEF superfamily	 - 	 - 	"Nucleotide exchange factor for Rab-like small GTPases (RabGEF), Mss4 type; RabGEF positely regulates the function of  Rab GTPase by promoting exchange of GDP for GTP; members of the Rab subfamily of Ras GTPases are important in vesicular transport;"
Q#7944 - 	CGI_10007740	superfamily	241865	1	151	4.37E-33	119.358	cl00440	BtpA superfamily	N	 - 	"BtpA family; The BtpA protein is tightly associated with the thylakoid membranes, where it stabilises the reaction centre proteins of photosystem I."
Q#7945 - 	CGI_10007741	superfamily	241572	10	91	2.35E-16	71.886	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#7945 - 	CGI_10007741	superfamily	241572	142	195	6.26E-08	49.1634	cl00050	CYCLIN superfamily	NC	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#7947 - 	CGI_10007743	superfamily	248401	226	516	2.62E-39	144.946	cl17847	Rsm22 superfamily	 - 	 - 	"Mitochondrial small ribosomal subunit Rsm22; Rsm22 has been identified as a mitochondrial small ribosomal subunit and is a methyltransferase. In Schizosaccharomyces pombe, Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria."
Q#7948 - 	CGI_10007744	superfamily	243072	64	194	2.96E-28	111.321	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7948 - 	CGI_10007744	superfamily	243072	137	296	6.01E-25	102.077	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7948 - 	CGI_10007744	superfamily	243072	248	364	5.30E-20	87.8242	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7948 - 	CGI_10007744	superfamily	247057	700	759	7.11E-27	105.342	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#7948 - 	CGI_10007744	superfamily	243072	39	67	0.000477809	39.0744	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#7949 - 	CGI_10007745	superfamily	242228	3	52	8.04E-18	69.9729	cl00977	Nop10p superfamily	 - 	 - 	"Nucleolar RNA-binding protein, Nop10p family; Nop10p is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10p is probably necessary for the stability of these RNPs."
Q#7951 - 	CGI_10005257	superfamily	221536	410	509	5.62E-06	46.6337	cl13732	SBF2 superfamily	NC	 - 	"Myotubularin protein; This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with pfam02141, pfam03456, pfam03455. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease."
Q#7952 - 	CGI_10005258	superfamily	204041	19	166	1.08E-40	137.328	cl07367	GLTP superfamily	 - 	 - 	Glycolipid transfer protein (GLTP); GLTP is a cytosolic protein that catalyzes the intermembrane transfer of glycolipids.
Q#7954 - 	CGI_10005260	superfamily	247725	11	130	1.21E-70	214.785	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7955 - 	CGI_10005261	superfamily	245201	84	412	1.16E-150	460.823	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7955 - 	CGI_10005261	superfamily	227318	458	518	0.0091015	38.3596	cl09222	COG4985 superfamily	N	 - 	"ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]"
Q#7956 - 	CGI_10005262	superfamily	243100	56	104	3.50E-06	44.2179	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#7957 - 	CGI_10005263	superfamily	247725	24	123	0.00150491	34.8317	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#7958 - 	CGI_10005264	superfamily	199156	141	156	0.000332125	36.6524	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#7960 - 	CGI_10006840	superfamily	219603	532	737	3.59E-34	132.572	cl06744	GCFC superfamily	 - 	 - 	"GC-rich sequence DNA-binding factor-like protein; Sequences found in this family are similar to a region of a human GC-rich sequence DNA-binding factor homolog. This is thought to be a protein involved in transcriptional regulation due to partial homologies to a transcription repressor and histone-interacting protein. This family also contains tuftelin interacting protein 11 which has been identified as both a nuclear and cytoplasmic protein, and has been implicated in the secretory pathway. Sip1, a septin interacting protein is also a member of this family."
Q#7961 - 	CGI_10006841	superfamily	245201	22	329	2.71E-60	204.307	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7963 - 	CGI_10006843	superfamily	245225	1	361	1.10E-78	259.896	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#7963 - 	CGI_10006843	superfamily	247986	378	497	2.53E-12	66.2426	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#7963 - 	CGI_10006843	superfamily	247986	613	746	7.81E-06	46.5974	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#7964 - 	CGI_10006844	superfamily	245225	10	389	2.17E-68	235.244	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#7964 - 	CGI_10006844	superfamily	247986	1085	1189	3.58E-11	63.5462	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#7964 - 	CGI_10006844	superfamily	247986	426	508	1.05E-10	62.0054	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#7964 - 	CGI_10006844	superfamily	197504	631	765	2.96E-47	167.466	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#7964 - 	CGI_10006844	superfamily	197504	1312	1445	7.16E-46	163.614	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#7964 - 	CGI_10006844	superfamily	245225	938	1088	1.36E-11	66.9501	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#7965 - 	CGI_10006845	superfamily	245225	41	422	2.95E-77	256.43	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#7965 - 	CGI_10006845	superfamily	247986	452	554	2.34E-14	72.791	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#7965 - 	CGI_10006845	superfamily	197504	669	801	3.93E-43	153.984	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#7966 - 	CGI_10006846	superfamily	197504	1	96	5.65E-34	119.702	cl18192	PBPe superfamily	N	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#7967 - 	CGI_10027629	superfamily	247792	23	75	1.24E-06	46.2848	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7968 - 	CGI_10027630	superfamily	247792	20	72	7.14E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#7968 - 	CGI_10027630	superfamily	241563	169	197	0.00503192	35.5328	cl00034	BBOX superfamily	C	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7969 - 	CGI_10027631	superfamily	246709	4	30	0.000369043	36.299	cl14782	RNase_H superfamily	N	 - 	"RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription."
Q#7972 - 	CGI_10027635	superfamily	247637	2	311	2.08E-139	404.338	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#7973 - 	CGI_10027636	superfamily	241600	132	203	2.50E-14	67.3022	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7974 - 	CGI_10027637	superfamily	241600	8	137	1.32E-31	113.104	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#7975 - 	CGI_10027638	superfamily	243035	107	183	1.87E-05	41.0662	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7975 - 	CGI_10027638	superfamily	241776	93	116	0.00639491	34.859	cl00315	RPS2 superfamily	NC	 - 	"Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane and subsequent signalling events, and has been linked to several diseases. Some evidence also suggests that the precursor of 67LR, 37LRP is also present in the nucleus in animals, where it appears associated with histones."
Q#7977 - 	CGI_10027640	superfamily	222225	19	130	6.41E-07	45.9764	cl18652	DoxX_2 superfamily	 - 	 - 	DoxX-like family; This family of uncharacterized proteins are related to DoxX pfam07681.
Q#7979 - 	CGI_10027642	superfamily	241563	123	162	5.31E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7980 - 	CGI_10027643	superfamily	241563	83	121	0.000161536	39.6279	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7980 - 	CGI_10027643	superfamily	242067	174	300	0.00353518	38.4879	cl00751	DUF155 superfamily	NC	 - 	"Uncharacterized ACR, YagE family COG1723; Uncharacterized ACR, YagE family COG1723.  "
Q#7980 - 	CGI_10027643	superfamily	243092	344	455	0.00558764	37.6996	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#7981 - 	CGI_10027644	superfamily	241563	117	156	4.11E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7982 - 	CGI_10027645	superfamily	216363	77	164	2.28E-16	70.9622	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#7984 - 	CGI_10027647	superfamily	241563	71	110	7.90E-07	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#7985 - 	CGI_10027648	superfamily	242611	36	286	1.76E-119	350.642	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#7986 - 	CGI_10027649	superfamily	220608	36	155	5.16E-34	128.193	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#7987 - 	CGI_10027650	superfamily	220608	36	114	9.99E-19	82.739	cl10859	G8 superfamily	C	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#7990 - 	CGI_10027653	superfamily	243035	30	97	1.40E-11	59.1705	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7990 - 	CGI_10027653	superfamily	243035	127	249	8.91E-11	56.8593	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7991 - 	CGI_10027654	superfamily	243035	51	160	3.41E-12	59.1705	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#7992 - 	CGI_10027655	superfamily	245596	53	354	5.47E-139	405.82	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#7992 - 	CGI_10027655	superfamily	247085	368	442	3.21E-05	42.4927	cl15820	RICIN superfamily	C	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#7993 - 	CGI_10027656	superfamily	245201	1	165	1.70E-41	142.376	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#7994 - 	CGI_10027657	superfamily	241584	175	267	2.61E-05	42.0983	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#7994 - 	CGI_10027657	superfamily	248016	117	174	0.00111516	36.9247	cl17462	T5orf172 superfamily	C	 - 	T5orf172 domain; This domain was identified by Iyer and colleagues.
Q#7999 - 	CGI_10027662	superfamily	243092	160	406	7.60E-17	78.916	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8000 - 	CGI_10027663	superfamily	246925	17	213	3.64E-06	46.1946	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#8001 - 	CGI_10027664	superfamily	241611	62	205	0.00349796	37.368	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#8002 - 	CGI_10027665	superfamily	245814	37	98	1.96E-05	44.4023	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8002 - 	CGI_10027665	superfamily	216347	1190	1612	3.73E-71	246.294	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#8002 - 	CGI_10027665	superfamily	245814	472	543	8.70E-08	51.7373	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8002 - 	CGI_10027665	superfamily	245814	558	623	6.27E-05	43.1132	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8002 - 	CGI_10027665	superfamily	245814	692	752	0.00383486	37.7204	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8003 - 	CGI_10027666	superfamily	245814	88	174	4.52E-07	44.3516	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8003 - 	CGI_10027666	superfamily	245814	12	70	5.75E-07	43.9348	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8004 - 	CGI_10027667	superfamily	245814	179	243	0.000574273	37.5604	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8004 - 	CGI_10027667	superfamily	245814	80	146	0.00325511	35.4092	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8008 - 	CGI_10027671	superfamily	245599	409	608	8.57E-84	263.772	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#8008 - 	CGI_10027671	superfamily	207662	143	220	4.11E-51	171.878	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#8010 - 	CGI_10027673	superfamily	243094	81	442	3.83E-115	369.364	cl02569	RasGAP superfamily	 - 	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#8010 - 	CGI_10027673	superfamily	128469	1595	1696	2.79E-13	69.0212	cl17971	VPS9 superfamily	 - 	 - 	Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
Q#8011 - 	CGI_10027674	superfamily	243039	367	549	3.77E-80	251.791	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#8011 - 	CGI_10027674	superfamily	190233	187	226	1.32E-05	43.2118	cl08341	zf-TRAF superfamily	C	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#8011 - 	CGI_10027674	superfamily	247792	43	82	0.00178233	36.7182	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8012 - 	CGI_10027675	superfamily	243072	19	100	1.70E-14	64.7122	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8013 - 	CGI_10027676	superfamily	241846	248	319	4.30E-20	87.851	cl00409	tgt superfamily	N	 - 	queuine tRNA-ribosyltransferase; Provisional
Q#8013 - 	CGI_10027676	superfamily	241846	86	143	0.00404403	37.0064	cl00409	tgt superfamily	NC	 - 	queuine tRNA-ribosyltransferase; Provisional
Q#8014 - 	CGI_10027677	superfamily	247723	147	221	4.41E-34	119.68	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#8015 - 	CGI_10027678	superfamily	243092	823	1074	2.41E-44	163.275	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8015 - 	CGI_10027678	superfamily	128914	44	95	8.05E-10	56.4254	cl15352	CTLH superfamily	 - 	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#8016 - 	CGI_10027679	superfamily	243082	376	604	1.99E-43	158.22	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#8016 - 	CGI_10027679	superfamily	245879	735	810	3.31E-17	78.5541	cl12116	DUSP superfamily	 - 	 - 	DUSP domain; The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Q#8016 - 	CGI_10027679	superfamily	245220	32	92	1.63E-16	75.9042	cl09957	zf-UBP superfamily	 - 	 - 	Zn-finger in ubiquitin-hydrolases and other protein; Zn-finger in ubiquitin-hydrolases and other protein.  
Q#8016 - 	CGI_10027679	superfamily	245879	631	693	8.40E-11	59.7935	cl12116	DUSP superfamily	 - 	 - 	DUSP domain; The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Q#8016 - 	CGI_10027679	superfamily	243082	174	209	7.48E-05	44.4986	cl02553	Peptidase_C19 superfamily	NC	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#8017 - 	CGI_10027680	superfamily	241574	482	707	1.43E-93	298.731	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#8017 - 	CGI_10027680	superfamily	241574	771	1001	1.55E-40	150.429	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#8017 - 	CGI_10027680	superfamily	238012	167	205	0.000368608	39.645	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8018 - 	CGI_10027681	superfamily	241568	2327	2384	1.30E-07	51.3096	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#8018 - 	CGI_10027681	superfamily	241568	2131	2183	1.94E-07	50.9244	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#8018 - 	CGI_10027681	superfamily	241568	2277	2323	0.000828701	40.1388	cl00043	CCP superfamily	C	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#8018 - 	CGI_10027681	superfamily	243061	1392	1493	1.52E-38	142.096	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	291	392	1.66E-38	142.096	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	513	613	1.95E-38	141.711	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	1282	1384	6.01E-38	140.555	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	1063	1161	8.41E-38	140.17	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	621	722	1.97E-37	139.014	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	182	282	3.49E-37	138.244	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	1737	1838	3.83E-37	138.244	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	952	1052	4.72E-37	137.859	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	1499	1601	1.51E-33	127.843	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	1171	1274	5.58E-33	126.303	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	1607	1706	5.38E-32	123.221	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	400	503	5.69E-32	123.221	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	839	943	2.91E-31	121.295	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	728	829	5.16E-31	120.525	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	243061	73	174	6.91E-30	117.058	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	111397	2193	2272	2.26E-17	80.463	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#8018 - 	CGI_10027681	superfamily	243061	11	64	2.13E-14	72.3746	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#8018 - 	CGI_10027681	superfamily	214531	1999	2041	1.86E-10	59.1524	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#8018 - 	CGI_10027681	superfamily	215683	1978	2015	8.11E-08	51.7871	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#8018 - 	CGI_10027681	superfamily	214531	1868	1910	0.000108978	42.5889	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#8018 - 	CGI_10027681	superfamily	214531	1922	1951	0.00132555	39.1221	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#8022 - 	CGI_10027685	superfamily	247724	16	87	7.02E-15	70.6323	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8024 - 	CGI_10027687	superfamily	241868	1178	1338	2.71E-52	183.476	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#8025 - 	CGI_10027688	superfamily	241696	123	438	6.47E-159	455.166	cl00218	Glyco_hydrolase_16 superfamily	 - 	 - 	"glycosyl hydrolase family 16; The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues."
Q#8026 - 	CGI_10027689	superfamily	241696	96	416	4.08E-165	470.189	cl00218	Glyco_hydrolase_16 superfamily	 - 	 - 	"glycosyl hydrolase family 16; The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues."
Q#8029 - 	CGI_10027692	superfamily	149426	344	493	1.39E-09	55.8653	cl18038	SEFIR superfamily	 - 	 - 	"SEFIR domain; This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways."
Q#8030 - 	CGI_10027693	superfamily	247755	31	239	7.24E-63	209.435	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8030 - 	CGI_10027693	superfamily	247789	372	578	1.17E-31	122.367	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#8032 - 	CGI_10027695	superfamily	238076	33	160	5.85E-79	244.251	cl18938	PAX superfamily	 - 	 - 	Paired Box domain
Q#8032 - 	CGI_10027695	superfamily	241599	269	324	2.89E-22	89.9952	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#8034 - 	CGI_10027697	superfamily	247057	200	260	5.22E-25	97.3757	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#8034 - 	CGI_10027697	superfamily	247057	129	189	2.61E-22	90.05	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#8034 - 	CGI_10027697	superfamily	247725	351	399	1.04E-18	82.2987	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8034 - 	CGI_10027697	superfamily	247725	393	418	2.58E-09	54.9495	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8035 - 	CGI_10027698	superfamily	243072	54	177	9.82E-36	133.278	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8035 - 	CGI_10027698	superfamily	243072	191	220	4.53E-05	42.156	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8036 - 	CGI_10027699	superfamily	242542	51	235	8.20E-37	129.658	cl01505	YhhN superfamily	 - 	 - 	"YhhN-like protein; The members of this family are similar to the hypothetical protein yhhN expressed by E. coli. Many of the members of this family are annotated as being possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues."
Q#8037 - 	CGI_10015249	superfamily	217293	1	173	7.08E-26	103.096	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#8037 - 	CGI_10015249	superfamily	202474	180	214	0.00393738	36.8629	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#8038 - 	CGI_10015250	superfamily	217293	24	224	4.72E-36	132.371	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#8038 - 	CGI_10015250	superfamily	202474	249	327	1.56E-07	50.3449	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#8039 - 	CGI_10015251	superfamily	191444	73	144	2.97E-11	55.7933	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#8040 - 	CGI_10015252	superfamily	247787	1	186	1.74E-102	297.573	cl17233	RecA-like_NTPases superfamily	N	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#8041 - 	CGI_10015253	superfamily	247765	15	44	3.42E-19	76.9507	cl17211	RecA superfamily	C	 - 	recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyzes an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination.
Q#8042 - 	CGI_10015254	superfamily	246680	261	312	0.00561802	34.288	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8044 - 	CGI_10015256	superfamily	245456	947	1262	1.07E-151	463.335	cl10970	AP_MHD_Cterm superfamily	 - 	 - 	"C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15."
Q#8045 - 	CGI_10015257	superfamily	245201	216	436	3.94E-14	72.2693	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8045 - 	CGI_10015257	superfamily	247792	110	151	0.00611552	35.9478	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8045 - 	CGI_10015257	superfamily	247792	18	59	0.00611552	35.9478	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8046 - 	CGI_10015258	superfamily	247805	566	709	1.91E-16	78.5332	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#8046 - 	CGI_10015258	superfamily	247905	821	945	7.06E-06	46.0769	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#8046 - 	CGI_10015258	superfamily	243778	1032	1122	1.64E-34	129.266	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#8046 - 	CGI_10015258	superfamily	219532	1161	1308	1.96E-21	91.9922	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#8046 - 	CGI_10015258	superfamily	245716	304	324	0.000528028	39.5349	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#8047 - 	CGI_10015259	superfamily	217380	62	342	1.91E-45	162.879	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#8047 - 	CGI_10015259	superfamily	248097	447	579	4.05E-19	83.8538	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#8048 - 	CGI_10015260	superfamily	247986	14	103	7.52E-10	56.2274	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#8049 - 	CGI_10015261	superfamily	241749	83	217	1.70E-18	78.5817	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#8060 - 	CGI_10015272	superfamily	241563	61	97	1.31E-05	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8062 - 	CGI_10015274	superfamily	245882	25	407	1.09E-180	516.844	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#8065 - 	CGI_10016677	superfamily	241563	60	99	9.45E-06	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8065 - 	CGI_10016677	superfamily	243092	301	452	0.00871822	36.9292	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8068 - 	CGI_10016680	superfamily	241563	13	41	0.00115205	37.3167	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8070 - 	CGI_10016682	superfamily	218231	248	367	4.44E-25	99.6602	cl04708	ELMO_CED12 superfamily	C	 - 	"ELMO/CED-12 family; This family represents a conserved domain which is found in a number of eukaryotic proteins including CED-12, ELMO I and ELMO II. ELMO1 is a component of signalling pathways that regulate phagocytosis and cell migration and is the mammalian orthologue of the C. elegans gene, ced-12. CED-12 is required for the engulfment of dying cells and cell migration. In mammalian cells, ELMO1 interacts with Dock180 as part of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. ELMO1 is ubiquitously expressed, although its expression is highest in the spleen, an organ rich in immune cells. ELMO1 has a PH domain and a polyproline sequence motif at its C terminus which are not present in this alignment."
Q#8071 - 	CGI_10016683	superfamily	218028	177	311	6.73E-10	57.7075	cl04479	AAA_4 superfamily	 - 	 - 	"Divergent AAA domain; This family is related to the pfam00004 family, and presumably has the same function (ATP-binding)."
Q#8073 - 	CGI_10016685	superfamily	110440	216	242	0.00739465	33.5353	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8074 - 	CGI_10016686	superfamily	245819	56	199	2.69E-49	160.052	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#8074 - 	CGI_10016686	superfamily	219526	1	42	2.85E-05	41.8359	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8075 - 	CGI_10016687	superfamily	245864	31	490	4.32E-102	316.528	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8076 - 	CGI_10016688	superfamily	245864	31	459	2.18E-99	308.438	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8078 - 	CGI_10016690	superfamily	243072	193	325	6.02E-25	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8078 - 	CGI_10016690	superfamily	243072	49	219	3.14E-23	94.7578	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8078 - 	CGI_10016690	superfamily	243073	440	479	7.78E-09	51.7021	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#8080 - 	CGI_10016692	superfamily	241583	188	311	2.27E-25	105.398	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8080 - 	CGI_10016692	superfamily	243060	499	586	0.00123788	38.1288	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#8081 - 	CGI_10016693	superfamily	241583	551	681	2.35E-25	105.398	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8083 - 	CGI_10016695	superfamily	241583	180	411	1.45E-24	102.702	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8083 - 	CGI_10016695	superfamily	243060	596	656	6.82E-05	41.9808	cl02507	SEA superfamily	N	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#8083 - 	CGI_10016695	superfamily	216572	8	122	0.0043289	36.8691	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#8085 - 	CGI_10016697	superfamily	247724	9	171	5.20E-60	188.503	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8087 - 	CGI_10016699	superfamily	207794	2	194	7.53E-59	193.962	cl02948	GH20_hexosaminidase superfamily	N	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#8087 - 	CGI_10016699	superfamily	191182	277	341	0.000523538	38.051	cl04917	Nsp1_C superfamily	C	 - 	Nsp1-like C-terminal region; This family probably forms a coiled-coil. This important region of Nsp1 is involved in binding Nup82.
Q#8089 - 	CGI_10016701	superfamily	247725	131	216	1.34E-42	141.66	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8089 - 	CGI_10016701	superfamily	246908	4	94	1.08E-32	115.653	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#8090 - 	CGI_10016702	superfamily	246680	91	168	1.49E-14	65.0494	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8091 - 	CGI_10016703	superfamily	243035	31	151	1.39E-24	93.0681	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8094 - 	CGI_10016730	superfamily	241563	59	98	2.85E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8094 - 	CGI_10016730	superfamily	191851	98	209	0.000546105	39.9207	cl06708	DUF1640 superfamily	 - 	 - 	Protein of unknown function (DUF1640); This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Q#8094 - 	CGI_10016730	superfamily	110440	476	502	0.00175327	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8094 - 	CGI_10016730	superfamily	110440	517	544	0.00859854	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8096 - 	CGI_10016732	superfamily	243100	176	229	8.92E-17	71.4909	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#8097 - 	CGI_10016733	superfamily	204198	35	118	2.32E-17	78.0154	cl07820	DUF1981 superfamily	 - 	 - 	Domain of unknown function (DUF1981); Members of this family of functionally uncharacterized domains are found in various plant and yeast protein transport proteins.
Q#8098 - 	CGI_10016734	superfamily	220692	41	354	1.75E-22	95.3489	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#8103 - 	CGI_10016739	superfamily	241563	73	110	7.63E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8103 - 	CGI_10016739	superfamily	128778	117	208	0.000392441	39.1703	cl17972	BBC superfamily	C	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#8104 - 	CGI_10016740	superfamily	128778	63	172	2.70E-08	51.8819	cl17972	BBC superfamily	C	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#8104 - 	CGI_10016740	superfamily	241563	19	56	0.000183617	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8105 - 	CGI_10016741	superfamily	241810	157	211	1.88E-28	103.749	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#8105 - 	CGI_10016741	superfamily	189761	76	152	8.02E-36	123.376	cl03010	Ribosomal_S4e superfamily	 - 	 - 	Ribosomal family S4e; Ribosomal family S4e.  
Q#8105 - 	CGI_10016741	superfamily	191938	1	22	4.42E-06	42.2606	cl06900	RS4NT superfamily	N	 - 	RS4NT (NUC023) domain; This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains.
Q#8106 - 	CGI_10016742	superfamily	222150	213	239	1.06E-05	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8106 - 	CGI_10016742	superfamily	222150	243	270	0.000108897	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8106 - 	CGI_10016742	superfamily	222150	154	181	0.00734424	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8107 - 	CGI_10016743	superfamily	244875	99	194	3.04E-07	48.1668	cl08255	Na_K-ATPase superfamily	NC	 - 	Sodium / potassium ATPase beta chain; Sodium / potassium ATPase beta chain.  
Q#8114 - 	CGI_10011342	superfamily	248097	24	159	4.66E-14	64.5938	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#8123 - 	CGI_10020879	superfamily	241564	74	141	4.46E-26	99.2623	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#8123 - 	CGI_10020879	superfamily	247792	312	351	0.000449614	37.4252	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8124 - 	CGI_10020880	superfamily	241600	35	134	5.48E-41	137.372	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8125 - 	CGI_10020881	superfamily	241600	370	566	2.35E-83	261.406	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8129 - 	CGI_10020885	superfamily	219542	48	157	2.57E-40	145.847	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#8129 - 	CGI_10020885	superfamily	215896	167	349	3.47E-20	88.8912	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#8129 - 	CGI_10020885	superfamily	219541	820	872	2.40E-14	71.7307	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#8129 - 	CGI_10020885	superfamily	215896	566	635	8.08E-07	48.8304	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#8129 - 	CGI_10020885	superfamily	219541	534	562	8.81E-05	42.0703	cl18516	Cu-oxidase_2 superfamily	NC	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#8130 - 	CGI_10020886	superfamily	245847	42	86	6.57E-06	41.003	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#8132 - 	CGI_10020888	superfamily	241574	94	300	4.35E-79	248.27	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#8134 - 	CGI_10020890	superfamily	246598	1273	1523	1.17E-171	517.565	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#8134 - 	CGI_10020890	superfamily	152569	966	1196	2.69E-157	478.424	cl13557	PRP8_domainIV superfamily	 - 	 - 	"PRP8 domain IV core; This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with pfam10597, pfam10596, pfam10598, pfam08083, pfam08082, pfam01398, pfam08084. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core."
Q#8134 - 	CGI_10020890	superfamily	151125	648	807	1.10E-107	339.066	cl18045	U6-snRNA_bdg superfamily	 - 	 - 	"U6-snRNA interacting domain of PrP8; This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor."
Q#8134 - 	CGI_10020890	superfamily	119117	414	549	3.05E-88	284.205	cl11217	U5_2-snRNA_bdg superfamily	 - 	 - 	"U5-snRNA binding site 2 of PrP8; The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor."
Q#8134 - 	CGI_10020890	superfamily	192639	192	285	1.60E-40	146.619	cl11218	RRM_4 superfamily	 - 	 - 	"RNA recognition motif of the spliceosomal PrP8; The large RNA-protein complex of the spliceosome catalyzes pre-mRNA splicing. One of the most conserved core proteins is PrP8 which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa. The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RRM are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain."
Q#8135 - 	CGI_10020891	superfamily	243116	713	1078	0	645.143	cl02626	DNA_pol_A superfamily	 - 	 - 	"Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase  beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains."
Q#8135 - 	CGI_10020891	superfamily	243116	414	456	1.66E-11	66.1885	cl02626	DNA_pol_A superfamily	C	 - 	"Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase  beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains."
Q#8135 - 	CGI_10020891	superfamily	245226	252	285	0.000118206	42.2877	cl10012	DnaQ_like_exo superfamily	NC	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#8137 - 	CGI_10020893	superfamily	227462	20	135	2.76E-35	122.027	cl18814	COG5133 superfamily	N	 - 	Uncharacterized conserved protein [Function unknown]
Q#8140 - 	CGI_10000860	superfamily	243072	178	285	0.00580601	35.8223	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8143 - 	CGI_10026580	superfamily	110440	484	508	0.00237925	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8143 - 	CGI_10026580	superfamily	217316	111	191	0.00397012	35.68	cl03832	DUF234 superfamily	 - 	 - 	Archaea bacterial proteins of unknown function; Archaea bacterial proteins of unknown function.  
Q#8146 - 	CGI_10026583	superfamily	238012	112	145	0.000753652	36.5634	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8150 - 	CGI_10026587	superfamily	241622	1418	1496	1.60E-16	77.607	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#8150 - 	CGI_10026587	superfamily	241622	781	853	1.07E-13	69.5178	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#8150 - 	CGI_10026587	superfamily	241622	686	767	1.64E-12	66.051	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#8150 - 	CGI_10026587	superfamily	241622	1552	1630	3.54E-07	50.2579	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#8150 - 	CGI_10026587	superfamily	247683	1652	1712	5.25E-17	78.5354	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8150 - 	CGI_10026587	superfamily	247744	1812	1970	7.15E-16	78.1035	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#8150 - 	CGI_10026587	superfamily	246680	6	89	6.48E-05	43.3288	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8150 - 	CGI_10026587	superfamily	247746	468	576	0.00368576	39.7996	cl17192	ATP-synt_B superfamily	C	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#8151 - 	CGI_10026588	superfamily	243172	54	412	1.63E-122	373.261	cl02773	VKG_Carbox superfamily	N	 - 	"Vitamin K-dependent gamma-carboxylase; Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl carboxylase post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase."
Q#8151 - 	CGI_10026588	superfamily	247772	464	514	0.0076315	34.9132	cl17218	Cupin_2 superfamily	N	 - 	Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).
Q#8152 - 	CGI_10026589	superfamily	112833	94	221	3.26E-65	210.67	cl04372	DUF367 superfamily	 - 	 - 	Domain of unknown function (DUF367); Domain of unknown function (DUF367).  
Q#8152 - 	CGI_10026589	superfamily	112833	341	468	3.26E-65	210.67	cl04372	DUF367 superfamily	 - 	 - 	Domain of unknown function (DUF367); Domain of unknown function (DUF367).  
Q#8152 - 	CGI_10026589	superfamily	217870	57	90	2.53E-09	53.6549	cl04386	RLI superfamily	 - 	 - 	"Possible Fer4-like domain in RNase L inhibitor, RLI; Possible metal-binding domain in endoribonuclease RNase L inhibitor. Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, pfam00037. Also often found adjacent to the DUF367 domain pfam04034 in uncharacterized proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons, and could possibly play a more general role in the regulation of RNA stability in mammalian cells. Inhibitory activity requires concentration-dependent association of RLI with RNase L."
Q#8152 - 	CGI_10026589	superfamily	217870	304	337	8.43E-09	52.1141	cl04386	RLI superfamily	 - 	 - 	"Possible Fer4-like domain in RNase L inhibitor, RLI; Possible metal-binding domain in endoribonuclease RNase L inhibitor. Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, pfam00037. Also often found adjacent to the DUF367 domain pfam04034 in uncharacterized proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons, and could possibly play a more general role in the regulation of RNA stability in mammalian cells. Inhibitory activity requires concentration-dependent association of RLI with RNase L."
Q#8153 - 	CGI_10026590	superfamily	219817	448	629	6.40E-18	83.0512	cl07129	Xpo1 superfamily	 - 	 - 	"Exportin 1-like protein; The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus."
Q#8153 - 	CGI_10026590	superfamily	244509	41	165	2.51E-10	60.2335	cl06793	PRKCSH superfamily	 - 	 - 	"Glucosidase II beta subunit-like protein; The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain."
Q#8153 - 	CGI_10026590	superfamily	243689	376	442	9.18E-07	48.3937	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#8154 - 	CGI_10026591	superfamily	245671	38	95	0.00363708	35.3016	cl11522	Tom22 superfamily	NC	 - 	"Mitochondrial import receptor subunit Tom22; The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins. The N terminal region of Tom22 has been shown to have chaperone-like activity, and the C terminal region faces the intermembrane face."
Q#8154 - 	CGI_10026591	superfamily	245671	118	175	0.00363708	35.3016	cl11522	Tom22 superfamily	NC	 - 	"Mitochondrial import receptor subunit Tom22; The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins. The N terminal region of Tom22 has been shown to have chaperone-like activity, and the C terminal region faces the intermembrane face."
Q#8155 - 	CGI_10026592	superfamily	191444	46	124	8.93E-07	42.6965	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#8156 - 	CGI_10026593	superfamily	216686	172	354	4.38E-47	160.566	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#8157 - 	CGI_10026594	superfamily	243092	201	477	2.58E-43	155.956	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8158 - 	CGI_10026595	superfamily	242899	27	176	5.23E-54	170.819	cl02135	TRAPP superfamily	 - 	 - 	"Transport protein particle (TRAPP) component; TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterized TRAPP proteins and has a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi."
Q#8159 - 	CGI_10026596	superfamily	241583	236	447	8.39E-91	291.064	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8159 - 	CGI_10026596	superfamily	216572	38	180	6.55E-30	116.605	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#8159 - 	CGI_10026596	superfamily	246918	544	595	4.23E-11	60.2931	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8159 - 	CGI_10026596	superfamily	204025	1062	1096	1.17E-06	46.8609	cl07344	PLAC superfamily	 - 	 - 	PLAC (protease and lacunin) domain; The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins. It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin.
Q#8159 - 	CGI_10026596	superfamily	246918	830	881	2.16E-05	43.7295	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8159 - 	CGI_10026596	superfamily	246918	884	941	0.000625126	39.1071	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8159 - 	CGI_10026596	superfamily	246918	948	999	0.00141204	37.9515	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8160 - 	CGI_10026597	superfamily	243035	1995	2115	3.20E-25	104.239	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8160 - 	CGI_10026597	superfamily	207627	1700	1776	2.87E-07	50.7159	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#8161 - 	CGI_10026598	superfamily	243119	158	206	2.83E-12	62.4613	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8161 - 	CGI_10026598	superfamily	243119	43	89	3.24E-10	56.6732	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8162 - 	CGI_10026599	superfamily	245303	28	372	2.20E-87	274.051	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8163 - 	CGI_10026600	superfamily	245303	25	379	1.89E-106	323.742	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8164 - 	CGI_10026601	superfamily	245303	27	360	6.06E-98	301.4	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8165 - 	CGI_10026602	superfamily	245303	23	387	0	599.545	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8165 - 	CGI_10026602	superfamily	243119	550	602	2.97E-13	65.1476	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8165 - 	CGI_10026602	superfamily	243119	442	492	1.08E-12	63.6068	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8166 - 	CGI_10026603	superfamily	245303	49	412	0	620.346	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8166 - 	CGI_10026603	superfamily	245303	626	989	0	617.264	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8166 - 	CGI_10026603	superfamily	245303	998	1091	5.45E-49	179.677	cl10447	GH18_chitinase-like superfamily	N	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8166 - 	CGI_10026603	superfamily	243119	1154	1204	3.55E-12	63.6068	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8166 - 	CGI_10026603	superfamily	243119	475	525	3.55E-12	63.6068	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8166 - 	CGI_10026603	superfamily	243119	578	622	1.43E-08	53.2064	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8166 - 	CGI_10026603	superfamily	243119	1257	1289	0.000715938	39.3393	cl02629	CBM_14 superfamily	C	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8167 - 	CGI_10026604	superfamily	245303	12	375	0	615.723	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8167 - 	CGI_10026604	superfamily	245303	429	791	0	594.922	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8167 - 	CGI_10026604	superfamily	243119	986	1038	1.43E-12	64.3772	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8167 - 	CGI_10026604	superfamily	243119	815	866	1.75E-12	63.992	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8168 - 	CGI_10026605	superfamily	245303	38	408	0	535.217	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#8168 - 	CGI_10026605	superfamily	243119	642	694	2.66E-13	65.918	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8168 - 	CGI_10026605	superfamily	243119	450	499	5.46E-05	41.6505	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#8169 - 	CGI_10026606	superfamily	248013	5	47	2.03E-11	58.8147	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#8170 - 	CGI_10026607	superfamily	241867	249	513	1.78E-32	129.842	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#8171 - 	CGI_10026608	superfamily	217869	5	215	4.73E-95	295.35	cl12286	Not3 superfamily	 - 	 - 	"Not1 N-terminal domain, CCR4-Not complex component; Not1 N-terminal domain, CCR4-Not complex component.  "
Q#8171 - 	CGI_10026608	superfamily	243016	533	663	9.22E-44	153.255	cl02384	NOT2_3_5 superfamily	 - 	 - 	"NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5."
Q#8172 - 	CGI_10026609	superfamily	245206	3	250	5.05E-86	262.599	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8173 - 	CGI_10026610	superfamily	245201	1648	1884	1.64E-29	119.649	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8173 - 	CGI_10026610	superfamily	243072	173	320	4.95E-29	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8173 - 	CGI_10026610	superfamily	243072	249	438	4.40E-18	83.587	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8173 - 	CGI_10026610	superfamily	243072	42	199	1.36E-14	73.5718	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8173 - 	CGI_10026610	superfamily	247724	1000	1158	3.20E-27	111.274	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8174 - 	CGI_10026611	superfamily	247724	6	169	9.68E-39	132.649	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8175 - 	CGI_10026612	superfamily	247724	1	94	2.41E-16	71.408	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8176 - 	CGI_10026614	superfamily	243035	90	144	7.50E-07	45.3034	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8179 - 	CGI_10026617	superfamily	216709	185	332	1.08E-46	160.52	cl03357	Nop superfamily	 - 	 - 	Putative snoRNA binding domain; This family consists of various Pre RNA processing ribonucleoproteins. The function of the aligned region is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Nop5p (Nop58p) from yeast is the protein component of a ribonucleoprotein protein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex. Nop56p and Nop5p interact with Nop1p and are required for ribosome biogenesis. Prp31p is required for pre-mRNA splicing in S. cerevisiae.
Q#8179 - 	CGI_10026617	superfamily	220400	334	463	5.70E-38	135.54	cl10762	Prp31_C superfamily	 - 	 - 	Prp31 C terminal domain; This is the C terminal domain of the pre-mRNA processing factor Prp31. Prp31 is required for U4/U6.U5 tri-snRNP formation. In humans this protein has been linked to autosomal dominant retinitis pigmentosa.
Q#8179 - 	CGI_10026617	superfamily	208568	90	141	2.85E-21	87.1772	cl06890	NOSIC superfamily	 - 	 - 	NOSIC (NUC001) domain; This is the central domain in Nop56/SIK1-like proteins.
Q#8180 - 	CGI_10026618	superfamily	218122	309	536	4.61E-68	226.71	cl04558	Choline_transpo superfamily	N	 - 	Plasma-membrane choline transporter; This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals.
Q#8182 - 	CGI_10026620	superfamily	241758	139	239	8.20E-19	82.4178	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#8182 - 	CGI_10026620	superfamily	247757	20	148	3.36E-45	155.877	cl17203	Fer4_NifH superfamily	C	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#8182 - 	CGI_10026620	superfamily	241619	306	359	8.74E-05	40.64	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8183 - 	CGI_10026621	superfamily	243040	1	95	7.42E-60	185.308	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#8184 - 	CGI_10026622	superfamily	241737	49	191	7.00E-18	82.544	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#8184 - 	CGI_10026622	superfamily	241617	968	1026	4.89E-16	75.1087	cl00110	MBD superfamily	 - 	 - 	"MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin.  MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family."
Q#8184 - 	CGI_10026622	superfamily	243114	1047	1159	3.62E-30	117.511	cl02622	Pre-SET superfamily	 - 	 - 	Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.
Q#8184 - 	CGI_10026622	superfamily	243091	1447	1515	1.09E-17	81.9971	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#8184 - 	CGI_10026622	superfamily	243091	1167	1233	1.66E-09	57.3443	cl02566	SET superfamily	C	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#8185 - 	CGI_10026623	superfamily	247805	6	220	1.18E-68	222.745	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#8185 - 	CGI_10026623	superfamily	247905	239	368	4.12E-29	112.331	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#8185 - 	CGI_10026623	superfamily	222474	399	462	1.22E-22	92.1009	cl16500	DUF4217 superfamily	 - 	 - 	Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many helicase proteins.
Q#8187 - 	CGI_10026625	superfamily	241599	1	39	1.60E-12	58.4089	cl00084	homeodomain superfamily	N	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#8189 - 	CGI_10026627	superfamily	217390	245	341	5.34E-06	44.4729	cl18407	TPT superfamily	N	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#8191 - 	CGI_10026629	superfamily	241648	270	321	2.56E-22	89.7394	cl00158	ZnF_GATA superfamily	 - 	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#8191 - 	CGI_10026629	superfamily	218566	122	214	4.61E-06	45.5794	cl18464	GATA-N superfamily	C	 - 	"GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell differentiation in a diverse range of tissues. Mutation are often associated with certain congenital human disorders. The six classical vertebrate GATA proteins, GATA-1 to GATA-6, are highly homologous and have two tandem zinc fingers. The classical GATA transcription factors function transcription activators. In lower metazoans GATA proteins carry a single canonical zinc finger. This family represents the N-terminal domain of the family of GATA transcription activators."
Q#8193 - 	CGI_10026631	superfamily	246680	493	576	1.75E-06	47.0352	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8194 - 	CGI_10026632	superfamily	245864	177	642	2.70E-76	253.355	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8194 - 	CGI_10026632	superfamily	245864	6	156	3.36E-32	128.935	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8196 - 	CGI_10026634	superfamily	243050	245	297	7.00E-21	86.495	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#8196 - 	CGI_10026634	superfamily	243050	362	414	7.00E-21	86.495	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#8196 - 	CGI_10026634	superfamily	243050	475	527	1.15E-20	86.1098	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#8196 - 	CGI_10026634	superfamily	243050	23	75	1.71E-20	85.3394	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#8196 - 	CGI_10026634	superfamily	243050	133	185	1.02E-13	66.4646	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#8197 - 	CGI_10026635	superfamily	241567	5	179	1.70E-35	126.176	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#8198 - 	CGI_10026636	superfamily	241587	5	61	1.06E-14	62.3066	cl00069	GGL superfamily	 - 	 - 	"G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors"
Q#8199 - 	CGI_10026637	superfamily	247727	161	221	4.20E-05	41.2615	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#8201 - 	CGI_10026639	superfamily	245814	132	206	2.42E-11	61.7363	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	444	517	4.54E-10	57.8843	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	339	415	2.19E-09	55.9583	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	26	100	8.50E-08	51.3359	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	1174	1227	7.33E-05	42.4763	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	544	619	0.000218218	40.9355	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	641	721	7.10E-11	60.5968	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	227	311	1.10E-08	54.0485	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8201 - 	CGI_10026639	superfamily	245814	939	1012	5.34E-06	46.1948	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8202 - 	CGI_10026640	superfamily	241645	161	220	2.10E-09	54.9658	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#8203 - 	CGI_10026641	superfamily	245201	2660	2906	1.59E-54	192.837	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8203 - 	CGI_10026641	superfamily	241584	1425	1517	3.85E-23	97.9523	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	1722	1811	5.87E-23	97.1819	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	245814	854	925	5.56E-21	91.1032	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	241584	929	1021	4.69E-20	88.7075	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	1030	1119	8.69E-19	85.2407	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	1829	1909	1.39E-18	84.4703	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	1324	1414	2.45E-18	83.6999	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	632	725	3.37E-18	83.3147	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	1621	1709	4.35E-18	83.3147	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	2504	2594	5.92E-18	82.9295	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	2213	2299	9.55E-18	82.1591	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	245814	2428	2500	1.10E-17	81.4732	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	241584	2112	2205	1.41E-17	81.7739	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	1131	1222	2.30E-17	81.0035	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	733	826	3.14E-17	80.6183	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	330	414	7.96E-15	73.6847	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	241584	431	513	2.68E-12	66.3659	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#8203 - 	CGI_10026641	superfamily	245814	160	218	3.39E-08	53.6471	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	1943	2010	4.40E-07	50.5655	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	72	140	0.000106851	43.2467	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	1247	1320	1.91E-17	80.7028	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	1545	1617	1.04E-15	75.6952	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	255	326	1.82E-14	71.8432	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	549	628	5.85E-14	70.6876	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	2323	2405	9.18E-10	58.6708	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8203 - 	CGI_10026641	superfamily	245814	2035	2108	1.52E-09	57.5908	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8204 - 	CGI_10026642	superfamily	245814	157	226	3.77E-13	64.8179	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8204 - 	CGI_10026642	superfamily	245814	258	325	1.35E-12	63.2771	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8204 - 	CGI_10026642	superfamily	245814	343	424	1.98E-08	51.3521	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8204 - 	CGI_10026642	superfamily	245814	1	59	2.74E-07	48.2705	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8205 - 	CGI_10026643	superfamily	241571	529	627	1.24E-17	80.149	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8205 - 	CGI_10026643	superfamily	241563	93	128	0.00288134	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8206 - 	CGI_10007825	superfamily	241564	53	121	4.13E-25	96.5659	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#8206 - 	CGI_10007825	superfamily	241564	272	325	1.92E-14	67.6759	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#8207 - 	CGI_10007826	superfamily	241563	68	108	6.22E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8208 - 	CGI_10007827	superfamily	245201	221	421	1.86E-38	140.45	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8208 - 	CGI_10007827	superfamily	216276	31	115	5.02E-16	73.7363	cl15639	Activin_recp superfamily	 - 	 - 	"Activin types I and II receptor domain; This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box."
Q#8208 - 	CGI_10007827	superfamily	243113	187	213	2.75E-07	47.4902	cl02621	TGF_beta_GS superfamily	 - 	 - 	Transforming growth factor beta type I GS-motif; This motif is found in the transforming growth factor beta (TGF-beta) type I which regulates cell growth and differentiation. The name of the GS motif comes from its highly conserved GSGSGLP signature in the cytoplasmic juxtamembrane region immediately preceding the protein's kinase domain. Point mutations in the GS motif modify the signaling ability of the type I receptor.
Q#8208 - 	CGI_10007827	superfamily	245201	341	508	1.10E-06	49.2284	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8209 - 	CGI_10007828	superfamily	247724	72	112	6.67E-12	60.2529	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8212 - 	CGI_10001137	superfamily	247856	33	91	4.83E-13	59.4837	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8213 - 	CGI_10001500	superfamily	130849	58	91	0.00140898	38.3072	cl17981	lycopene_cycl superfamily	C	 - 	lycopene cyclase; This model represents a family of bacterial lycopene cyclases catalyzing the transformation of lycopene to carotene. These enzymes are found in a limited spectrum of alpha and gamma proteobacteria as well as Flavobacterium.
Q#8214 - 	CGI_10001501	superfamily	115363	204	232	2.04E-06	43.5146	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8215 - 	CGI_10001502	superfamily	115363	82	115	4.99E-07	42.7442	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8215 - 	CGI_10001502	superfamily	115363	38	65	0.00568945	31.9586	cl05972	MIB_HERC2 superfamily	N	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8216 - 	CGI_10008467	superfamily	219974	585	772	4.20E-51	181.301	cl18538	Dna2 superfamily	 - 	 - 	"DNA replication factor Dna2; Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways."
Q#8216 - 	CGI_10008467	superfamily	221913	1253	1427	1.99E-41	152.695	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#8216 - 	CGI_10008467	superfamily	222258	1075	1281	9.36E-11	61.8151	cl18656	AAA_30 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#8216 - 	CGI_10008467	superfamily	241999	750	886	8.83E-06	46.2537	cl00641	Cas4_I-A_I-B_I-C_I-D_II-B superfamily	N	 - 	CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster
Q#8217 - 	CGI_10008468	superfamily	244906	51	116	6.26E-30	114.93	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#8217 - 	CGI_10008468	superfamily	244906	192	257	7.68E-30	114.93	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#8217 - 	CGI_10008468	superfamily	149105	930	1023	9.04E-05	44.7333	cl12353	TMPIT superfamily	C	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#8218 - 	CGI_10008469	superfamily	245596	51	279	1.30E-82	253.288	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#8219 - 	CGI_10008470	superfamily	245610	8	361	0	741.875	cl11424	nitrilase superfamily	 - 	 - 	"Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy."
Q#8220 - 	CGI_10008471	superfamily	227718	71	119	0.00241822	34.4839	cl02254	COG5431 superfamily	NC	 - 	Uncharacterized metal-binding protein [Function unknown]
Q#8221 - 	CGI_10008472	superfamily	241559	992	1093	3.96E-23	96.6111	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#8223 - 	CGI_10008474	superfamily	247755	158	184	0.00107921	38.5705	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8225 - 	CGI_10008476	superfamily	245206	9	353	1.56E-72	231.627	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8227 - 	CGI_10008478	superfamily	241624	1	309	1.61E-44	159.799	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#8228 - 	CGI_10008479	superfamily	241862	118	276	8.33E-24	97.0416	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#8230 - 	CGI_10008481	superfamily	243058	287	380	0.000298784	38.8348	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#8230 - 	CGI_10008481	superfamily	248012	4	78	4.20E-07	47.5725	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#8232 - 	CGI_10005784	superfamily	216056	40	189	5.82E-24	97.3803	cl08279	Peptidase_M16 superfamily	 - 	 - 	Insulinase (Peptidase family M16); Insulinase (Peptidase family M16).  
Q#8232 - 	CGI_10005784	superfamily	218490	270	407	2.40E-05	43.6191	cl08432	Peptidase_M16_C superfamily	N	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#8233 - 	CGI_10005785	superfamily	219525	50	89	4.09E-05	40.095	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#8234 - 	CGI_10005786	superfamily	245213	38	74	1.17E-08	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8234 - 	CGI_10005786	superfamily	245213	114	150	1.50E-08	51.4834	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8234 - 	CGI_10005786	superfamily	245213	76	112	2.30E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8234 - 	CGI_10005786	superfamily	245213	1	36	3.06E-07	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8234 - 	CGI_10005786	superfamily	221370	348	504	3.80E-09	55.8405	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#8234 - 	CGI_10005786	superfamily	243086	497	534	4.73E-08	50.0662	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#8234 - 	CGI_10005786	superfamily	243029	259	299	0.00361832	35.9533	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#8235 - 	CGI_10005787	superfamily	215647	78	116	1.76E-05	41.4401	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#8236 - 	CGI_10005788	superfamily	241754	84	249	6.03E-116	349.962	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#8236 - 	CGI_10005788	superfamily	111612	36	78	1.33E-06	44.009	cl03686	Myosin_N superfamily	 - 	 - 	Myosin N-terminal SH3-like domain; This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown.
Q#8237 - 	CGI_10009522	superfamily	248458	26	170	5.36E-15	75.0429	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8237 - 	CGI_10009522	superfamily	248458	255	436	5.81E-14	71.9613	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8238 - 	CGI_10009523	superfamily	246975	241	262	0.00669731	34.2449	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#8239 - 	CGI_10009524	superfamily	247755	1145	1239	1.32E-70	236.038	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8239 - 	CGI_10009524	superfamily	247755	45	206	2.67E-64	218.319	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8239 - 	CGI_10009524	superfamily	244201	578	693	1.66E-32	124.265	cl05797	SMC_hinge superfamily	 - 	 - 	SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.
Q#8240 - 	CGI_10009525	superfamily	217740	9	255	4.84E-91	271.542	cl18427	Scramblase superfamily	 - 	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#8241 - 	CGI_10009526	superfamily	247639	53	304	4.13E-40	142.6	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#8243 - 	CGI_10009528	superfamily	241748	324	531	6.76E-125	369.968	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#8243 - 	CGI_10009528	superfamily	216431	12	138	8.85E-13	65.7673	cl08317	Creatinase_N superfamily	 - 	 - 	Creatinase/Prolidase N-terminal domain; This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.
Q#8243 - 	CGI_10009528	superfamily	216431	183	276	0.000145935	40.7293	cl08317	Creatinase_N superfamily	C	 - 	Creatinase/Prolidase N-terminal domain; This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.
Q#8244 - 	CGI_10009529	superfamily	241599	20	73	1.73E-05	37.6081	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#8245 - 	CGI_10009530	superfamily	243072	202	362	1.44E-33	125.959	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8245 - 	CGI_10009530	superfamily	243072	103	260	4.20E-29	113.247	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8246 - 	CGI_10009531	superfamily	219673	105	271	7.16E-40	140.126	cl06835	COPIIcoated_ERV superfamily	N	 - 	"Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localisation. All proteins identified biochemically as Erv41p-Erv46p interactors are localised to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi."
Q#8246 - 	CGI_10009531	superfamily	206021	5	105	7.79E-13	62.8973	cl16436	ERGIC_N superfamily	 - 	 - 	"Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ERGIC proteins, ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, pfam07970."
Q#8247 - 	CGI_10009532	superfamily	243540	41	262	2.74E-12	63.8061	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#8248 - 	CGI_10009533	superfamily	243540	54	276	1.21E-17	78.8288	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#8249 - 	CGI_10009534	superfamily	241754	437	1140	0	677.832	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#8249 - 	CGI_10009534	superfamily	243072	126	281	2.88E-28	113.247	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8249 - 	CGI_10009534	superfamily	243072	69	168	4.25E-15	74.7274	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8252 - 	CGI_10009537	superfamily	241625	1	122	8.87E-16	68.8896	cl00123	PROF superfamily	 - 	 - 	"Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway."
Q#8253 - 	CGI_10009538	superfamily	242894	2	181	2.50E-35	125.953	cl02122	TFIIF_beta superfamily	 - 	 - 	"Transcription initiation factor IIF, beta subunit; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter."
Q#8254 - 	CGI_10009539	superfamily	247743	53	192	3.10E-23	93.7499	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#8256 - 	CGI_10001634	superfamily	241563	61	99	0.000569982	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8259 - 	CGI_10004436	superfamily	243092	15	296	2.88E-31	119.362	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8260 - 	CGI_10004437	superfamily	247684	8	447	0	702.797	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#8260 - 	CGI_10004437	superfamily	247743	780	854	7.58E-06	46.5196	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#8261 - 	CGI_10004438	superfamily	241578	1617	1795	2.15E-75	253.812	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8265 - 	CGI_10013143	superfamily	245226	50	143	5.40E-50	159.188	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#8270 - 	CGI_10013148	superfamily	242406	4	105	3.51E-13	62.6089	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#8273 - 	CGI_10013151	superfamily	241958	234	489	3.58E-82	263.222	cl00573	SDF superfamily	N	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#8273 - 	CGI_10013151	superfamily	241958	26	167	2.66E-06	48.2806	cl00573	SDF superfamily	C	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#8276 - 	CGI_10013154	superfamily	241571	40	125	1.67E-11	57.8074	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8277 - 	CGI_10013155	superfamily	246921	319	371	1.01E-12	65.0893	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#8277 - 	CGI_10013155	superfamily	246921	241	297	6.84E-06	45.0589	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#8277 - 	CGI_10013155	superfamily	246921	383	435	0.000472787	39.6661	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#8277 - 	CGI_10013155	superfamily	246921	185	236	0.0021374	37.3549	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#8278 - 	CGI_10013156	superfamily	218987	12	86	9.49E-35	116.378	cl05685	GCN5L1 superfamily	N	 - 	GCN5-like protein 1 (GCN5L1); This family consists of several eukaryotic GCN5-like protein 1 (GCN5L1) sequences. The function of this family is unknown.
Q#8286 - 	CGI_10021284	superfamily	241600	1	72	1.36E-18	75.7399	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8287 - 	CGI_10021285	superfamily	245531	42	123	0.000279694	36.1878	cl11158	BEN superfamily	 - 	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#8290 - 	CGI_10021288	superfamily	243384	26	151	3.28E-42	139.914	cl03312	Flavokinase superfamily	 - 	 - 	Riboflavin kinase; This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism. This domain is thought to have kinase activity.
Q#8291 - 	CGI_10021289	superfamily	241610	45	98	9.89E-19	76.905	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#8291 - 	CGI_10021289	superfamily	241610	107	159	1.81E-18	76.1346	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#8291 - 	CGI_10021289	superfamily	241610	170	222	5.91E-17	71.8974	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#8291 - 	CGI_10021289	superfamily	241610	11	38	2.46E-07	45.7038	cl00101	KU superfamily	N	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#8292 - 	CGI_10021290	superfamily	248458	92	450	1.84E-07	51.5457	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8293 - 	CGI_10021291	superfamily	245814	223	284	0.000373351	38.2391	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8294 - 	CGI_10021292	superfamily	245847	83	198	0.000600948	38.6376	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#8294 - 	CGI_10021292	superfamily	245847	279	394	0.00262326	37.0968	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#8299 - 	CGI_10021297	superfamily	245206	5	104	4.16E-36	128.785	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8299 - 	CGI_10021297	superfamily	242406	101	195	1.26E-16	73.3945	cl01271	DUF1768 superfamily	C	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#8300 - 	CGI_10021298	superfamily	245206	1	64	2.77E-19	77.9382	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8301 - 	CGI_10021299	superfamily	245206	1	278	2.35E-123	355.282	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8303 - 	CGI_10021301	superfamily	243092	24	110	1.43E-09	56.5744	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8304 - 	CGI_10003509	superfamily	248247	53	300	3.10E-75	240.199	cl17693	Integrin_beta superfamily	N	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#8304 - 	CGI_10003509	superfamily	219677	303	330	0.00792165	33.9504	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#8305 - 	CGI_10003510	superfamily	149701	114	155	6.72E-10	53.3741	cl07373	Integrin_b_cyt superfamily	 - 	 - 	"Integrin beta cytoplasmic domain; Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion. Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit. Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity. This domain corresponds to the cytoplasmic domain of the beta subunit."
Q#8305 - 	CGI_10003510	superfamily	219677	38	62	0.000129831	38.5728	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#8309 - 	CGI_10017734	superfamily	243072	13	118	1.51E-23	90.5206	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8311 - 	CGI_10017736	superfamily	245010	8	109	1.48E-16	70.1085	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#8312 - 	CGI_10017737	superfamily	242432	66	223	3.19E-28	107.815	cl01321	SURF1 superfamily	C	 - 	"SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring complex of the respiratory chain, is an assemblage of nuclear and mitochondrially-encoded subunits. Its assembly is mediated by nuclear encoded assembly factors, one of which is Surf1/Shy1. Mutations in human Surf1 are a major cause of Leigh syndrome, a severe neurodegenerative disorder."
Q#8313 - 	CGI_10017738	superfamily	247744	25	231	3.42E-104	303.322	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#8314 - 	CGI_10017739	superfamily	247792	37	82	5.61E-05	41.2772	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8314 - 	CGI_10017739	superfamily	241563	177	211	0.00117608	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8315 - 	CGI_10017740	superfamily	247745	20	315	9.01E-47	166.338	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#8316 - 	CGI_10017741	superfamily	247856	83	142	3.11E-08	50.6241	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8316 - 	CGI_10017741	superfamily	215754	278	368	5.35E-31	114.658	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#8316 - 	CGI_10017741	superfamily	215754	187	275	1.89E-27	105.028	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#8316 - 	CGI_10017741	superfamily	215754	373	462	5.71E-19	81.916	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#8316 - 	CGI_10017741	superfamily	247856	21	78	0.00343951	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8317 - 	CGI_10017742	superfamily	247044	195	305	3.09E-27	103.485	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#8317 - 	CGI_10017742	superfamily	247044	12	126	8.97E-20	82.684	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#8319 - 	CGI_10017744	superfamily	247856	45	99	0.00128058	34.4457	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8321 - 	CGI_10017746	superfamily	190614	255	334	4.04E-30	116.121	cl15647	YEATS superfamily	 - 	 - 	"YEATS family; We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity"
Q#8322 - 	CGI_10017747	superfamily	219448	911	1015	2.62E-33	125.505	cl06523	DRMBL superfamily	 - 	 - 	DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.
Q#8322 - 	CGI_10017747	superfamily	241867	723	810	2.77E-08	53.7114	cl00446	Lactamase_B superfamily	NC	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#8323 - 	CGI_10017748	superfamily	216686	67	132	8.37E-05	39.999	cl18377	Galactosyl_T superfamily	N	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#8323 - 	CGI_10017748	superfamily	245230	29	60	0.000446009	38.3918	cl10017	Tubulin_FtsZ superfamily	N	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#8326 - 	CGI_10017751	superfamily	207716	73	141	9.08E-15	64.971	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#8327 - 	CGI_10017752	superfamily	245206	40	307	1.03E-60	197.447	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8328 - 	CGI_10017753	superfamily	247684	12	185	8.71E-19	82.6367	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#8329 - 	CGI_10017754	superfamily	245206	51	102	0.00290341	35.2779	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8330 - 	CGI_10017755	superfamily	245206	1	27	1.18E-06	42.9819	cl09931	NADB_Rossmann superfamily	NC	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8331 - 	CGI_10017756	superfamily	245206	40	126	3.41E-25	96.9098	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8332 - 	CGI_10017757	superfamily	247684	12	185	4.23E-19	83.4071	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#8333 - 	CGI_10017758	superfamily	207716	22	89	3.93E-22	86.157	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#8334 - 	CGI_10017759	superfamily	207716	41	114	4.66E-20	78.453	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#8335 - 	CGI_10017760	superfamily	215866	83	240	1.08E-27	107.411	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#8335 - 	CGI_10017760	superfamily	243212	258	413	6.40E-24	97.029	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#8336 - 	CGI_10017761	superfamily	215866	23	178	1.31E-33	123.589	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#8336 - 	CGI_10017761	superfamily	243212	198	354	1.76E-28	108.97	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#8337 - 	CGI_10017762	superfamily	248136	3	135	5.41E-53	166.339	cl17582	Sybindin superfamily	 - 	 - 	"Sybindin-like family; Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses."
Q#8338 - 	CGI_10017763	superfamily	245835	746	937	0.00357634	39.2614	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#8338 - 	CGI_10017763	superfamily	213465	887	993	0.00390679	38.752	cl17074	PRK03963 superfamily	C	 - 	V-type ATP synthase subunit E; Provisional
Q#8339 - 	CGI_10017764	superfamily	246925	311	651	9.28E-11	62.7582	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#8339 - 	CGI_10017764	superfamily	246925	70	329	0.00803881	37.7202	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#8340 - 	CGI_10017765	superfamily	245622	773	891	7.35E-22	93.8282	cl11446	Rhomboid superfamily	 - 	 - 	"Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite."
Q#8341 - 	CGI_10017766	superfamily	245864	11	499	2.05E-74	245.008	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8342 - 	CGI_10003803	superfamily	241583	1	93	3.53E-25	96.4862	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8343 - 	CGI_10003804	superfamily	241609	140	218	1.02E-23	92.4411	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#8343 - 	CGI_10003804	superfamily	245213	106	138	0.000869955	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8344 - 	CGI_10003805	superfamily	241609	43	111	3.11E-20	79.7295	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#8346 - 	CGI_10000368	superfamily	243161	3	60	7.73E-05	36.6034	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#8348 - 	CGI_10001062	superfamily	245847	48	170	4.30E-10	53.6604	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#8349 - 	CGI_10001119	superfamily	241691	32	264	1.60E-32	121.737	cl00213	DNA_BRE_C superfamily	 - 	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#8351 - 	CGI_10001154	superfamily	222429	6	80	8.76E-16	67.6508	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#8354 - 	CGI_10015859	superfamily	248097	285	408	7.29E-27	103.499	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#8354 - 	CGI_10015859	superfamily	248022	40	241	2.60E-17	81.9403	cl17468	Aa_trans superfamily	N	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#8355 - 	CGI_10015860	superfamily	245601	568	681	4.22E-16	78.9552	cl11399	HP superfamily	C	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#8355 - 	CGI_10015860	superfamily	245601	806	949	4.64E-09	56.9988	cl11399	HP superfamily	N	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#8355 - 	CGI_10015860	superfamily	245601	392	432	1.32E-05	47.442	cl11399	HP superfamily	C	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#8355 - 	CGI_10015860	superfamily	247809	248	347	0.00150066	39.7481	cl17255	ATP-grasp_4 superfamily	N	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#8356 - 	CGI_10015861	superfamily	247916	58	169	3.25E-17	77.8262	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#8357 - 	CGI_10015862	superfamily	247724	26	44	1.72E-05	39.5156	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8358 - 	CGI_10015863	superfamily	216942	23	71	0.00083894	34.9092	cl03494	CDI superfamily	 - 	 - 	Cyclin-dependent kinase inhibitor; Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.
Q#8361 - 	CGI_10015866	superfamily	241760	577	613	2.77E-11	59.7555	cl00295	ZZ superfamily	C	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#8361 - 	CGI_10015866	superfamily	217473	171	365	1.45E-40	149.052	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#8363 - 	CGI_10015868	superfamily	218186	173	610	0	577.433	cl18446	PA26 superfamily	 - 	 - 	PA26 p53-induced protein (sestrin); PA26 is a p53-inducible protein. Its function is unknown. It has similarity to pfam04636 in its N-terminus.
Q#8364 - 	CGI_10015869	superfamily	243096	812	995	6.20E-24	101.22	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#8364 - 	CGI_10015869	superfamily	243074	117	160	5.68E-08	50.9681	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#8364 - 	CGI_10015869	superfamily	247725	1060	1141	3.77E-07	49.9455	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8364 - 	CGI_10015869	superfamily	247725	987	1076	0.00184973	39.1767	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8364 - 	CGI_10015869	superfamily	222625	400	484	0.00554402	37.5107	cl16748	DUF4347 superfamily	C	 - 	"Domain of unknown function (DUF4347); This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. There are two completely conserved residues (C and G) that may be functionally important."
Q#8367 - 	CGI_10015872	superfamily	248458	143	273	2.16E-19	89.6805	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8367 - 	CGI_10015872	superfamily	248458	332	478	3.22E-13	70.8057	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8367 - 	CGI_10015872	superfamily	245864	587	992	3.38E-57	204.434	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8368 - 	CGI_10015873	superfamily	245814	41	108	5.07E-07	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8369 - 	CGI_10015874	superfamily	245864	3	385	3.60E-36	137.025	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8377 - 	CGI_10001563	superfamily	241632	138	369	6.90E-80	256.796	cl00137	SERPIN superfamily	C	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#8380 - 	CGI_10001646	superfamily	247684	17	425	2.01E-99	312.674	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#8381 - 	CGI_10001503	superfamily	245864	1	180	1.22E-63	204.82	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#8384 - 	CGI_10001358	superfamily	241563	59	96	2.12E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8384 - 	CGI_10001358	superfamily	128778	101	213	0.00839823	35.3183	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#8388 - 	CGI_10002151	superfamily	219525	274	313	0.000233362	39.3246	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#8391 - 	CGI_10002630	superfamily	241750	137	465	1.88E-130	383.908	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#8395 - 	CGI_10003128	superfamily	243091	196	263	1.23E-09	54.8056	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#8397 - 	CGI_10009672	superfamily	247743	149	205	8.81E-05	40.5923	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#8397 - 	CGI_10009672	superfamily	248372	7	125	2.00E-11	58.75	cl17818	Nuc_deoxyrib_tr superfamily	 - 	 - 	Nucleoside 2-deoxyribosyltransferase; Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyzes the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides.
Q#8398 - 	CGI_10009673	superfamily	110440	105	132	0.00270046	32.7649	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8402 - 	CGI_10009677	superfamily	246598	24	289	1.10E-170	478.616	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#8403 - 	CGI_10009678	superfamily	245147	154	359	0.00438272	37.2555	cl09743	RNA_lig_T4_1 superfamily	 - 	 - 	"RNA ligase; Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns."
Q#8404 - 	CGI_10009679	superfamily	191163	1	190	1.23E-127	360.201	cl04888	DUF667 superfamily	 - 	 - 	"Protein of unknown function (DUF667); This family of proteins are highly conserved in eukaryotes. Some proteins in the family are annotated as transcription factors. However, there is currently no support for this in the literature."
Q#8405 - 	CGI_10009680	superfamily	245201	37	322	1.12E-55	186.151	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8407 - 	CGI_10009682	superfamily	241874	31	601	0	788.392	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#8408 - 	CGI_10009683	superfamily	247727	125	219	0.000575769	37.4095	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#8410 - 	CGI_10009685	superfamily	243092	31	252	1.72E-21	94.324	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8410 - 	CGI_10009685	superfamily	243141	355	420	0.0098793	35.0255	cl02687	RWD superfamily	N	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#8413 - 	CGI_10009688	superfamily	243074	4	48	5.61E-08	46.7309	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#8414 - 	CGI_10009689	superfamily	192915	102	233	6.10E-09	54.2965	cl13451	DUF3506 superfamily	 - 	 - 	Domain of unknown function (DUF3506); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 131 to 148 amino acids in length. This domain has a conserved KLTGD sequence motif.
Q#8416 - 	CGI_10003357	superfamily	248293	110	179	0.00120145	36.1778	cl17739	MADF_DNA_bdg superfamily	 - 	 - 	Alcohol dehydrogenase transcription factor Myb/SANT-like; The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains.
Q#8418 - 	CGI_10004066	superfamily	215647	340	541	2.67E-34	131.192	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#8418 - 	CGI_10004066	superfamily	221370	118	310	2.31E-11	62.7741	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#8418 - 	CGI_10004066	superfamily	243029	35	87	2.79E-07	48.5009	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#8418 - 	CGI_10004066	superfamily	243035	660	706	0.00397938	36.6337	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8419 - 	CGI_10004067	superfamily	245818	37	144	6.88E-11	58.5653	cl11966	Rel-Spo_like superfamily	C	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#8419 - 	CGI_10004067	superfamily	220744	150	281	5.84E-30	113.096	cl11075	OAS1_C superfamily	C	 - 	"2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus; This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between 320 and 344 at the extreme C-terminal end. Oligoadenylate synthetases are antiviral enzymes that counteract vial attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication. This domain is often associated with NTP_transf_2 pfam01909."
Q#8422 - 	CGI_10010613	superfamily	245201	249	518	4.15E-48	167.799	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8423 - 	CGI_10010614	superfamily	243035	116	236	7.50E-21	84.9789	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8424 - 	CGI_10010615	superfamily	243035	178	298	3.55E-20	83.8233	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8425 - 	CGI_10010616	superfamily	219755	1	47	1.78E-18	73.5255	cl07021	SYF2 superfamily	N	 - 	SYF2 splicing factor; Proteins in this family are involved in cell cycle progression and pre-mRNA splicing.
Q#8426 - 	CGI_10010617	superfamily	216152	1	214	1.48E-56	185.21	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#8428 - 	CGI_10010619	superfamily	242406	4	59	6.84E-05	36.8005	cl01271	DUF1768 superfamily	NC	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#8429 - 	CGI_10010620	superfamily	216152	1	214	4.20E-53	175.965	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#8430 - 	CGI_10010621	superfamily	248458	31	194	0.00407806	35.7525	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8431 - 	CGI_10010622	superfamily	246902	1318	1497	4.52E-97	311.416	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#8431 - 	CGI_10010622	superfamily	246902	618	764	1.00E-86	280.602	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#8431 - 	CGI_10010622	superfamily	247725	461	592	3.87E-52	181.689	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8431 - 	CGI_10010622	superfamily	243088	342	473	2.56E-39	145.217	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#8431 - 	CGI_10010622	superfamily	195686	55	217	6.62E-54	187.987	cl08291	TCTP superfamily	 - 	 - 	Translationally controlled tumour protein; Translationally controlled tumour protein.  
Q#8432 - 	CGI_10010623	superfamily	222150	756	781	0.00581993	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8432 - 	CGI_10010623	superfamily	222150	728	753	0.00994065	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8434 - 	CGI_10010625	superfamily	245367	6	198	9.84E-72	238.297	cl10727	DUF2042 superfamily	C	 - 	Uncharacterized conserved protein (DUF2042); This entry is the conserved N-terminal 300 residues of a group of proteins found from protozoa to Humans. The function is unknown.
Q#8434 - 	CGI_10010625	superfamily	245367	196	833	3.98E-60	218.538	cl10727	DUF2042 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2042); This entry is the conserved N-terminal 300 residues of a group of proteins found from protozoa to Humans. The function is unknown.
Q#8438 - 	CGI_10012816	superfamily	204985	68	124	2.65E-08	52.1739	cl14987	Chorein_N superfamily	N	 - 	"N-terminal region of Chorein, a TM vesicle-mediated sorter; Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport."
Q#8439 - 	CGI_10012817	superfamily	221585	258	353	6.81E-22	92.1373	cl13842	hSac2 superfamily	 - 	 - 	"Inositol phosphatase; This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam02383. hSac2 functions as an inositol polyphosphate 5-phosphatase."
Q#8439 - 	CGI_10012817	superfamily	217007	3	74	2.33E-21	94.589	cl11995	Syja_N superfamily	N	 - 	SacI homology domain; This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
Q#8440 - 	CGI_10012818	superfamily	247907	789	946	2.26E-24	101.341	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#8440 - 	CGI_10012818	superfamily	245213	621	657	1.38E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8440 - 	CGI_10012818	superfamily	245213	699	735	3.44E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8440 - 	CGI_10012818	superfamily	245213	667	697	1.57E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8440 - 	CGI_10012818	superfamily	245213	546	581	0.00180031	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8440 - 	CGI_10012818	superfamily	245213	751	785	0.00854612	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8440 - 	CGI_10012818	superfamily	248288	1016	1076	8.31E-08	51.2501	cl17734	DAN superfamily	 - 	 - 	"DAN domain; This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family after the first member to be reported. This family includes DAN, Cerberus and Gremlin. The gremlin protein is an antagonist of bone morphogenetic protein signaling. It is postulated that all members of this family antagonise different TGF beta pfam00019 ligands. Recent work shows that the DAN protein is not an efficient antagonist of BMP-2/4 class signals, we found that DAN was able to interact with GDF-5 in a frog embryo assay, suggesting that DAN may regulate signaling by the GDF-5/6/7 class of BMPs in vivo."
Q#8440 - 	CGI_10012818	superfamily	243030	114	145	4.87E-05	42.3047	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#8440 - 	CGI_10012818	superfamily	243030	353	384	6.79E-05	41.9195	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#8440 - 	CGI_10012818	superfamily	199168	402	425	7.05E-05	41.5684	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#8440 - 	CGI_10012818	superfamily	214507	46	95	0.00021192	40.4912	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#8440 - 	CGI_10012818	superfamily	199168	165	188	0.000258602	40.0276	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#8440 - 	CGI_10012818	superfamily	199168	450	471	0.00318243	36.946	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#8442 - 	CGI_10012820	superfamily	243092	38	332	2.34E-25	106.65	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8443 - 	CGI_10012821	superfamily	245226	9	115	4.82E-13	63.0884	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#8444 - 	CGI_10012822	superfamily	241583	120	306	1.25E-64	218.209	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8444 - 	CGI_10012822	superfamily	247097	428	464	0.000757376	38.8997	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#8444 - 	CGI_10012822	superfamily	247097	761	795	0.00712124	36.2033	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#8446 - 	CGI_10012824	superfamily	246612	579	671	1.03E-13	68.9853	cl14057	BPL_LplA_LipB superfamily	N	 - 	"Biotin/lipoate A/B protein ligase family; This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Lipoate-protein ligase A (LPLA) catalyzes the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor."
Q#8446 - 	CGI_10012824	superfamily	241555	397	475	0.00110701	40.7866	cl00020	GAT_1 superfamily	NC	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#8447 - 	CGI_10012825	superfamily	241832	7	75	9.44E-20	80.3084	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#8447 - 	CGI_10012825	superfamily	243175	89	208	9.03E-13	61.8109	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#8448 - 	CGI_10012826	superfamily	245814	189	259	2.77E-10	55.1879	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8448 - 	CGI_10012826	superfamily	245814	54	136	7.48E-07	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8450 - 	CGI_10012828	superfamily	241782	34	302	8.14E-98	297.558	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#8453 - 	CGI_10001473	superfamily	243179	7	90	8.91E-21	81.5809	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#8454 - 	CGI_10003828	superfamily	247727	75	171	0.00568455	33.8212	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#8455 - 	CGI_10003829	superfamily	207921	269	385	6.21E-40	139.225	cl03350	Ribosomal_L28e superfamily	 - 	 - 	Ribosomal L28e protein family; Ribosomal L28e protein family.  
Q#8456 - 	CGI_10003830	superfamily	241550	56	124	2.61E-16	71.8685	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#8458 - 	CGI_10003239	superfamily	248458	139	510	1.10E-20	92.3769	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8459 - 	CGI_10003240	superfamily	248458	139	476	6.23E-19	86.9841	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8460 - 	CGI_10003241	superfamily	248458	162	511	2.42E-19	88.1397	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8461 - 	CGI_10003242	superfamily	248458	166	477	7.49E-19	86.5989	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8462 - 	CGI_10005641	superfamily	248012	43	135	2.20E-13	63.0613	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#8464 - 	CGI_10005643	superfamily	241597	34	99	2.43E-32	115.088	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#8466 - 	CGI_10005645	superfamily	247743	869	1000	5.10E-23	97.6019	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#8466 - 	CGI_10005645	superfamily	247743	586	731	3.67E-06	47.1407	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#8466 - 	CGI_10005645	superfamily	220158	60	135	1.08E-14	71.4639	cl07772	PEX-1N superfamily	 - 	 - 	"Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation."
Q#8467 - 	CGI_10005646	superfamily	241647	137	167	1.55E-08	50.6042	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#8467 - 	CGI_10005646	superfamily	241647	64	108	9.75E-06	42.515	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#8468 - 	CGI_10021060	superfamily	243035	27	70	5.72E-05	37.9846	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8470 - 	CGI_10021062	superfamily	243092	9	167	6.25E-30	112.428	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8471 - 	CGI_10021063	superfamily	241607	85	119	0.000139473	39.1754	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#8472 - 	CGI_10021064	superfamily	241600	510	682	4.22E-62	207.863	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8472 - 	CGI_10021064	superfamily	241619	443	493	2.02E-05	43.3397	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8473 - 	CGI_10021065	superfamily	241600	96	267	7.61E-68	212.486	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8473 - 	CGI_10021065	superfamily	241619	31	79	4.13E-05	40.6433	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8477 - 	CGI_10021069	superfamily	242884	7	102	8.98E-36	119.253	cl02104	Ribosomal_L36e superfamily	 - 	 - 	Ribosomal protein L36e; Ribosomal protein L36e.  
Q#8478 - 	CGI_10021070	superfamily	245814	329	381	0.000442871	38.6243	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8480 - 	CGI_10021072	superfamily	149667	1	120	1.01E-18	83.9591	cl07343	GON superfamily	C	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#8480 - 	CGI_10021072	superfamily	243093	142	221	6.27E-18	78.7262	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#8481 - 	CGI_10021073	superfamily	241611	89	224	5.99E-14	71.2656	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#8481 - 	CGI_10021073	superfamily	243093	587	663	1.85E-05	44.4434	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#8481 - 	CGI_10021073	superfamily	238012	1016	1044	0.00332072	37.3338	cl11390	EGF_Lam superfamily	N	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8483 - 	CGI_10021075	superfamily	215827	144	255	5.98E-11	59.7896	cl02830	Tyrosinase superfamily	C	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#8484 - 	CGI_10021076	superfamily	215827	144	311	2.80E-24	101.391	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#8485 - 	CGI_10021077	superfamily	241599	76	130	5.49E-08	48.7789	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#8485 - 	CGI_10021077	superfamily	243166	132	282	1.01E-35	129.336	cl02759	TRAM_LAG1_CLN8 superfamily	C	 - 	TLC domain; TLC domain.  
Q#8487 - 	CGI_10021079	superfamily	247856	79	133	1.12E-17	72.5805	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8487 - 	CGI_10021079	superfamily	247856	7	63	4.77E-11	54.4761	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8488 - 	CGI_10021080	superfamily	215754	24	118	5.24E-23	91.546	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#8488 - 	CGI_10021080	superfamily	215754	124	223	9.86E-23	90.7756	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#8488 - 	CGI_10021080	superfamily	215754	230	351	2.94E-15	70.36	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#8489 - 	CGI_10021081	superfamily	245213	3332	3365	2.34E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	496	536	0.000120683	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	756	788	0.000295771	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	1133	1173	0.000729915	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	1006	1039	0.000969351	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	3081	3114	0.00120169	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	3458	3493	0.00152092	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	798	828	0.0022604	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	669	706	0.00256141	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	245213	2656	2698	0.00280058	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	243124	98	192	1.65E-14	74.3857	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#8489 - 	CGI_10021081	superfamily	243065	2223	2392	1.21E-08	56.6813	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#8489 - 	CGI_10021081	superfamily	241578	2697	2737	2.00E-07	53.5427	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8489 - 	CGI_10021081	superfamily	241578	328	368	6.25E-07	52.0019	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8489 - 	CGI_10021081	superfamily	243060	3588	3655	5.68E-05	44.6772	cl02507	SEA superfamily	N	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#8489 - 	CGI_10021081	superfamily	245213	2909	2948	0.00045505	41.1804	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	241578	834	868	0.000649714	43.1424	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8489 - 	CGI_10021081	superfamily	241578	404	450	0.000909931	42.372	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8489 - 	CGI_10021081	superfamily	245213	2740	2778	0.00120138	40.0248	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8489 - 	CGI_10021081	superfamily	241578	361	411	0.00199896	41.6016	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8489 - 	CGI_10021081	superfamily	241578	578	619	0.00475525	40.446	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8490 - 	CGI_10008783	superfamily	218329	11	410	5.64E-80	255.125	cl04845	DIE2_ALG10 superfamily	 - 	 - 	"DIE2/ALG10 family; The ALG10 protein from Saccharomyces cerevisiae encodes the alpha-1,2 glucosyltransferase of the endoplasmic reticulum. This protein has been characterized in rat as potassium channel regulator 1."
Q#8491 - 	CGI_10008784	superfamily	244901	5	233	3.17E-108	326.505	cl08306	Peptidase_C12 superfamily	 - 	 - 	"Cysteine peptidase C12 contains ubiquitin carboxyl-terminal hydrolase (UCH) families L1, L3, L5 and BAP1; The ubiquitin C-terminal hydrolase (UCH; ubiquitinyl hydrolase; ubiquitin thiolesterase) family of deubiquitinating enzymes (DUBs) consists of four members to date: UCH-L1, UCH-L3, UCH-L5 (UCH37) and BRCA1-associated protein-1 (BAP1), all containing a conserved catalytic domain with cysteine peptidase activity.  UCH-L1 hydrolyzes carboxyl terminal esters and amides of ubiquitin (Ub). Dysfunction of this hydrolase activity can lead to an accumulation of alpha-synuclein, which is linked to Parkinson's disease (PD) and neurofibrillary tangles, linked to Alzheimer's disease (AD).  UCH-L1, in its dimeric form, has additional enzymatic activity as a ubiquitin ligase. UCH-L3 hydrolyzes isopeptide bonds at the C-terminal glycine of either Ub or Nedd8, a ubiquitin-like protein. UCH-L3 can also interact with Lys48-linked Ub dimers to protect it from degradation while inhibiting its hydrolase activity at the same time.  UCH-L1 and UCH-L3 are the most closely related of the UCH members. UCH-L5 (UCH37) is involved in the deubiquitinating activity in the 19S proteasome regulatory complex. It is also associated with the human Ino80 chromatin-remodeling complex (hINO80) in the nucleus. BAP1 binds to the wild-type BRCA1 RING finger domain, localized in the nucleus.  It consists of the N-terminal UCH domain and two predicted nuclear localization signals (NLSs), only one of which is functional. The full-length human BRCA1 is a ubiquitin ligase. However, BAP1 does not appear to function in the deubiquitination of autoubiquitinated  BRCA1. There is growing evidence that UCH enzymes and human malignancies are closely correlated. Studies show that UCH enzymes play a crucial role in some signaling pathways and in cell-cycle regulation."
Q#8492 - 	CGI_10008785	superfamily	243039	423	513	8.93E-14	68.1746	cl02446	MATH superfamily	N	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#8492 - 	CGI_10008785	superfamily	247792	14	63	1.39E-06	45.5144	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8492 - 	CGI_10008785	superfamily	241563	163	192	0.0039013	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8493 - 	CGI_10008786	superfamily	242889	256	356	5.65E-20	83.8065	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#8496 - 	CGI_10008789	superfamily	247724	1	200	1.18E-74	232.041	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8500 - 	CGI_10008793	superfamily	243110	166	375	1.08E-18	85.5589	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#8501 - 	CGI_10008794	superfamily	243110	270	333	5.56E-05	43.9573	cl02616	MACPF superfamily	N	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#8503 - 	CGI_10007205	superfamily	241619	65	126	2.89E-05	39.4877	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8504 - 	CGI_10007206	superfamily	217293	2	160	9.64E-25	99.6295	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#8504 - 	CGI_10007206	superfamily	202474	167	249	1.89E-08	53.0413	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#8505 - 	CGI_10007207	superfamily	217293	2	165	4.07E-29	111.956	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#8505 - 	CGI_10007207	superfamily	202474	172	269	1.18E-11	62.2861	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#8506 - 	CGI_10007208	superfamily	192929	2	460	0	547.439	cl13492	HSNSD superfamily	 - 	 - 	heparan sulfate-N-deacetylase; This family of proteins is are heparan sulfate N-deacetylase enzymes. This protein is found in eukaryotes. This proteinenzyme is often found associated with pfam00685.
Q#8507 - 	CGI_10007209	superfamily	247692	210	788	0	836.045	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#8508 - 	CGI_10007210	superfamily	247723	300	367	3.78E-11	60.0113	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#8509 - 	CGI_10007211	superfamily	202711	61	231	1.61E-98	287.326	cl04190	Mob1_phocein superfamily	 - 	 - 	"Mob1/phocein family; Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin."
Q#8510 - 	CGI_10007212	superfamily	247723	389	463	3.45E-37	132.073	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#8510 - 	CGI_10007212	superfamily	247723	43	120	2.86E-35	126.712	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#8510 - 	CGI_10007212	superfamily	247723	125	218	1.38E-47	161.679	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#8512 - 	CGI_10006326	superfamily	241580	761	834	2.98E-29	113.418	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#8512 - 	CGI_10006326	superfamily	241572	82	166	4.62E-10	58.0188	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#8514 - 	CGI_10006328	superfamily	247683	2181	2223	3.75E-05	43.6055	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8514 - 	CGI_10006328	superfamily	243142	1468	1600	3.78E-08	53.7843	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#8520 - 	CGI_10023311	superfamily	216686	92	269	5.33E-41	149.396	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#8520 - 	CGI_10023311	superfamily	245847	432	579	2.54E-15	74.1301	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#8520 - 	CGI_10023311	superfamily	241619	304	353	0.00245101	37.1765	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8521 - 	CGI_10023312	superfamily	222150	259	282	0.000179006	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8521 - 	CGI_10023312	superfamily	222150	147	171	0.000427341	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8521 - 	CGI_10023312	superfamily	222150	288	312	0.000515344	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8521 - 	CGI_10023312	superfamily	222150	204	228	0.00197631	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8521 - 	CGI_10023312	superfamily	222150	92	114	0.00610447	34.2897	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#8522 - 	CGI_10023313	superfamily	245819	578	627	1.69E-13	68.7599	cl11967	Nucleotidyl_cyc_III superfamily	C	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#8522 - 	CGI_10023313	superfamily	245225	2	304	4.07E-42	156.639	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#8522 - 	CGI_10023313	superfamily	245201	395	501	2.95E-09	56.776	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8522 - 	CGI_10023313	superfamily	219526	517	564	9.14E-07	48.7695	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8523 - 	CGI_10023314	superfamily	241574	1	86	8.81E-35	129.628	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#8523 - 	CGI_10023314	superfamily	241574	173	336	1.12E-09	57.2105	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#8528 - 	CGI_10023319	superfamily	243035	336	406	0.00037691	38.755	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8528 - 	CGI_10023319	superfamily	241619	27	93	0.00105367	37.1765	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8528 - 	CGI_10023319	superfamily	243035	123	203	0.0035209	35.8633	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8528 - 	CGI_10023319	superfamily	241619	237	305	0.00474003	35.2505	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8529 - 	CGI_10023320	superfamily	243058	177	264	0.000104112	42.6868	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#8529 - 	CGI_10023320	superfamily	245201	459	727	4.80E-146	453.498	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8529 - 	CGI_10023320	superfamily	216347	1417	1843	4.08E-131	417.322	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#8530 - 	CGI_10023321	superfamily	241889	79	214	7.79E-48	161.244	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#8531 - 	CGI_10023322	superfamily	245201	507	771	2.24E-53	184.362	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8532 - 	CGI_10023323	superfamily	247755	60	277	7.93E-77	243.612	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8532 - 	CGI_10023323	superfamily	247789	350	509	7.19E-17	79.225	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#8533 - 	CGI_10023324	superfamily	247684	47	384	9.27E-63	212.908	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#8534 - 	CGI_10023325	superfamily	247725	436	556	3.55E-57	195.147	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8534 - 	CGI_10023325	superfamily	241645	306	391	1.74E-20	88.7335	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#8535 - 	CGI_10023326	superfamily	247065	46	138	7.86E-18	75.459	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#8536 - 	CGI_10023327	superfamily	241574	272	501	1.60E-68	226.313	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#8537 - 	CGI_10023328	superfamily	187408	309	642	7.52E-126	394.735	cl14654	V_Alix_like superfamily	 - 	 - 	"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain."
Q#8537 - 	CGI_10023328	superfamily	187403	3	304	5.30E-111	355.197	cl14649	BRO1_Alix_like superfamily	N	 - 	"Protein-interacting Bro1-like domain of mammalian Alix and related domains; This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, HD-PTP, and Brox) and Snf7 (in the case of yeast Bro1, and Rim20). The single domain protein human Brox, and the isolated Bro1-like domains of Alix, HD-PTP and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V) domain, which in the case of Alix, has been shown to be a dimerization domain and to contain a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in this superfamily. Alix, HD-PTP and Bro1 also have a proline-rich region (PRR); the Alix PRR binds multiple partners. Rhophilin-1, and -2, in addition to this Bro1-like domain, have an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This protein has a C-terminal, catalytically inactive tyrosine phosphatase domain."
Q#8538 - 	CGI_10023329	superfamily	241884	6	151	2.55E-92	271.143	cl00467	Ntn_hydrolase superfamily	N	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#8542 - 	CGI_10023335	superfamily	116100	195	344	1.24E-60	193.568	cl08454	NAD_Gly3P_dh_C superfamily	 - 	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain.
Q#8542 - 	CGI_10023335	superfamily	201664	6	170	8.29E-55	178.961	cl18216	NAD_Gly3P_dh_N superfamily	 - 	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
Q#8543 - 	CGI_10023336	superfamily	221075	81	195	1.26E-21	86.8055	cl12855	Med30 superfamily	 - 	 - 	"Mediator complex subunit 30; Med30 is a metazoan-specific subunit of Mediator, having no homologues in yeasts."
Q#8545 - 	CGI_10023338	superfamily	146451	91	108	3.97E-05	36.9535	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#8546 - 	CGI_10001125	superfamily	242274	27	174	9.35E-10	53.4872	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#8550 - 	CGI_10005171	superfamily	247097	133	169	0.000442721	39.7418	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#8550 - 	CGI_10005171	superfamily	247097	877	913	0.000667185	38.9714	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#8553 - 	CGI_10005174	superfamily	203591	88	221	4.60E-34	129.028	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#8553 - 	CGI_10005174	superfamily	226728	186	258	3.94E-06	48.3873	cl18775	COG4278 superfamily	NC	 - 	Uncharacterized conserved protein [Function unknown]
Q#8553 - 	CGI_10005174	superfamily	203591	14	91	0.00201623	38.5064	cl06275	DUF1399 superfamily	N	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#8554 - 	CGI_10005175	superfamily	114894	1	217	1.61E-52	175.206	cl17945	GDE_C superfamily	NC	 - 	"Amylo-alpha-1,6-glucosidase; This family includes human glycogen branching enzyme. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homologue that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33)."
Q#8556 - 	CGI_10014412	superfamily	220766	70	250	5.09E-53	175.239	cl11103	MENTAL superfamily	 - 	 - 	"Cholesterol-capturing domain; Human meta-static lymph node (MLN) 64 is a late endosomal membrane protein, and carries this MENTAL (MLN64N-terminal) domain at its N-terminus. The domain is composed of four trans-membrane helices with three short intervening loops. The function of the domain is to capture cholesterol and pass it to the associated START domain pfam01852 for transfer to a cytosolic acceptor protein or membrane. In mammals, the MENTAL domain is involved in the localisation of MLN64 and MENTHO in late endosomes, and also in homo-and of hetero-interactions of these two proteins."
Q#8556 - 	CGI_10014412	superfamily	246681	282	367	1.67E-12	64.6834	cl14643	SRPBCC superfamily	C	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#8559 - 	CGI_10014415	superfamily	245814	71	140	0.000703763	36.6983	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8559 - 	CGI_10014415	superfamily	245814	171	250	5.98E-06	42.6815	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8561 - 	CGI_10014417	superfamily	201778	23	142	6.41E-17	76.8638	cl18219	GFO_IDH_MocA superfamily	 - 	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#8561 - 	CGI_10014417	superfamily	217272	154	217	6.65E-06	44.4476	cl18400	GFO_IDH_MocA_C superfamily	C	 - 	"Oxidoreductase family, C-terminal alpha/beta domain; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#8561 - 	CGI_10014417	superfamily	217272	240	300	0.00937657	34.8176	cl18400	GFO_IDH_MocA_C superfamily	C	 - 	"Oxidoreductase family, C-terminal alpha/beta domain; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#8562 - 	CGI_10014418	superfamily	199528	7	114	0.000202016	38.1533	cl15392	PRK10429 superfamily	C	 - 	melibiose:sodium symporter; Provisional
Q#8563 - 	CGI_10014419	superfamily	201778	21	140	3.75E-21	88.805	cl18219	GFO_IDH_MocA superfamily	 - 	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#8563 - 	CGI_10014419	superfamily	217272	152	215	3.54E-07	48.2996	cl18400	GFO_IDH_MocA_C superfamily	C	 - 	"Oxidoreductase family, C-terminal alpha/beta domain; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#8566 - 	CGI_10014422	superfamily	241563	1	40	5.80E-07	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8567 - 	CGI_10014423	superfamily	245226	55	150	2.76E-09	51.5325	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#8569 - 	CGI_10014425	superfamily	245814	15	84	3.80E-05	40.5503	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8569 - 	CGI_10014425	superfamily	245814	125	208	1.41E-08	50.1965	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8572 - 	CGI_10014428	superfamily	247912	32	277	6.57E-20	89.0976	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#8575 - 	CGI_10014431	superfamily	244539	20	436	8.30E-154	444.842	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#8576 - 	CGI_10014432	superfamily	242895	18	146	1.18E-56	179.351	cl02125	Med6 superfamily	 - 	 - 	MED6 mediator sub complex component; Component of RNA polymerase II holoenzyme and mediator sub complex.
Q#8579 - 	CGI_10014436	superfamily	247724	38	202	2.83E-70	214.715	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8580 - 	CGI_10014437	superfamily	247724	9	178	2.67E-56	177.736	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8581 - 	CGI_10014438	superfamily	248458	96	218	1.08E-05	45.7677	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8588 - 	CGI_10007301	superfamily	245847	22	105	0.00015375	39.7932	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#8589 - 	CGI_10014985	superfamily	241581	25	94	3.46E-09	55.8554	cl00062	FHA superfamily	N	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#8590 - 	CGI_10014986	superfamily	241874	46	566	0	727.163	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#8591 - 	CGI_10014987	superfamily	246671	113	256	1.17E-27	105.198	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#8593 - 	CGI_10014989	superfamily	243555	22	218	3.52E-07	49.3118	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#8595 - 	CGI_10014991	superfamily	193473	1	342	3.61E-43	157.173	cl15668	Acatn superfamily	N	 - 	Acetyl-coenzyme A transporter 1; The mouse Acatn is a 61 kDa hydrophobic protein with six to 10 transmembrane domains. It appears to promote 9-O-acetylation in gangliosides.
Q#8599 - 	CGI_10014995	superfamily	246935	14	97	7.21E-12	58.4484	cl15347	CBM20 superfamily	 - 	 - 	"The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch."
Q#8600 - 	CGI_10014996	superfamily	202715	134	234	7.89E-20	81.4704	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#8601 - 	CGI_10014997	superfamily	241872	104	184	5.60E-16	78.1828	cl00453	CDP-OH_P_transf superfamily	C	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#8602 - 	CGI_10014998	superfamily	246918	31	74	1.45E-07	44.1147	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8603 - 	CGI_10014999	superfamily	245595	477	766	2.70E-177	538.717	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#8603 - 	CGI_10014999	superfamily	245595	31	317	1.41E-151	469.123	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#8603 - 	CGI_10014999	superfamily	248053	770	845	9.82E-31	118.396	cl17499	Peptidase_M14NE-CP-C_like superfamily	 - 	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#8603 - 	CGI_10014999	superfamily	248053	321	396	5.15E-30	116.084	cl17499	Peptidase_M14NE-CP-C_like superfamily	 - 	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#8603 - 	CGI_10014999	superfamily	245595	1230	1495	2.76E-41	156.213	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#8603 - 	CGI_10014999	superfamily	245595	897	1130	4.79E-19	89.1794	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#8603 - 	CGI_10014999	superfamily	248053	1147	1221	1.26E-09	57.2917	cl17499	Peptidase_M14NE-CP-C_like superfamily	 - 	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#8603 - 	CGI_10014999	superfamily	248053	1625	1707	5.51E-05	43.4345	cl17499	Peptidase_M14NE-CP-C_like superfamily	 - 	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#8603 - 	CGI_10014999	superfamily	248053	1562	1618	0.00132696	39.1973	cl17499	Peptidase_M14NE-CP-C_like superfamily	C	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#8604 - 	CGI_10015000	superfamily	241596	511	571	3.64E-15	71.4763	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#8605 - 	CGI_10015001	superfamily	243092	91	363	4.03E-18	82.768	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8605 - 	CGI_10015001	superfamily	245010	366	408	0.00259244	36.1737	cl09111	Prefoldin superfamily	N	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#8606 - 	CGI_10015002	superfamily	150464	46	152	1.83E-14	66.1186	cl10773	Transmemb_17 superfamily	 - 	 - 	Predicted membrane protein; This is a 100 amino acid region of a family of proteins conserved from nematodes to humans. It is predicted to be a transmembrane region but its function is not known.
Q#8607 - 	CGI_10015003	superfamily	241574	131	268	5.61E-30	111.161	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#8607 - 	CGI_10015003	superfamily	241626	9	106	3.49E-09	52.892	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#8608 - 	CGI_10015004	superfamily	247749	2	278	3.90E-173	483.915	cl17195	LDH_MDH_like superfamily	 - 	 - 	"NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others."
Q#8610 - 	CGI_10015006	superfamily	247724	3	74	3.74E-22	88.3611	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8611 - 	CGI_10015007	superfamily	243072	279	404	4.10E-31	118.255	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8611 - 	CGI_10015007	superfamily	243072	494	614	2.38E-29	113.247	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8611 - 	CGI_10015007	superfamily	243072	423	548	1.33E-27	108.24	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8611 - 	CGI_10015007	superfamily	243072	72	197	4.85E-27	106.699	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8611 - 	CGI_10015007	superfamily	243072	138	272	5.89E-25	100.921	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8612 - 	CGI_10015008	superfamily	243072	33	158	5.94E-31	116.329	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8612 - 	CGI_10015008	superfamily	243072	231	356	1.61E-30	114.788	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8612 - 	CGI_10015008	superfamily	243072	297	422	5.68E-28	107.855	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8612 - 	CGI_10015008	superfamily	243072	363	498	1.80E-27	106.699	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8612 - 	CGI_10015008	superfamily	243072	99	224	1.23E-24	98.995	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8613 - 	CGI_10015009	superfamily	248013	63	113	7.97E-07	46.1031	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#8614 - 	CGI_10015010	superfamily	243072	9	76	6.41E-16	71.2606	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8615 - 	CGI_10025236	superfamily	244824	159	565	0	855.761	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#8615 - 	CGI_10025236	superfamily	245008	62	157	1.41E-46	160.006	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#8615 - 	CGI_10025236	superfamily	243149	583	677	2.61E-19	83.941	cl02706	Alpha-amylase_C superfamily	 - 	 - 	"Alpha amylase, C-terminal all-beta domain; Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain."
Q#8616 - 	CGI_10025237	superfamily	217584	226	348	3.63E-22	91.6498	cl04100	MOSC_N superfamily	 - 	 - 	"MOSC N-terminal beta barrel domain; This domain is found to the N-terminus of pfam03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold."
Q#8616 - 	CGI_10025237	superfamily	217583	366	474	1.93E-13	67.0027	cl04097	MOSC superfamily	C	 - 	"MOSC domain; The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters."
Q#8617 - 	CGI_10025238	superfamily	241782	42	382	1.53E-14	73.8446	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#8618 - 	CGI_10025239	superfamily	247799	13	74	8.26E-21	85.6059	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#8618 - 	CGI_10025239	superfamily	247799	273	333	9.06E-18	77.2151	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#8618 - 	CGI_10025239	superfamily	247799	93	157	2.58E-13	64.8051	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#8619 - 	CGI_10025240	superfamily	243035	40	150	6.98E-22	93.4533	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8619 - 	CGI_10025240	superfamily	245814	503	561	0.00923362	35.9279	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8619 - 	CGI_10025240	superfamily	243086	799	842	9.27E-16	73.5633	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#8619 - 	CGI_10025240	superfamily	215647	947	1019	2.52E-13	69.9448	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#8619 - 	CGI_10025240	superfamily	241571	174	269	5.75E-05	42.7847	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8619 - 	CGI_10025240	superfamily	215647	868	926	0.000159216	43.3661	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#8622 - 	CGI_10025243	superfamily	245835	306	465	0.000493439	40.8117	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#8623 - 	CGI_10025244	superfamily	241622	32	118	2.01E-16	74.5254	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#8624 - 	CGI_10025245	superfamily	245814	195	272	0.000462899	38.1759	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8626 - 	CGI_10025247	superfamily	243179	142	240	6.70E-16	71.4099	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#8629 - 	CGI_10025250	superfamily	220695	43	214	9.84E-05	42.1807	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#8630 - 	CGI_10025251	superfamily	247724	66	240	3.07E-104	317.168	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#8630 - 	CGI_10025251	superfamily	243185	251	336	1.90E-32	120.637	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#8630 - 	CGI_10025251	superfamily	243183	468	546	7.46E-31	116.052	cl02785	Elongation_Factor_C superfamily	 - 	 - 	"Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p.  This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain.  EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown."
Q#8630 - 	CGI_10025251	superfamily	203441	555	660	2.76E-36	131.948	cl05759	LepA_C superfamily	 - 	 - 	GTP-binding protein LepA C-terminus; This family consists of the C-terminal region of several pro- and eukaryotic GTP-binding LepA proteins.
Q#8633 - 	CGI_10025254	superfamily	241571	315	414	2.43E-27	107.498	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8633 - 	CGI_10025254	superfamily	241571	79	183	1.78E-17	79.3786	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8633 - 	CGI_10025254	superfamily	241571	457	542	1.64E-13	67.8226	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8633 - 	CGI_10025254	superfamily	241571	209	280	1.80E-09	55.8814	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8633 - 	CGI_10025254	superfamily	241571	3	59	6.92E-05	41.6068	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8636 - 	CGI_10025257	superfamily	245819	421	603	1.94E-54	184.32	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#8636 - 	CGI_10025257	superfamily	219526	203	407	2.82E-100	306.468	cl06648	HNOBA superfamily	 - 	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8636 - 	CGI_10025257	superfamily	203730	2	172	2.34E-69	224.071	cl18246	HNOB superfamily	 - 	 - 	"Heme NO binding; The HNOB (Heme NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8637 - 	CGI_10025258	superfamily	245819	563	741	1.39E-53	183.164	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#8637 - 	CGI_10025258	superfamily	219526	355	550	7.21E-66	219.028	cl06648	HNOBA superfamily	 - 	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8637 - 	CGI_10025258	superfamily	203730	230	313	5.01E-11	61.5164	cl18246	HNOB superfamily	N	 - 	"Heme NO binding; The HNOB (Heme NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8638 - 	CGI_10025259	superfamily	247068	450	550	2.04E-28	109.71	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8638 - 	CGI_10025259	superfamily	247068	233	329	2.56E-26	103.932	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8638 - 	CGI_10025259	superfamily	247068	346	442	4.10E-17	77.7389	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8638 - 	CGI_10025259	superfamily	247068	119	224	2.90E-14	69.6497	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8638 - 	CGI_10025259	superfamily	247068	27	109	6.35E-06	44.6118	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1083	1180	4.39E-29	115.103	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	547	641	1.09E-26	108.17	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1291	1388	1.50E-25	104.703	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	340	436	2.31E-25	104.318	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1188	1283	2.46E-25	104.318	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	650	749	2.73E-25	103.932	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	973	1075	1.67E-24	101.621	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1623	1705	2.58E-23	98.1545	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	444	538	3.18E-23	98.1545	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	235	332	3.49E-22	95.0729	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	871	964	4.63E-22	94.6877	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	2023	2125	3.45E-21	91.9913	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1814	1909	6.80E-20	88.5245	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1926	2013	8.52E-20	88.1393	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1504	1599	4.24E-18	83.1317	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	43	122	2.09E-16	78.1241	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	760	843	5.99E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	131	227	6.62E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1397	1489	3.33E-15	74.6573	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	1713	1806	1.38E-14	73.1165	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	2242	2344	1.05E-10	61.5605	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	247068	2137	2232	2.46E-10	60.4049	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#8639 - 	CGI_10025260	superfamily	216265	2573	2610	0.00224382	39.5932	cl03079	Cadherin_C superfamily	N	 - 	Cadherin cytoplasmic region; Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
Q#8640 - 	CGI_10025261	superfamily	241874	137	508	6.90E-72	246.339	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#8640 - 	CGI_10025261	superfamily	241874	579	707	0.00724425	38.3309	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#8642 - 	CGI_10025264	superfamily	241763	503	712	7.40E-99	305.702	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#8642 - 	CGI_10025264	superfamily	245040	17	90	2.76E-10	58.2544	cl09238	CY superfamily	 - 	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#8642 - 	CGI_10025264	superfamily	245040	101	198	1.21E-06	47.0836	cl09238	CY superfamily	 - 	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#8642 - 	CGI_10025264	superfamily	244586	418	474	4.47E-13	65.3426	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#8644 - 	CGI_10025266	superfamily	245622	175	310	1.19E-21	89.591	cl11446	Rhomboid superfamily	 - 	 - 	"Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite."
Q#8648 - 	CGI_10025270	superfamily	241862	364	514	6.60E-22	94.7304	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#8649 - 	CGI_10025271	superfamily	191243	11	37	3.41E-08	49.3631	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8649 - 	CGI_10025271	superfamily	191243	43	69	1.16E-06	45.1259	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8650 - 	CGI_10025272	superfamily	191243	11	37	0.000133608	38.1923	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8650 - 	CGI_10025272	superfamily	191243	43	69	0.0013096	35.4959	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8651 - 	CGI_10025273	superfamily	191243	324	350	5.72E-05	40.8887	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8651 - 	CGI_10025273	superfamily	191243	11	37	6.37E-05	40.8887	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8651 - 	CGI_10025273	superfamily	191243	299	322	0.000338147	38.5775	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8651 - 	CGI_10025273	superfamily	191243	43	69	0.0010783	37.0367	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#8652 - 	CGI_10025274	superfamily	245230	1	460	0	637.825	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#8653 - 	CGI_10025275	superfamily	247792	25	74	5.06E-09	52.0628	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8653 - 	CGI_10025275	superfamily	110440	299	326	0.00032846	38.1577	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8653 - 	CGI_10025275	superfamily	110440	339	366	0.00174356	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8654 - 	CGI_10025276	superfamily	192535	51	173	0.00623392	36.4198	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#8655 - 	CGI_10025277	superfamily	197509	17	55	0.000284784	37.5477	cl09965	PAC superfamily	 - 	 - 	Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Q#8656 - 	CGI_10025278	superfamily	241596	70	123	2.00E-13	62.2315	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#8656 - 	CGI_10025278	superfamily	243045	155	218	1.92E-09	52.2503	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#8657 - 	CGI_10025279	superfamily	241782	46	393	1.03E-139	405.406	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#8658 - 	CGI_10025280	superfamily	245835	1227	1405	8.53E-40	149.39	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#8658 - 	CGI_10025280	superfamily	243096	1032	1176	1.31E-26	110.465	cl02571	RhoGEF superfamily	N	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#8658 - 	CGI_10025280	superfamily	247683	28	77	1.83E-13	68.2582	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8658 - 	CGI_10025280	superfamily	247683	435	486	9.74E-12	63.2507	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8658 - 	CGI_10025280	superfamily	247683	1663	1719	3.76E-14	70.4783	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8658 - 	CGI_10025280	superfamily	247683	302	353	8.62E-13	66.5944	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8658 - 	CGI_10025280	superfamily	247683	166	215	8.21E-12	63.5278	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8658 - 	CGI_10025280	superfamily	247683	1495	1550	1.33E-11	63.0832	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8658 - 	CGI_10025280	superfamily	247683	95	142	2.15E-10	59.6828	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#8660 - 	CGI_10004439	superfamily	243199	5	87	9.22E-09	53.8342	cl02808	RT_like superfamily	N	 - 	"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs."
Q#8661 - 	CGI_10004440	superfamily	215847	98	147	4.00E-10	58.6119	cl09510	Lipoxygenase superfamily	NC	 - 	Lipoxygenase; Lipoxygenase.  
Q#8662 - 	CGI_10019460	superfamily	217064	157	302	6.54E-18	82.1572	cl03617	CLN3 superfamily	N	 - 	CLN3 protein; This is a family of proteins from the CLN3 gene. A missense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease).
Q#8662 - 	CGI_10019460	superfamily	217064	7	119	3.12E-09	55.9636	cl03617	CLN3 superfamily	C	 - 	CLN3 protein; This is a family of proteins from the CLN3 gene. A missense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease).
Q#8664 - 	CGI_10019462	superfamily	198738	366	453	4.06E-44	150.881	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#8664 - 	CGI_10019462	superfamily	247057	122	190	1.03E-20	85.8505	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#8672 - 	CGI_10019470	superfamily	247787	83	127	6.11E-05	43.2957	cl17233	RecA-like_NTPases superfamily	C	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#8673 - 	CGI_10019471	superfamily	222432	534	618	1.54E-15	73.4962	cl16451	Bravo_FIGEY superfamily	N	 - 	C-terminal domain of Fibronectin type III; This is the very C-terminal region of neural adhesion molecule L1 proteins that are also known as Bravo or NrCAM. It lies upstream of the IG and Fn3 domains and has the highly conserved motif FIGEY. The function is not known.
Q#8673 - 	CGI_10019471	superfamily	245814	193	275	2.45E-11	60.5968	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8673 - 	CGI_10019471	superfamily	245814	47	115	6.49E-08	50.4586	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8673 - 	CGI_10019471	superfamily	245814	297	383	0.00147184	37.379	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#8674 - 	CGI_10019472	superfamily	190271	871	979	1.54E-44	157.476	cl03521	Alpha_adaptin_C superfamily	 - 	 - 	"Alpha adaptin AP2, C-terminal domain; Alpha adaptin is a hetero tetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site."
Q#8674 - 	CGI_10019472	superfamily	243521	767	865	2.08E-20	88.4542	cl03759	Alpha_adaptinC2 superfamily	 - 	 - 	"Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins."
Q#8675 - 	CGI_10019473	superfamily	241636	186	354	3.05E-93	279.473	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#8676 - 	CGI_10019474	superfamily	241636	186	211	2.12E-10	56.0568	cl00145	TBOX superfamily	C	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#8678 - 	CGI_10019476	superfamily	243072	148	312	1.23E-17	79.3498	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8678 - 	CGI_10019476	superfamily	243072	253	383	3.56E-17	77.809	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8679 - 	CGI_10019477	superfamily	243072	227	389	2.69E-15	72.8014	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8679 - 	CGI_10019477	superfamily	243072	162	250	2.59E-12	63.9418	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8679 - 	CGI_10019477	superfamily	243072	329	498	2.65E-09	55.0822	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8680 - 	CGI_10019478	superfamily	218330	158	279	1.35E-48	166.654	cl04847	SHQ1 superfamily	N	 - 	SHQ1 protein; S. cerevisiae SHQ1 protein is required for SnoRNAs of the box H/ACA Quantitative accumulation (unpublished).
Q#8680 - 	CGI_10019478	superfamily	218330	310	413	6.55E-36	131.601	cl04847	SHQ1 superfamily	N	 - 	SHQ1 protein; S. cerevisiae SHQ1 protein is required for SnoRNAs of the box H/ACA Quantitative accumulation (unpublished).
Q#8681 - 	CGI_10019479	superfamily	245598	91	395	6.42E-149	428.983	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#8682 - 	CGI_10019480	superfamily	219963	282	374	9.47E-23	91.1301	cl08487	GCV_T_C superfamily	 - 	 - 	"Glycine cleavage T-protein C-terminal barrel domain; This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyzes the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase."
Q#8683 - 	CGI_10019481	superfamily	221887	11	107	2.86E-24	95.659	cl15229	ING superfamily	 - 	 - 	"Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterized C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail."
Q#8683 - 	CGI_10019481	superfamily	247999	343	390	7.23E-10	54.4188	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#8684 - 	CGI_10019482	superfamily	243083	1197	1308	1.29E-50	175.773	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#8684 - 	CGI_10019482	superfamily	248279	322	441	5.64E-53	182.537	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#8684 - 	CGI_10019482	superfamily	243084	613	710	3.10E-49	171.428	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#8684 - 	CGI_10019482	superfamily	220792	107	248	4.88E-23	97.8618	cl11150	EPL1 superfamily	 - 	 - 	Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.
Q#8684 - 	CGI_10019482	superfamily	247999	282	314	1.24E-14	70.3671	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#8685 - 	CGI_10019483	superfamily	241583	14	163	1.77E-67	228.277	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8685 - 	CGI_10019483	superfamily	149667	1350	1545	8.99E-64	217.238	cl07343	GON superfamily	 - 	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#8685 - 	CGI_10019483	superfamily	246918	947	998	1.96E-05	44.1147	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8685 - 	CGI_10019483	superfamily	246918	611	664	0.000218452	41.0331	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8685 - 	CGI_10019483	superfamily	246918	721	775	0.000684712	39.4923	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8685 - 	CGI_10019483	superfamily	246918	1064	1113	0.00219653	37.9515	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8685 - 	CGI_10019483	superfamily	246918	669	719	0.00671664	36.4107	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#8687 - 	CGI_10019485	superfamily	243072	52	172	2.05E-15	72.031	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8687 - 	CGI_10019485	superfamily	243072	114	239	4.10E-14	68.5642	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8687 - 	CGI_10019485	superfamily	243072	182	315	6.15E-13	65.0974	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8690 - 	CGI_10014037	superfamily	244881	956	1192	1.68E-49	180.162	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#8690 - 	CGI_10014037	superfamily	215788	727	817	2.06E-25	103.413	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#8690 - 	CGI_10014037	superfamily	203720	1365	1445	6.98E-15	72.9662	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#8690 - 	CGI_10014037	superfamily	243064	1466	1558	1.37E-10	61.256	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#8690 - 	CGI_10014037	superfamily	216731	116	192	3.14E-06	47.2535	cl12258	A2M_N superfamily	 - 	 - 	MG2 domain; This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin.
Q#8690 - 	CGI_10014037	superfamily	221351	19	106	0.00774736	36.5187	cl13419	MG1 superfamily	 - 	 - 	Alpha-2-macroglobulin MG1 domain; This is the N-terminal MG1 domain from alpha-2-macroglobulin.
Q#8691 - 	CGI_10014038	superfamily	241596	25	75	3.55E-07	46.0531	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#8691 - 	CGI_10014038	superfamily	243123	93	134	2.70E-07	46.3974	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#8692 - 	CGI_10014039	superfamily	241596	16	66	2.98E-07	46.4383	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#8692 - 	CGI_10014039	superfamily	243123	84	125	4.24E-08	48.3233	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#8693 - 	CGI_10014040	superfamily	243072	856	956	5.20E-18	82.4314	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8693 - 	CGI_10014040	superfamily	243072	915	1001	3.05E-07	50.0746	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8693 - 	CGI_10014040	superfamily	218536	977	1257	5.50E-59	207.968	cl05038	AAR2 superfamily	N	 - 	AAR2 protein; This family consists of several eukaryotic AAR2-like proteins. The yeast protein AAR2 is involved in splicing pre-mRNA of the a1 cistron and other genes that are important for cell growth.
Q#8693 - 	CGI_10014040	superfamily	115363	357	424	1.04E-21	91.2793	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8693 - 	CGI_10014040	superfamily	241760	81	125	1.19E-16	76.3431	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#8693 - 	CGI_10014040	superfamily	241760	441	480	1.50E-11	61.7055	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#8693 - 	CGI_10014040	superfamily	115363	8	70	2.73E-11	61.2337	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8693 - 	CGI_10014040	superfamily	115363	543	574	2.30E-05	43.8998	cl05972	MIB_HERC2 superfamily	N	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8695 - 	CGI_10014042	superfamily	241754	12	688	0	1091.86	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#8695 - 	CGI_10014042	superfamily	218855	832	1025	2.49E-32	125.877	cl10652	Myosin_TH1 superfamily	 - 	 - 	Myosin tail; Myosin tail.  
Q#8698 - 	CGI_10014045	superfamily	243109	1	45	2.74E-33	114.732	cl02614	SPRY superfamily	N	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#8698 - 	CGI_10014045	superfamily	243073	50	91	5.12E-17	68.8678	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#8699 - 	CGI_10014046	superfamily	245836	332	514	1.82E-98	308.497	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#8699 - 	CGI_10014046	superfamily	244947	520	658	8.75E-85	269.233	cl08424	OBF_DNA_ligase_family superfamily	 - 	 - 	"The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain."
Q#8699 - 	CGI_10014046	superfamily	189650	9	95	2.46E-25	101.59	cl02913	zf-PARP superfamily	 - 	 - 	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
Q#8699 - 	CGI_10014046	superfamily	204434	763	788	2.46E-08	51.4265	cl10963	zf-CCHH superfamily	 - 	 - 	"Zinc-finger (CX5CX6HX5H) motif; This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism."
Q#8700 - 	CGI_10014047	superfamily	247095	54	467	1.97E-140	412.435	cl15837	alkPPc superfamily	 - 	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#8702 - 	CGI_10014049	superfamily	243045	346	435	1.26E-10	60.3395	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#8702 - 	CGI_10014049	superfamily	221427	931	962	0.000686027	40.8908	cl13540	Period_C superfamily	NC	 - 	Period protein 2/3C-terminal region; This domain is found in eukaryotes. This domain is typically between 164 to 200 amino acids in length. This domain is found associated with pfam08447.
Q#8703 - 	CGI_10014050	superfamily	243034	180	296	2.14E-09	53.538	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#8703 - 	CGI_10014050	superfamily	215821	29	90	2.33E-05	41.8423	cl18346	FKBP_C superfamily	C	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#8704 - 	CGI_10014051	superfamily	221999	391	612	8.77E-117	365.776	cl16180	CLU superfamily	 - 	 - 	"Clustered mitochondria; The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in proteins from fungi, protozoa, plants to humans. It is required for correct functioning of the mitochondria and mitochondrial transport although the exact function of the domain is unknown. In Dictyostelium the full-length protein is required for a very late step in fission of the outer mitochondrial membrane suggesting that mitochondria are transported along microtubules, as in mammalian cells, rather than along actin filaments, as in budding yeast. Disruption of the protein-impaired cytokinesis and caused mitochondria to cluster at the cell centre. It is likely that CLU functions in a novel pathway that positions mitochondria within the cell based on their physiological state. Disruption of the CLU pathway may enhance oxidative damage, alter gene expression, cause mitochondria to cluster at microtubule plus ends, and lead eventually to mitochondrial failure."
Q#8704 - 	CGI_10014051	superfamily	221783	801	987	4.41E-58	199.528	cl15102	eIF3_p135 superfamily	 - 	 - 	"Translation initiation factor eIF3 subunit 135; Translation initiation factor eIF3 is a multi-subunit protein complex required for initiation of protein biosynthesis in eukaryotic cells. The complex promotes ribosome dissociation, the binding of the initiator methionyl-tRNA to the 40 S ribosomal subunit, and mRNA recruitment to the ribosome. The protein product from TIF31 genes in yeast is p135 which associates with the eIF3 but does not seem to be necessary for protein translation initiation."
Q#8704 - 	CGI_10014051	superfamily	248006	1058	1098	0.000255408	40.6323	cl17452	TPR_10 superfamily	 - 	 - 	Tetratricopeptide repeat; Tetratricopeptide repeat.  
Q#8704 - 	CGI_10014051	superfamily	248006	1183	1222	0.000671873	39.0915	cl17452	TPR_10 superfamily	 - 	 - 	Tetratricopeptide repeat; Tetratricopeptide repeat.  
Q#8705 - 	CGI_10014052	superfamily	242921	24	197	4.18E-82	244.437	cl02175	Rer1 superfamily	 - 	 - 	Rer1 family; RER1 family protein are involved in involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi compartment. The C terminus of yeast Rer1p interacts with a coatomer complex.
Q#8706 - 	CGI_10014053	superfamily	247755	570	806	7.08E-138	411.163	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8706 - 	CGI_10014053	superfamily	216049	249	525	5.16E-44	160.529	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#8707 - 	CGI_10014054	superfamily	243092	221	466	9.49E-60	206.417	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8708 - 	CGI_10014055	superfamily	242912	1	175	3.55E-101	292.203	cl02161	Ssu72 superfamily	 - 	 - 	"Ssu72-like protein; The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs."
Q#8709 - 	CGI_10014056	superfamily	245225	1107	1161	3.39E-06	49.464	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#8709 - 	CGI_10014056	superfamily	245225	949	1032	0.00543024	39.2764	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	NC	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#8710 - 	CGI_10014057	superfamily	245819	669	845	3.07E-61	205.506	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#8710 - 	CGI_10014057	superfamily	245201	371	596	1.13E-23	101.459	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8710 - 	CGI_10014057	superfamily	219526	614	655	0.000497132	41.0655	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8711 - 	CGI_10014058	superfamily	248279	7	41	0.00680124	34.2643	cl17725	zf-HC5HC2H superfamily	NC	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#8712 - 	CGI_10014059	superfamily	202484	7	66	5.62E-16	68.0244	cl03798	zf-Tim10_DDP superfamily	 - 	 - 	Tim10/DDP family zinc finger; Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein TIMM8A. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localised to the mitochondrial intermembrane space.
Q#8713 - 	CGI_10014060	superfamily	247097	120	153	0.00948862	31.9661	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#8714 - 	CGI_10002449	superfamily	245226	261	472	1.22E-50	175.174	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#8714 - 	CGI_10002449	superfamily	224570	531	723	2.00E-10	59.3966	cl18705	COG1656 superfamily	 - 	 - 	Uncharacterized conserved protein [Function unknown]
Q#8716 - 	CGI_10002451	superfamily	247684	1	238	4.60E-121	352.324	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#8717 - 	CGI_10002452	superfamily	242232	111	160	1.47E-11	56.4124	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#8718 - 	CGI_10002453	superfamily	220783	2	92	1.33E-13	66.6863	cl11136	Syntaxin-18_N superfamily	 - 	 - 	"SNARE-complex protein Syntaxin-18 N-terminus; This is the conserved N-terminal of Syntaxin-18. Syntaxin-18 is found in the SNARE complex of the endoplasmic reticulum and functions in the trafficking between the ER intermediate compartment and the cis-Golgi vesicle. In particular, the N-terminal region is important for the formation of ER aggregates. More specifically, syntaxin-18 is involved in endoplasmic reticulum-mediated phagocytosis, presumably by regulating the specific and direct fusion of the ER with the plasma or phagosomal membranes."
Q#8727 - 	CGI_10004075	superfamily	245599	220	423	7.83E-144	412.452	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#8727 - 	CGI_10004075	superfamily	207662	124	200	1.42E-54	178.125	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#8730 - 	CGI_10004078	superfamily	243072	697	831	3.58E-21	91.291	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8730 - 	CGI_10004078	superfamily	243072	391	520	4.25E-19	85.513	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8730 - 	CGI_10004078	superfamily	243072	548	655	1.24E-16	78.1942	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8730 - 	CGI_10004078	superfamily	243072	759	922	9.33E-15	72.8014	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8730 - 	CGI_10004078	superfamily	243072	293	452	0.00068426	39.6743	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8731 - 	CGI_10004079	superfamily	243072	387	463	3.95E-16	75.4978	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8736 - 	CGI_10014021	superfamily	241600	18	65	1.37E-15	67.2655	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8737 - 	CGI_10014022	superfamily	241600	107	282	5.66E-63	200.159	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8737 - 	CGI_10014022	superfamily	241600	3	91	6.75E-32	118.882	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8739 - 	CGI_10014025	superfamily	241600	67	199	7.67E-57	180.899	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8745 - 	CGI_10014031	superfamily	219673	159	377	1.64E-112	331.185	cl06835	COPIIcoated_ERV superfamily	 - 	 - 	"Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localisation. All proteins identified biochemically as Erv41p-Erv46p interactors are localised to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi."
Q#8745 - 	CGI_10014031	superfamily	206021	9	113	1.83E-56	182.694	cl16436	ERGIC_N superfamily	 - 	 - 	"Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ERGIC proteins, ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, pfam07970."
Q#8746 - 	CGI_10014032	superfamily	220650	12	78	2.71E-17	69.6589	cl10931	Romo1 superfamily	 - 	 - 	"Reactive mitochondrial oxygen species modulator 1; This is a family of small, approximately 100 amino acid, proteins found from yeasts to humans. The majority of endogenous reactive oxygen species (ROS) in cells are produced by the mitochondrial respiratory chain. An increase or imbalance in ROS alters the intracellular redox homeostasis, triggers DNA damage, and may contribute to cancer development and progression. Members of this family are mitochondrial reactive oxygen species modulator 1 (Romo1) proteins that are responsible for increasing the level of ROS in cells. Increased Romo1 expression can have a number of other effects including: inducing premature senescence of cultured human fibroblasts and increased resistance to 5-fluorouracil."
Q#8748 - 	CGI_10014034	superfamily	247805	336	491	6.51E-18	82.3852	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#8748 - 	CGI_10014034	superfamily	247905	684	817	1.73E-13	68.8036	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#8748 - 	CGI_10014034	superfamily	246680	118	197	1.78E-08	53.0742	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8748 - 	CGI_10014034	superfamily	213148	548	678	9.29E-08	51.5438	cl17041	helicase_insert_domain superfamily	 - 	 - 	"helical domain inserted in SF2-type helicase domain in Hef-, MDA5- and FancM-like proteins; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex."
Q#8749 - 	CGI_10014035	superfamily	246680	120	211	4.75E-08	49.9926	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8749 - 	CGI_10014035	superfamily	246680	30	112	0.000109585	39.9774	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8750 - 	CGI_10010799	superfamily	238012	305	353	3.23E-06	43.8822	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8750 - 	CGI_10010799	superfamily	238012	219	255	4.69E-05	40.4154	cl11390	EGF_Lam superfamily	N	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8750 - 	CGI_10010799	superfamily	238012	50	90	8.35E-05	39.645	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8750 - 	CGI_10010799	superfamily	238012	258	299	0.000293401	38.1042	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8750 - 	CGI_10010799	superfamily	238012	4	45	0.000361491	37.719	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8750 - 	CGI_10010799	superfamily	238012	159	205	0.000940214	36.5634	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#8753 - 	CGI_10010802	superfamily	245205	35	91	0.000801621	36.0617	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#8754 - 	CGI_10010803	superfamily	243091	6	57	0.000574695	36.5435	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#8755 - 	CGI_10010804	superfamily	241600	176	248	1.35E-18	80.399	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8756 - 	CGI_10010805	superfamily	247637	2	331	3.73E-156	443.628	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#8757 - 	CGI_10010806	superfamily	241600	75	162	2.77E-43	145.461	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8757 - 	CGI_10010806	superfamily	241619	10	54	2.00E-05	40.2581	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#8759 - 	CGI_10010808	superfamily	242296	235	273	0.00899913	33.6535	cl01090	SlyX superfamily	C	 - 	SlyX; The SlyX protein has no known function. It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure.
Q#8760 - 	CGI_10010809	superfamily	219097	7	203	7.73E-91	283.632	cl18491	Muskelin_N superfamily	 - 	 - 	"Muskelin N-terminus; This family represents the N-terminal region of muskelin and is found in conjunction with several pfam01344 repeats. Muskelin is an intracellular, kelch repeat protein that is needed in cell-spreading responses to the matrix adhesion molecule, thrombospondin-1."
Q#8760 - 	CGI_10010809	superfamily	243146	278	330	1.03E-06	46.5135	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#8761 - 	CGI_10010810	superfamily	216101	55	653	1.38E-176	537.647	cl08288	Carn_acyltransf superfamily	 - 	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#8762 - 	CGI_10010811	superfamily	222557	26	201	2.01E-76	231.716	cl16634	DUF4291 superfamily	 - 	 - 	Domain of unknown function (DUF4291); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 190 and 214 amino acids in length. There are two conserved sequence motifs: VYQAY and RMTW.
Q#8763 - 	CGI_10019317	superfamily	243035	34	106	9.70E-07	47.9998	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8763 - 	CGI_10019317	superfamily	243035	678	751	1.06E-06	47.9998	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8763 - 	CGI_10019317	superfamily	243035	142	258	6.12E-06	45.3034	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8763 - 	CGI_10019317	superfamily	241568	606	660	0.0013419	37.8276	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#8767 - 	CGI_10019321	superfamily	245213	1518	1552	3.66E-08	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8767 - 	CGI_10019321	superfamily	245213	1558	1584	0.000789137	39.3822	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#8770 - 	CGI_10019324	superfamily	243109	874	1006	3.99E-70	234.117	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#8770 - 	CGI_10019324	superfamily	243109	439	588	1.17E-68	230.662	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#8770 - 	CGI_10019324	superfamily	243109	1422	1567	5.00E-63	214.472	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#8770 - 	CGI_10019324	superfamily	216456	234	440	3.52E-72	243	cl03182	RYDR_ITPR superfamily	 - 	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#8770 - 	CGI_10019324	superfamily	216456	2119	2363	2.81E-54	191.383	cl03182	RYDR_ITPR superfamily	 - 	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#8770 - 	CGI_10019324	superfamily	202095	758	851	4.03E-37	137.75	cl03409	RyR superfamily	 - 	 - 	RyR domain; This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
Q#8770 - 	CGI_10019324	superfamily	202095	643	735	5.78E-32	123.113	cl03409	RyR superfamily	 - 	 - 	RyR domain; This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
Q#8770 - 	CGI_10019324	superfamily	197746	7	60	0.00040581	40.7875	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#8770 - 	CGI_10019324	superfamily	197746	66	92	0.000745481	40.0171	cl02624	MIR superfamily	C	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#8771 - 	CGI_10019325	superfamily	247856	757	812	1.42E-12	65.2617	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8771 - 	CGI_10019325	superfamily	219849	553	675	5.43E-36	134.234	cl09597	RIH_assoc superfamily	 - 	 - 	"RyR and IP3R Homology associated; This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815."
Q#8771 - 	CGI_10019325	superfamily	219038	1113	1244	2.11E-35	136.371	cl05786	RR_TM4-6 superfamily	N	 - 	Ryanodine Receptor TM 4-6; This region covers TM regions 4-6 of the ryanodine receptor 1 family.
Q#8771 - 	CGI_10019325	superfamily	247739	471	516	0.00183332	38.2676	cl17185	LPLAT superfamily	N	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#8775 - 	CGI_10019329	superfamily	245201	55	288	1.27E-81	264.382	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8775 - 	CGI_10019329	superfamily	247694	749	846	7.50E-71	229.256	cl17070	AMPKA_C_like superfamily	 - 	 - 	"C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha subunit and similar domains; This family is composed of AMPKs, microtubule-associated protein/microtubule affinity regulating kinases (MARKs), yeast Kcc4p-like proteins, plant calcineurin B-Like (CBL)-interacting protein kinases (CIPKs), and similar proteins. They are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. AMPKs act as sensors for the energy status of the cell and are activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. MARKs phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Kcc4p and related proteins are septin-associated proteins that are involved in septin organization and in the yeast morphogenesis checkpoint coordinating the cell cycle with bud formation. CIPKs interact with the calcineurin B-like (CBL) calcium sensors to form a signaling network that decode specific calcium signals triggered by a variety of environmental stimuli including salinity, drought, cold, light, and mechanical perturbation, among others. All members of this family contain an N-terminal catalytic kinase domain and a C-terminal regulatory domain which is also called kinase associated domain 1 (KA1) in some cases. The C-terminal regulatory domain serves as a protein interaction domain in AMPKs and CIPKs. In MARKs and Kcc4p-like proteins, this domain binds phospholipids and may be involved in membrane localization."
Q#8775 - 	CGI_10019329	superfamily	241643	362	398	0.00137688	37.466	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#8776 - 	CGI_10019330	superfamily	150144	14	113	1.01E-17	77.1282	cl09624	Tex_N superfamily	C	 - 	Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Bordetella pertussis tex. This protein defines a novel family of prokaryotic transcriptional accessory factors.
Q#8777 - 	CGI_10019331	superfamily	245202	91	150	5.38E-22	84.592	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#8778 - 	CGI_10019332	superfamily	247787	63	306	1.97E-63	202.428	cl17233	RecA-like_NTPases superfamily	 - 	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#8780 - 	CGI_10019334	superfamily	241550	382	627	7.51E-70	233.663	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#8780 - 	CGI_10019334	superfamily	241550	64	178	1.74E-42	157.009	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#8780 - 	CGI_10019334	superfamily	245839	631	724	2.59E-06	47.1344	cl12020	Anticodon_Ia_like superfamily	C	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#8782 - 	CGI_10019336	superfamily	206088	10	31	0.00166821	34.6191	cl16476	zf-CCHC_3 superfamily	C	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#8783 - 	CGI_10011123	superfamily	244824	103	561	4.68E-119	365.143	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#8785 - 	CGI_10011125	superfamily	243034	388	484	1.60E-22	92.8283	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#8785 - 	CGI_10011125	superfamily	243034	10	109	1.51E-20	87.0503	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#8785 - 	CGI_10011125	superfamily	243034	253	352	1.71E-14	69.7163	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#8785 - 	CGI_10011125	superfamily	128966	513	552	2.32E-05	42.2546	cl17974	STI1 superfamily	 - 	 - 	Heat shock chaperonin-binding motif; Heat shock chaperonin-binding motif.  
Q#8786 - 	CGI_10011126	superfamily	241580	132	210	1.32E-42	146.93	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#8787 - 	CGI_10011127	superfamily	241758	1	194	7.19E-83	261.002	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#8787 - 	CGI_10011127	superfamily	245229	415	535	5.59E-30	114.734	cl10015	YjgF_YER057c_UK114_family superfamily	 - 	 - 	"YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site."
Q#8787 - 	CGI_10011127	superfamily	245229	308	387	7.48E-17	76.9121	cl10015	YjgF_YER057c_UK114_family superfamily	 - 	 - 	"YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site."
Q#8790 - 	CGI_10011130	superfamily	245201	571	830	1.05E-108	342.979	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8791 - 	CGI_10011131	superfamily	241563	13	46	0.00307776	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8793 - 	CGI_10011133	superfamily	216062	79	308	1.60E-55	186.104	cl02928	TGFb_propeptide superfamily	 - 	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#8793 - 	CGI_10011133	superfamily	243062	360	461	2.87E-54	178.238	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#8794 - 	CGI_10011134	superfamily	243092	843	1117	2.78E-64	220.284	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8794 - 	CGI_10011134	superfamily	243074	467	507	8.16E-10	56.3609	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#8795 - 	CGI_10011135	superfamily	203311	30	180	1.73E-34	122.438	cl18239	CDKN3 superfamily	 - 	 - 	Cyclin-dependent kinase inhibitor 3 (CDKN3); This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a human dual specificity protein phosphatase that dephosphorylates Cdk2 on threonine 160 in a cyclin-dependent manner.
Q#8796 - 	CGI_10028418	superfamily	241578	5	180	1.42E-12	63.739	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#8797 - 	CGI_10028419	superfamily	248119	17	123	3.37E-12	59.232	cl17565	TerD_like superfamily	N	 - 	"Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Tellurium resistance terD like proteins. This family is composed of uncharacterized proteins involved in stress response, such as the tellurium resistance proteins, chemical-damaging agent resistance proteins, and general stress proteins from a variety of organisms. The tellurium resistance proteins are homologous terA,-D,-E,-F,-Z,-X gene products, which confer tellurium resistance mediated by plasmids. Currently, the biochemical mechanism of tellurium resistance remains unknown. The family also contains several ter gene homologues, YceC, YceD, YceE, for which there is no clear evidence for any involvement in the tellurium resistance. A putative cAMP-binding protin CABP1 shows a significant similarity to the terD protein and is also included in this family."
Q#8798 - 	CGI_10028420	superfamily	243092	29	148	0.00042299	42.7072	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8799 - 	CGI_10028421	superfamily	243092	687	952	1.12E-65	222.981	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8799 - 	CGI_10028421	superfamily	248020	28	387	4.16E-48	175.345	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#8799 - 	CGI_10028421	superfamily	208922	538	607	5.67E-13	67.2183	cl08418	TAF5_NTD2 superfamily	C	 - 	"TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID); The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs.  In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. TAF5 has a paralog gene (TAF5L) which has a redundant function. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. C-terminus of TAF5 contains six WD40 repeats that likely form a closed beta propeller structure and may be involved in protein-protein interaction. The first part of the TAF5 N-terminal (TAF5_NTD1) homodimerizes in the absence of other TAFs. The second conserved N-terminal part of TAF5 (TAF5_NTD2) has an alpha-helical domain. One study has shown that TAF5_NTD2 homodimerizes only at high concentration of calcium but not any other metals. No dimerization was observed in other structural studies of TAF_NTD2. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. However, TAF5 does not have a HFD motif."
Q#8802 - 	CGI_10028424	superfamily	216981	35	73	0.000453279	38.2826	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#8802 - 	CGI_10028424	superfamily	243176	131	154	0.00449485	37.2783	cl02777	chaperonin_like superfamily	NC	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#8806 - 	CGI_10028428	superfamily	245226	80	230	2.58E-18	80.0372	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#8806 - 	CGI_10028428	superfamily	244936	262	312	0.00813789	35.3212	cl08398	MltA superfamily	C	 - 	MltA specific insert domain; This beta barrel domain is found inserted in the MltA a murein degrading transglycosylase enzyme. This domain may be involved in peptidoglycan binding.
Q#8808 - 	CGI_10028430	superfamily	243051	26	135	2.65E-10	55.0493	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#8809 - 	CGI_10028431	superfamily	246664	303	679	2.81E-148	449.718	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#8809 - 	CGI_10028431	superfamily	246664	893	995	1.47E-30	126.27	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#8809 - 	CGI_10028431	superfamily	246664	154	240	1.83E-05	46.894	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#8810 - 	CGI_10028432	superfamily	243027	8	84	6.47E-22	83.4811	cl02418	Hormone_5 superfamily	 - 	 - 	"Neurohypophysial hormones, C-terminal Domain; N-terminal Domain is in hormone5"
Q#8813 - 	CGI_10028435	superfamily	241780	17	299	2.78E-127	373.719	cl00319	Gn_AT_II superfamily	 - 	 - 	"Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate.  Asparagine synthetase B  synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the formation of the beta-lactam ring in the beta-lactamase inhibitor clavulanic acid. GltS synthesizes L-glutamate from 2-oxoglutarate and L-glutamine. These enzymes are generally dimers, but GPATase also exists as a homotetramer."
Q#8813 - 	CGI_10028435	superfamily	241770	310	445	2.08E-15	72.8136	cl00309	PRTases_typeI superfamily	 - 	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#8814 - 	CGI_10028436	superfamily	241708	7	257	4.42E-164	464.458	cl00231	SAICAR_synt superfamily	 - 	 - 	"5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; SAICAR synthetase (the PurC gene product) catalyzes the seventh step of the de novo biosynthesis of purine nucleotides (also reported as eighth step). It converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP, and phosphate."
Q#8814 - 	CGI_10028436	superfamily	241771	267	417	3.22E-48	163.555	cl00310	AIRC superfamily	 - 	 - 	AIR carboxylase; Members of this family catalyze the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyze the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain.
Q#8817 - 	CGI_10028439	superfamily	245201	965	1217	3.65E-83	273.643	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8817 - 	CGI_10028439	superfamily	247856	1256	1307	8.20E-05	42.1497	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8817 - 	CGI_10028439	superfamily	245201	582	847	1.63E-28	116.795	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8817 - 	CGI_10028439	superfamily	247725	188	319	2.40E-16	78.1464	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8817 - 	CGI_10028439	superfamily	246908	430	502	8.40E-11	60.7613	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#8817 - 	CGI_10028439	superfamily	246908	305	377	9.58E-10	57.6797	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#8818 - 	CGI_10028440	superfamily	247057	499	569	2.39E-32	119.063	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#8818 - 	CGI_10028440	superfamily	248259	129	227	7.16E-39	137.766	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#8818 - 	CGI_10028440	superfamily	248259	23	118	1.25E-36	131.603	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#8818 - 	CGI_10028440	superfamily	221437	305	415	2.58E-35	128.627	cl13561	DUF3588 superfamily	 - 	 - 	"Protein of unknown function (DUF3588); This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 866 amino acids in length, and the family is found in association with pfam02820. The exact function of this family is not known."
Q#8819 - 	CGI_10028441	superfamily	248458	1	274	3.74E-11	61.9461	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8820 - 	CGI_10028442	superfamily	248458	73	435	1.36E-17	82.7469	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#8821 - 	CGI_10028443	superfamily	215847	72	111	5.65E-06	43.2039	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#8822 - 	CGI_10028445	superfamily	215847	109	232	1.54E-19	86.7314	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#8823 - 	CGI_10028446	superfamily	243199	37	78	4.43E-13	62.2277	cl02808	RT_like superfamily	C	 - 	"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs."
Q#8824 - 	CGI_10028447	superfamily	206130	85	114	0.000342324	38.3387	cl16501	DUF4218 superfamily	NC	 - 	Domain of unknown function (DUF4218); Domain of unknown function (DUF4218).  
Q#8829 - 	CGI_10028452	superfamily	246675	19	292	4.39E-101	300.312	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#8831 - 	CGI_10028454	superfamily	245201	7	119	3.40E-19	81.5141	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8832 - 	CGI_10028455	superfamily	243072	129	250	2.17E-32	123.648	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8832 - 	CGI_10028455	superfamily	246680	799	873	5.20E-07	48.5955	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#8834 - 	CGI_10028457	superfamily	243082	561	800	1.77E-34	136.561	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#8834 - 	CGI_10028457	superfamily	243082	79	227	1.56E-22	99.9674	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#8834 - 	CGI_10028457	superfamily	177476	942	1046	0.0058396	38.9543	cl14386	PHA02694 superfamily	C	 - 	hypothetical protein; Provisional
Q#8835 - 	CGI_10028458	superfamily	245201	489	739	2.27E-67	224.706	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8835 - 	CGI_10028458	superfamily	241645	97	174	1.64E-11	61.4365	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#8836 - 	CGI_10028459	superfamily	241645	24	105	3.71E-22	84.1632	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#8838 - 	CGI_10028461	superfamily	246908	61	147	3.26E-42	146.355	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#8838 - 	CGI_10028461	superfamily	241566	228	277	3.94E-15	70.2135	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#8838 - 	CGI_10028461	superfamily	243095	288	483	1.75E-72	230.867	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#8845 - 	CGI_10028468	superfamily	241766	298	406	0.000137146	42.4155	cl00303	PNP_UDP_1 superfamily	C	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#8846 - 	CGI_10028469	superfamily	247723	43	120	1.09E-42	144.821	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#8846 - 	CGI_10028469	superfamily	247723	134	206	3.93E-27	102.336	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#8847 - 	CGI_10028470	superfamily	241569	128	181	2.40E-20	80.834	cl00044	ChSh superfamily	 - 	 - 	"Chromo Shadow Domain,  found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2)"
Q#8847 - 	CGI_10028470	superfamily	248013	32	75	3.81E-13	61.1259	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#8848 - 	CGI_10028471	superfamily	245208	90	461	0	633.769	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#8850 - 	CGI_10028473	superfamily	247792	99	146	0.000339004	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8855 - 	CGI_10028478	superfamily	247792	247	293	3.61E-07	47.8256	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8855 - 	CGI_10028478	superfamily	243092	392	587	1.88E-09	58.1152	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8856 - 	CGI_10028479	superfamily	242307	44	135	1.49E-20	81.1556	cl01110	Sdh5 superfamily	 - 	 - 	"Flavinator of succinate dehydrogenase; This family of uncharacterized proteins. Based on personal observation it was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true.This family is now found to be a highly conserved mitochondrial protein, Sdh5. Both yeast and human Sdh5 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Mutational inactivation of Sdh5 confers tumor susceptibility in humans."
Q#8857 - 	CGI_10028480	superfamily	243056	53	249	2.76E-08	51.9761	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#8858 - 	CGI_10028481	superfamily	247057	388	443	4.29E-06	44.1525	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#8858 - 	CGI_10028481	superfamily	221744	30	140	0.00212626	38.1859	cl18614	CABIT superfamily	N	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#8862 - 	CGI_10028485	superfamily	207668	68	107	9.82E-16	66.061	cl02609	TFIIS_C superfamily	 - 	 - 	Transcription factor S-II (TFIIS); Transcription factor S-II (TFIIS).  
Q#8862 - 	CGI_10028485	superfamily	243156	4	53	3.77E-11	53.9281	cl02717	RNA_POL_M_15KD superfamily	 - 	 - 	RNA polymerases M/15 Kd subunit; RNA polymerases M/15 Kd subunit.  
Q#8867 - 	CGI_10028490	superfamily	243072	51	158	4.04E-19	79.3498	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8868 - 	CGI_10028491	superfamily	243035	41	81	5.70E-05	41.0662	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#8868 - 	CGI_10028491	superfamily	243091	119	231	1.85E-08	51.9515	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#8870 - 	CGI_10028493	superfamily	239753	143	269	4.34E-80	239.981	cl15890	Sina superfamily	 - 	 - 	"Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins that function as E3 ubiquitin ligases, acting either as single proteins or as a part of multiprotein complexes. Sina is expressed in many cells in the developing eye but is essential specifically for R7 photoreceptor cell development. Sina cooperates with Phyllopod (Phyl), Ebi and the E2 ubiquitin-conjugating enzyme Ubcd1 to catalyze the ubiquitination and subsequent degradation of Tramtrack (Ttk88); Ttk88 is a transcriptional repressor that blocks photoreceptor differentiation. Similarly, the mammalian homologue Siah1 cooperates with SIP (Siah-interacting protein), Ebi and the adaptor protein Skp1, to target beta-catenin for ubiquitination and degradation via a p53-dependent mechanism. SINAT5 targets NAC1 for ubiquitin-mediated degradation resulting in the downregulation of auxin, a hormone that controls many aspects of plant development. Other targets of Sina family proteins include c-Myb, synaptophysin, group 1 glutamate receptors, promyelocytic leukemia protein, alpha-synuclein, synphilin-1 and alpha-ketoglutarate dehydrogenase, among others. Sina proteins also bind proteins that are not targets for ubiquitination such as Phyl, adenomatous polyposis coli, VAV, BAG-1 and Dab-1. Siah binds to a consensus motif, PXAXVXP, which is present in Siah-binding proteins. Siah is a dimeric protein consisting of an N-terminal RING domain, two zinc finger motifs and a C-terminal substrate-binding domain (SBD); this SBD contains an eight-stranded antiparallel beta-sandwich fold similar to the MATH (meprin and TRAF-C homology) domain."
Q#8870 - 	CGI_10028493	superfamily	247792	28	67	0.00721554	33.5732	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#8872 - 	CGI_10028495	superfamily	241547	71	239	1.77E-32	120.08	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#8872 - 	CGI_10028495	superfamily	241547	44	96	1.85E-05	43.8417	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#8873 - 	CGI_10028496	superfamily	241867	75	286	1.07E-17	81.0606	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#8874 - 	CGI_10028497	superfamily	241609	31	117	2.02E-19	79.3443	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#8877 - 	CGI_10028500	superfamily	216574	74	214	4.60E-30	114.612	cl14794	FAD_binding_4 superfamily	 - 	 - 	"FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan."
Q#8877 - 	CGI_10028500	superfamily	219706	478	514	3.82E-06	44.4492	cl06869	BBE superfamily	 - 	 - 	Berberine and berberine like; This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyze the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine.
Q#8879 - 	CGI_10028502	superfamily	245201	99	338	1.96E-12	64.5653	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#8882 - 	CGI_10028505	superfamily	243034	292	373	1.13E-07	51.2268	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#8883 - 	CGI_10028506	superfamily	241566	264	313	3.84E-14	67.5171	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#8883 - 	CGI_10028506	superfamily	241566	337	387	3.58E-10	55.9612	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#8883 - 	CGI_10028506	superfamily	247725	75	169	2.44E-33	121.683	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8883 - 	CGI_10028506	superfamily	248019	423	498	6.22E-28	107.768	cl17465	DAGK_cat superfamily	C	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#8885 - 	CGI_10028508	superfamily	244875	18	309	5.11E-60	195.698	cl08255	Na_K-ATPase superfamily	 - 	 - 	Sodium / potassium ATPase beta chain; Sodium / potassium ATPase beta chain.  
Q#8886 - 	CGI_10028509	superfamily	243092	142	448	1.21E-83	263.812	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8886 - 	CGI_10028509	superfamily	199226	6	32	1.13E-07	48.4679	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#8887 - 	CGI_10028510	superfamily	247725	16	135	5.57E-18	77.1987	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8888 - 	CGI_10028511	superfamily	245602	353	746	4.81E-154	457.401	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#8888 - 	CGI_10028511	superfamily	241612	81	122	0.009986	35.0122	cl00103	Trefoil superfamily	N	 - 	"P or trefoil or TFF domain; Trefoil factor family domain peptides are mucin-associated molecules, largely found in epithelia of gastrointestinal tissues. Function is not known but it was originally identified from mucosal tissues, where it may have a regulatory or structural role and has also been implicated as a growth fractor in other tissues.The domain is found in 1 to 6 copies where it occurs."
Q#8889 - 	CGI_10028512	superfamily	245602	369	726	1.54E-126	388.45	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#8890 - 	CGI_10028513	superfamily	245602	332	727	5.79E-179	526.737	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#8891 - 	CGI_10028514	superfamily	241583	130	282	1.84E-76	241.339	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#8891 - 	CGI_10028514	superfamily	243048	312	501	5.69E-48	166.718	cl02471	HX superfamily	 - 	 - 	Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat.
Q#8891 - 	CGI_10028514	superfamily	216518	52	102	1.60E-11	60.2365	cl18368	PG_binding_1 superfamily	 - 	 - 	Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.
Q#8892 - 	CGI_10028515	superfamily	247098	32	158	7.80E-72	215.082	cl15841	COG0229 superfamily	 - 	 - 	"Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]"
Q#8896 - 	CGI_10009337	superfamily	218493	48	195	1.77E-43	146.348	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#8897 - 	CGI_10009338	superfamily	218493	441	588	5.63E-47	162.141	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#8898 - 	CGI_10009339	superfamily	246722	4	115	4.48E-30	115.932	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#8898 - 	CGI_10009339	superfamily	246724	117	256	1.95E-20	85.8673	cl14815	H3TH_StructSpec-5'-nucleases superfamily	 - 	 - 	"H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases."
Q#8899 - 	CGI_10009340	superfamily	243609	1	136	7.10E-34	118.091	cl04000	Cornichon superfamily	 - 	 - 	Cornichon protein; Cornichon protein.  
Q#8900 - 	CGI_10009341	superfamily	192997	310	399	5.65E-09	55.6655	cl18184	Sterol-sensing superfamily	N	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#8900 - 	CGI_10009341	superfamily	241888	719	860	4.60E-05	44.4817	cl00473	BI-1-like superfamily	C	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#8907 - 	CGI_10009348	superfamily	243074	7	53	9.37E-10	54.4349	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#8908 - 	CGI_10009349	superfamily	115363	583	640	1.42E-08	52.3742	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8909 - 	CGI_10009350	superfamily	115363	5	64	1.53E-07	44.6702	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8910 - 	CGI_10009351	superfamily	115363	58	107	0.000199191	38.1218	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8911 - 	CGI_10009352	superfamily	115363	267	321	1.34E-05	42.7442	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#8913 - 	CGI_10001195	superfamily	247057	256	311	1.50E-05	42.2265	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#8916 - 	CGI_10001198	superfamily	245040	51	79	0.00927424	31.2445	cl09238	CY superfamily	NC	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#8917 - 	CGI_10001316	superfamily	206088	28	49	0.00413798	33.4635	cl16476	zf-CCHC_3 superfamily	C	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#8923 - 	CGI_10008365	superfamily	244859	4	118	0.00545723	33.6741	cl08171	HtrL_YibB superfamily	C	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#8924 - 	CGI_10008366	superfamily	243072	430	555	2.14E-31	118.64	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8924 - 	CGI_10008366	superfamily	243072	4	125	7.97E-31	117.099	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8924 - 	CGI_10008366	superfamily	243072	165	290	8.56E-31	116.714	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8924 - 	CGI_10008366	superfamily	243072	368	489	2.22E-28	110.166	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8924 - 	CGI_10008366	superfamily	243072	264	390	3.05E-28	109.781	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8926 - 	CGI_10008368	superfamily	245206	22	94	5.94E-16	69.3981	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#8927 - 	CGI_10008369	superfamily	193256	596	643	2.18E-05	45.3236	cl18189	AAA_8 superfamily	N	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#8927 - 	CGI_10008369	superfamily	110440	471	498	0.000256337	39.3133	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#8927 - 	CGI_10008369	superfamily	241563	60	96	0.00151979	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#8929 - 	CGI_10004220	superfamily	241874	28	605	0	681.983	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#8933 - 	CGI_10001889	superfamily	217293	81	283	8.05E-30	115.037	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#8933 - 	CGI_10001889	superfamily	202474	290	375	1.13E-07	51.1153	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#8934 - 	CGI_10002066	superfamily	247858	1	114	1.25E-18	78.5838	cl17304	2OG-FeII_Oxy_3 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#8935 - 	CGI_10002067	superfamily	219677	41	69	0.00947167	35.106	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#8938 - 	CGI_10010354	superfamily	247905	186	325	3.67E-21	88.4488	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#8938 - 	CGI_10010354	superfamily	247805	5	156	9.29E-14	67.7476	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#8939 - 	CGI_10010355	superfamily	243092	117	299	3.16E-16	79.3012	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8939 - 	CGI_10010355	superfamily	243092	224	492	4.06E-11	63.8932	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8941 - 	CGI_10010357	superfamily	243072	19	112	6.49E-15	68.5642	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8941 - 	CGI_10010357	superfamily	243073	206	246	1.87E-06	43.6129	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#8944 - 	CGI_10010360	superfamily	247725	46	180	7.41E-16	76.0273	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8944 - 	CGI_10010360	superfamily	206020	369	419	1.22E-12	64.0662	cl18286	Y_phosphatase_m superfamily	 - 	 - 	"Myotubularin Y_phosphatase-like; This short region is highly conserved and seems to be common to many myotubularin proteins with protein tyrosine pyrophosphate activity. As the family has a number of highly conserved residues such as histidine, cysteine, glutamine and aspartate, it is possible that this represents a catalytic core of the active enzymatic part of the proteins."
Q#8944 - 	CGI_10010360	superfamily	221647	582	626	1.05E-08	53.2103	cl13953	3-PAP superfamily	NC	 - 	"Myotubularin-associated protein; This domain family is found in eukaryotes, and is typically between 115 and 138 amino acids in length. Myotubularin is a dual-specific phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bisphosphate. 3-PAP is a catalytically inactive member of the myotubularin gene family, which coprecipitates lipid phosphatidylinositol 3-phosphate-3-phosphatase activity from lysates of human platelets."
Q#8944 - 	CGI_10010360	superfamily	219103	218	269	3.40E-06	45.8252	cl05893	Myotub-related superfamily	C	 - 	"Myotubularin-related; This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease."
Q#8950 - 	CGI_10010514	superfamily	241624	925	1167	8.37E-29	118.198	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#8950 - 	CGI_10010514	superfamily	247725	182	363	6.84E-39	145.765	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#8950 - 	CGI_10010514	superfamily	246925	680	898	1.62E-07	53.8986	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#8950 - 	CGI_10010514	superfamily	246925	573	738	0.000181821	44.2686	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#8951 - 	CGI_10010516	superfamily	215647	32	254	1.19E-18	81.886	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#8952 - 	CGI_10010517	superfamily	241600	106	184	2.36E-29	110.023	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8953 - 	CGI_10010518	superfamily	247908	118	305	7.81E-65	204.064	cl17354	NIF superfamily	 - 	 - 	NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.
Q#8954 - 	CGI_10010519	superfamily	248259	471	563	1.25E-39	142.389	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#8954 - 	CGI_10010519	superfamily	248259	371	460	4.85E-27	106.565	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#8954 - 	CGI_10010519	superfamily	248259	141	241	2.15E-26	105.024	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#8954 - 	CGI_10010519	superfamily	247057	770	836	2.34E-26	103.989	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#8954 - 	CGI_10010519	superfamily	248259	252	347	5.79E-24	98.0906	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#8955 - 	CGI_10010520	superfamily	114912	7	41	3.46E-11	57.0609	cl17946	zf-U1 superfamily	 - 	 - 	"U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family."
Q#8955 - 	CGI_10010520	superfamily	241647	130	155	0.00108225	35.9666	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#8956 - 	CGI_10010521	superfamily	247775	302	551	2.28E-69	231.372	cl17221	ArsB_NhaD_permease superfamily	N	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#8956 - 	CGI_10010521	superfamily	247775	91	266	2.62E-54	190.541	cl17221	ArsB_NhaD_permease superfamily	C	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#8958 - 	CGI_10010523	superfamily	243072	63	173	7.66E-09	54.697	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#8958 - 	CGI_10010523	superfamily	149414	180	242	3.50E-29	111.98	cl07091	TRP_2 superfamily	 - 	 - 	Transient receptor ion channel II; This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023).
Q#8962 - 	CGI_10010528	superfamily	241571	47	83	0.00392895	34.3103	cl00049	CUB superfamily	NC	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#8963 - 	CGI_10010529	superfamily	241785	85	483	0	630.198	cl00324	Ribosomal_L3 superfamily	 - 	 - 	Ribosomal protein L3; Ribosomal protein L3.  
Q#8964 - 	CGI_10010530	superfamily	118773	39	164	3.40E-34	118.724	cl10933	NDUFB10 superfamily	 - 	 - 	"NADH-ubiquinone oxidoreductase subunit 10; NDUFB10 is a family of conserved proteins of up to 180 residues. It is one of the 41 protein subunits within the hydrophobic fraction of the NADH:ubiquinone oxidoreductase (complex I), a multiprotein complex located in the inner mitochondrial membrane whose main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. NDUFB10 is encoded in the nucleus."
Q#8965 - 	CGI_10010531	superfamily	243092	424	647	4.02E-47	171.749	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#8966 - 	CGI_10010532	superfamily	241782	26	438	2.50E-142	417.355	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#8969 - 	CGI_10010887	superfamily	241607	94	117	3.21E-05	38.0198	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#8970 - 	CGI_10010888	superfamily	241607	66	89	9.40E-07	41.8718	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#8970 - 	CGI_10010888	superfamily	241607	28	62	3.77E-06	40.331	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#8971 - 	CGI_10010889	superfamily	241547	61	207	3.11E-49	163.594	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#8972 - 	CGI_10010890	superfamily	205516	307	467	4.67E-79	245.392	cl18271	AcetylCoA_hyd_C superfamily	 - 	 - 	"Acetyl-CoA hydrolase/transferase C-terminal domain; This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 utilises acyl-CoA and acetate to form acetyl-CoA."
Q#8972 - 	CGI_10010890	superfamily	217098	44	222	3.13E-22	93.7549	cl15896	AcetylCoA_hydro superfamily	 - 	 - 	"Acetyl-CoA hydrolase/transferase N-terminal domain; This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 utilises acyl-CoA and acetate to form acetyl-CoA."
Q#8973 - 	CGI_10010891	superfamily	203238	1	131	4.06E-58	179.417	cl12307	GMP_PDE_delta superfamily	 - 	 - 	"GMP-PDE, delta subunit; GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE)(EC:3.1.4.35). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport."
Q#8977 - 	CGI_10010895	superfamily	241596	121	171	3.84E-15	66.8539	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#8978 - 	CGI_10010896	superfamily	241596	140	180	6.87E-11	55.2979	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#8980 - 	CGI_10010898	superfamily	247755	58	285	1.70E-75	232.056	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8981 - 	CGI_10010899	superfamily	247789	90	270	4.00E-20	85.3882	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#8982 - 	CGI_10010900	superfamily	247755	47	210	4.76E-56	180.825	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8983 - 	CGI_10010901	superfamily	247789	16	229	1.46E-23	96.9441	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#8983 - 	CGI_10010901	superfamily	247755	377	424	1.11E-06	47.5458	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#8984 - 	CGI_10010902	superfamily	218284	43	96	1.12E-15	70.3611	cl04786	SOUL superfamily	C	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#8984 - 	CGI_10010902	superfamily	247750	124	156	2.53E-06	44.9509	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#8992 - 	CGI_10008844	superfamily	245819	426	601	2.51E-60	201.269	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#8992 - 	CGI_10008844	superfamily	219526	208	411	3.30E-61	204.775	cl06648	HNOBA superfamily	 - 	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8992 - 	CGI_10008844	superfamily	203730	1	158	5.54E-45	158.202	cl18246	HNOB superfamily	 - 	 - 	"Heme NO binding; The HNOB (Heme NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#8993 - 	CGI_10008845	superfamily	241600	136	354	4.73E-102	303.778	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#8997 - 	CGI_10008849	superfamily	243179	112	220	9.43E-11	56.3587	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#8998 - 	CGI_10008850	superfamily	247856	325	384	2.17E-05	41.7645	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#8998 - 	CGI_10008850	superfamily	247856	174	227	6.84E-05	40.6089	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9000 - 	CGI_10008852	superfamily	243034	125	219	1.07E-06	45.4488	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9001 - 	CGI_10008853	superfamily	247727	171	306	3.66E-13	66.9365	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#9002 - 	CGI_10008854	superfamily	221135	7	149	9.45E-32	115.932	cl13079	PI31_Prot_N superfamily	 - 	 - 	PI31 proteasome regulator N-terminal; PI31 is a regulatory subunit of the immuno-proteasome which is an inhibitor of the 20 S proteasome in vitro.PI31 is also an F-box protein Fbxo7.Skp1 binding partner which requires an N terminal FP domain in both proteins for the interaction to occur via the FP beta sheets. The structure of PI31 FP domain contains a novel alpha/beta-fold and two intermolecular contact surfaces. This is the N-terminal domain of the members.
Q#9002 - 	CGI_10008854	superfamily	219914	198	250	1.42E-05	41.5874	cl07260	PI31_Prot_C superfamily	 - 	 - 	PI31 proteasome regulator; PI31 is a cellular regulator of proteasome formation and of proteasome-mediated antigen processing.
Q#9004 - 	CGI_10008856	superfamily	243072	452	531	5.16E-14	68.9494	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9004 - 	CGI_10008856	superfamily	242183	134	421	2.65E-144	420.114	cl00907	Glutaminase superfamily	 - 	 - 	Glutaminase; This family of enzymes deaminates glutamine to glutamate EC:3.5.1.2.
Q#9006 - 	CGI_10008858	superfamily	248458	167	328	1.26E-06	48.4641	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9006 - 	CGI_10008858	superfamily	248458	24	108	0.000247003	41.1453	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9007 - 	CGI_10008860	superfamily	218267	25	113	8.01E-24	100.972	cl04754	LMBR1 superfamily	C	 - 	"LMBR1-like membrane protein; Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought. Vertebrate members of this family may play a role in limb development. A member of this family has been shown to be a lipocalin membrane receptor"
Q#9009 - 	CGI_10008862	superfamily	241563	68	109	8.16E-07	46.7036	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9009 - 	CGI_10008862	superfamily	241563	28	59	0.00158551	37.0736	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9010 - 	CGI_10002688	superfamily	247916	501	568	0.000209174	40.4618	cl17362	Transglut_core superfamily	C	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#9013 - 	CGI_10021342	superfamily	222429	7	85	3.61E-16	68.8064	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#9015 - 	CGI_10021344	superfamily	151671	10	475	1.20E-43	162.131	cl12777	DUF3028 superfamily	 - 	 - 	Protein of unknown function (DUF3028); This eukaryotic family of proteins has no known function.
Q#9016 - 	CGI_10021345	superfamily	247724	14	94	6.31E-53	165.756	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9017 - 	CGI_10021346	superfamily	243050	1	38	0.000114632	37.0139	cl02475	LIM superfamily	N	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#9018 - 	CGI_10021347	superfamily	245201	501	714	2.71E-47	167.414	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9019 - 	CGI_10021348	superfamily	238191	61	527	8.82E-102	319.278	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9019 - 	CGI_10021348	superfamily	238191	2	30	0.000817394	40.7784	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9020 - 	CGI_10021350	superfamily	241838	73	115	1.93E-18	84.4222	cl00395	FMT_core superfamily	C	 - 	"Formyltransferase, catalytic core domain; Formyltransferase, catalytic core domain. The proteins of this superfamily contain a formyltransferase domain that hydrolyzes the removal of a formyl group from its substrate as part of a multistep transfer mechanism, and this alignment model represents the catalytic core of the formyltransferase domain.  This family includes the following known members; Glycinamide Ribonucleotide Transformylase (GART), Formyl-FH4 Hydrolase, Methionyl-tRNA Formyltransferase, ArnA, and 10-Formyltetrahydrofolate Dehydrogenase (FDH).  Glycinamide Ribonucleotide Transformylase  (GART) catalyzes the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Methionyl-tRNA Formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA, which plays important role in translation initiation. ArnA is required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. 10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. Members of this family are multidomain proteins. The formyltransferase domain is located at the N-terminus of FDH, Methionyl-tRNA Formyltransferase and ArnA, and at the C-terminus of Formyl-FH4 Hydrolase.  Prokaryotic Glycinamide Ribonucleotide Transformylase (GART) is a single domain protein while eukaryotic GART is a trifunctional protein that catalyzes the second, third and fifth steps in de novo purine biosynthesis."
Q#9020 - 	CGI_10021350	superfamily	245201	620	691	6.68E-15	73.8101	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9020 - 	CGI_10021350	superfamily	247724	293	413	1.14E-07	51.0082	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9020 - 	CGI_10021350	superfamily	247724	187	225	2.36E-07	50.2378	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9021 - 	CGI_10021351	superfamily	238191	29	204	1.39E-57	191.777	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9022 - 	CGI_10021352	superfamily	241971	22	269	1.06E-101	300.263	cl00599	Extradiol_Dioxygenase_3B_like superfamily	 - 	 - 	"Subunit B of Class III Extradiol ring-cleavage dioxygenases; Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be further divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two-domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B. This model represents the catalytic subunit B of extradiol dioxygenase class III enzymes. Enzymes belonging to this family include Protocatechuate 4,5-dioxygenase (LigAB), 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB), 4,5-DOPA Dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase, and 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD). There are also some family members that do not show the typical dioxygenase activity."
Q#9024 - 	CGI_10021354	superfamily	245847	22	143	2.44E-07	48.2676	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#9025 - 	CGI_10021355	superfamily	241574	189	389	3.74E-67	221.306	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9025 - 	CGI_10021355	superfamily	241574	542	629	1.20E-11	63.7589	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9027 - 	CGI_10021357	superfamily	243064	17	95	1.18E-07	47.3534	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#9028 - 	CGI_10021358	superfamily	241563	61	102	2.49E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9029 - 	CGI_10021359	superfamily	248458	9	104	1.29E-07	50.3901	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9030 - 	CGI_10021360	superfamily	242173	188	338	3.58E-32	118.902	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#9031 - 	CGI_10021361	superfamily	241782	136	497	3.55E-149	457.849	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#9031 - 	CGI_10021361	superfamily	241782	535	896	6.19E-179	539.574	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#9031 - 	CGI_10021361	superfamily	241782	898	1190	1.17E-136	428.252	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#9032 - 	CGI_10021362	superfamily	242173	33	184	5.09E-37	128.918	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#9033 - 	CGI_10021363	superfamily	247675	8	388	0	793.138	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#9036 - 	CGI_10021366	superfamily	241644	79	213	5.67E-64	197.425	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#9038 - 	CGI_10023035	superfamily	243035	2	54	2.59E-09	48.385	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9039 - 	CGI_10023037	superfamily	247046	93	245	4.09E-09	53.9781	cl15705	DUF563 superfamily	N	 - 	Protein of unknown function (DUF563); Family of uncharacterized proteins.
Q#9043 - 	CGI_10023041	superfamily	243051	599	757	1.12E-22	95.9077	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#9043 - 	CGI_10023041	superfamily	241571	331	446	2.65E-12	64.3558	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#9043 - 	CGI_10023041	superfamily	241583	103	284	3.59E-33	126.532	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#9053 - 	CGI_10023051	superfamily	247915	16	55	0.00493939	31.9745	cl17361	Glucosaminidase superfamily	NC	 - 	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; This family includes Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase EC:3.2.1.96, as well as the flageller protein J, which has been shown to hydrolyse peptidoglycan."
Q#9056 - 	CGI_10023054	superfamily	241554	223	355	1.93E-22	93.8643	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#9056 - 	CGI_10023054	superfamily	241554	321	395	1.20E-06	47.9213	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#9058 - 	CGI_10023056	superfamily	203013	436	461	0.00444759	34.909	cl04519	zf-HIT superfamily	 - 	 - 	HIT zinc finger; This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) that specifically interacts with the ligand binding domain of the thyroid receptor.
Q#9063 - 	CGI_10023062	superfamily	222090	148	293	2.05E-15	73.0758	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#9064 - 	CGI_10023063	superfamily	247866	131	374	4.51E-48	164.548	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#9064 - 	CGI_10023063	superfamily	247866	11	114	4.29E-07	48.988	cl17312	PhyH superfamily	C	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#9065 - 	CGI_10023064	superfamily	216101	18	599	0	675.548	cl08288	Carn_acyltransf superfamily	 - 	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#9067 - 	CGI_10023066	superfamily	243094	509	828	1.15E-171	517.522	cl02569	RasGAP superfamily	 - 	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#9067 - 	CGI_10023066	superfamily	246669	374	517	1.04E-63	214.478	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#9067 - 	CGI_10023066	superfamily	247725	315	422	7.77E-35	133.666	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9070 - 	CGI_10023069	superfamily	218940	104	568	0	609.496	cl05625	COBRA1 superfamily	 - 	 - 	"Cofactor of BRCA1 (COBRA1); This family consists of several cofactor of BRCA1 (COBRA1) like proteins. It is thought that COBRA1 along with BRCA1 is involved in chromatin unfolding. COBRA1 is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. It is thought that that reorganisation of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions."
Q#9071 - 	CGI_10023071	superfamily	247057	141	191	1.58E-06	46.8489	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#9071 - 	CGI_10023071	superfamily	246908	253	373	2.45E-37	137.851	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#9071 - 	CGI_10023071	superfamily	243053	748	820	1.24E-13	70.7444	cl02485	RasGEF superfamily	C	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#9072 - 	CGI_10023072	superfamily	243069	41	169	1.09E-48	165.807	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#9073 - 	CGI_10023074	superfamily	247639	74	251	1.64E-07	50.0607	cl16914	O-FucT_like superfamily	N	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#9075 - 	CGI_10009660	superfamily	247986	456	543	1.06E-08	55.0718	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#9075 - 	CGI_10009660	superfamily	245225	8	385	1.30E-126	391.05	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#9075 - 	CGI_10009660	superfamily	197504	663	792	1.58E-38	141.273	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#9075 - 	CGI_10009660	superfamily	119082	839	865	2.83E-09	54.4926	cl11191	CaM_bdg_C0 superfamily	 - 	 - 	"Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue."
Q#9076 - 	CGI_10009661	superfamily	247723	332	422	4.24E-46	156.999	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9076 - 	CGI_10009661	superfamily	247723	200	290	5.29E-46	156.54	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9077 - 	CGI_10009662	superfamily	116164	71	97	9.76E-07	44.102	cl06534	Vg_Tdu superfamily	C	 - 	"Vestigial/Tondu family; The mammalian TEF and the Drosophila scalloped genes belong to a conserved family of transcriptional factors that possesses a TEA/ATTS DNA-binding domain. Transcriptional activation by these proteins likely requires interactions with specific coactivators. In Drosophila, Scalloped (Sd) interacts with Vestigial (Vg) to form a complex, which binds DNA through the Sd TEA/ATTS domain. The Sd-Vg heterodimer is a key regulator of wing development, which directly controls several target genes and is able to induce wing outgrowth when ectopically expressed. This short conserved region is needed for interaction with Sd."
Q#9086 - 	CGI_10003144	superfamily	243035	20	96	1.28E-11	57.6297	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9087 - 	CGI_10003145	superfamily	243092	359	554	1.86E-14	74.6788	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9087 - 	CGI_10003145	superfamily	243092	688	774	0.000817055	41.9368	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9087 - 	CGI_10003145	superfamily	243092	101	170	0.00954782	38.47	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9091 - 	CGI_10012656	superfamily	245596	530	794	6.93E-76	252.614	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#9091 - 	CGI_10012656	superfamily	245596	440	496	4.15E-09	57.3176	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#9091 - 	CGI_10012656	superfamily	245166	881	945	0.00611376	37.955	cl09823	Trep_Strep superfamily	C	 - 	"Hypothetical bacterial integral membrane protein (Trep_Strep); This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. It is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6."
Q#9091 - 	CGI_10012656	superfamily	216554	1138	1216	0.00828521	37.459	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#9095 - 	CGI_10028231	superfamily	241832	438	532	2.51E-14	70.3321	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9095 - 	CGI_10028231	superfamily	241832	570	653	0.00110302	38.4726	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9097 - 	CGI_10028233	superfamily	247978	414	447	0.00853678	36.394	cl17424	CsbD superfamily	NC	 - 	"CsbD-like; CsbD is a bacterial general stress response protein. It's expression is mediated by sigma-B, an alternative sigma factor. The role of CsbD in stress response is unclear."
Q#9098 - 	CGI_10028234	superfamily	220695	49	206	1.20E-05	44.8771	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#9099 - 	CGI_10028235	superfamily	218140	210	487	9.58E-89	289.113	cl04579	Anoctamin superfamily	C	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#9099 - 	CGI_10028235	superfamily	218140	544	711	3.61E-48	176.25	cl04579	Anoctamin superfamily	N	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#9100 - 	CGI_10028236	superfamily	248264	13	50	4.13E-09	49.543	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#9101 - 	CGI_10028237	superfamily	245596	75	266	1.01E-99	303.734	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#9104 - 	CGI_10028240	superfamily	241563	38	77	8.40E-07	46.1763	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9104 - 	CGI_10028240	superfamily	245027	76	189	0.00779474	35.832	cl09176	FlgN superfamily	C	 - 	FlgN protein; This family includes the FlgN protein and export chaperone involved in flagellar synthesis.
Q#9107 - 	CGI_10028243	superfamily	110440	354	381	0.00582978	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9107 - 	CGI_10028243	superfamily	243092	134	269	0.0063365	36.544	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9108 - 	CGI_10028244	superfamily	241563	60	99	1.17E-05	43.8651	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9108 - 	CGI_10028244	superfamily	243362	355	396	0.00916357	36.6343	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#9110 - 	CGI_10028246	superfamily	243072	852	978	1.15E-25	104.388	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9110 - 	CGI_10028246	superfamily	243072	569	694	1.16E-23	98.6098	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9110 - 	CGI_10028246	superfamily	243072	474	628	1.28E-23	98.6098	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9110 - 	CGI_10028246	superfamily	243072	754	912	5.03E-22	93.9874	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9110 - 	CGI_10028246	superfamily	243072	361	500	8.43E-21	90.5206	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9110 - 	CGI_10028246	superfamily	243072	250	387	6.23E-20	87.8242	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9110 - 	CGI_10028246	superfamily	248318	1092	1147	1.20E-19	85.1801	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#9110 - 	CGI_10028246	superfamily	243072	919	1050	9.34E-18	81.661	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9110 - 	CGI_10028246	superfamily	243066	59	156	2.25E-13	68.0277	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#9111 - 	CGI_10028247	superfamily	245210	31	406	8.15E-172	490.513	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#9113 - 	CGI_10028249	superfamily	245226	122	284	3.81E-22	90.8228	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9114 - 	CGI_10028250	superfamily	217865	60	338	1.18E-159	455.548	cl12285	Not1 superfamily	N	 - 	"CCR4-Not complex component, Not1; The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID."
Q#9115 - 	CGI_10028251	superfamily	207662	73	109	8.94E-17	73.6336	cl02596	NR_DBD_like superfamily	C	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#9115 - 	CGI_10028251	superfamily	207662	251	287	2.23E-11	58.996	cl02596	NR_DBD_like superfamily	NC	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#9117 - 	CGI_10028254	superfamily	221482	479	680	3.59E-29	115.752	cl13649	Angiomotin_C superfamily	 - 	 - 	"Angiomotin C terminal; This domain family is found in eukaryotes, and is typically between 197 and 211 amino acids in length. This family is the C terminal region of angiomotin. Angiomotin regulates the action of angiogenesis inhibitor angiostatin. The C terminal region of angiomotin appears to be involved in directing the protein chemotactically."
Q#9118 - 	CGI_10028255	superfamily	187751	116	260	2.09E-35	130.117	cl18153	RNase_H2-B superfamily	C	 - 	"Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder."
Q#9118 - 	CGI_10028255	superfamily	187751	344	384	9.90E-05	41.906	cl18153	RNase_H2-B superfamily	N	 - 	"Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder."
Q#9120 - 	CGI_10028257	superfamily	220695	327	455	2.31E-08	54.5071	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#9123 - 	CGI_10028260	superfamily	241750	312	514	4.38E-32	123.067	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#9124 - 	CGI_10028261	superfamily	222413	90	149	5.94E-11	59.9762	cl16433	DDE_Tnp_1_7 superfamily	C	 - 	Transposase IS4; Transposase IS4.  
Q#9124 - 	CGI_10028261	superfamily	222412	204	233	1.79E-06	43.5133	cl16432	Tnp_zf-ribbon_2 superfamily	 - 	 - 	DDE_Tnp_1-like zinc-ribbon; This zinc-ribbon domain is frequently found at the C-terminal of proteins derived from transposable elements.
Q#9127 - 	CGI_10028264	superfamily	242274	134	250	2.82E-05	42.7846	cl01053	SGNH_hydrolase superfamily	N	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#9130 - 	CGI_10028267	superfamily	243077	106	157	3.81E-15	71.0373	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#9130 - 	CGI_10028267	superfamily	214946	220	459	2.56E-18	85.4879	cl15345	Sec63 superfamily	C	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#9130 - 	CGI_10028267	superfamily	214946	612	692	0.000193512	42.7307	cl15345	Sec63 superfamily	N	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#9131 - 	CGI_10028268	superfamily	247916	105	150	6.54E-05	41.2143	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#9135 - 	CGI_10028272	superfamily	246664	250	745	1.09E-149	450.223	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#9136 - 	CGI_10028273	superfamily	247799	75	197	4.93E-59	191.688	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#9137 - 	CGI_10028274	superfamily	241568	30	85	3.28E-07	45.9168	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9138 - 	CGI_10028275	superfamily	241563	68	109	8.96E-07	46.3184	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9138 - 	CGI_10028275	superfamily	241563	28	59	0.00337337	35.918	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9139 - 	CGI_10028276	superfamily	247044	141	206	2.33E-28	104.612	cl15697	ADF_gelsolin superfamily	C	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#9141 - 	CGI_10028278	superfamily	248097	69	186	4.12E-16	74.2238	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9141 - 	CGI_10028278	superfamily	248097	354	413	0.00854139	34.9334	cl17543	C1q superfamily	NC	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9144 - 	CGI_10028281	superfamily	245603	94	117	0.000190592	36.1604	cl11403	pepsin_retropepsin_like superfamily	C	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#9145 - 	CGI_10028283	superfamily	241574	627	815	3.51E-71	235.558	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9145 - 	CGI_10028283	superfamily	243072	98	189	5.70E-15	72.8014	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9148 - 	CGI_10028286	superfamily	218570	166	194	0.00107341	35.4561	cl05109	Pacifastin_I superfamily	 - 	 - 	"Pacifastin inhibitor (LCMII); Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors."
Q#9149 - 	CGI_10028287	superfamily	215754	61	133	4.21E-16	70.7452	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#9149 - 	CGI_10028287	superfamily	215754	136	199	2.68E-07	46.0924	cl02813	Mito_carr superfamily	C	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#9150 - 	CGI_10028288	superfamily	245814	200	276	0.000498845	40.1651	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9150 - 	CGI_10028288	superfamily	215647	751	928	1.47E-15	77.6488	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#9150 - 	CGI_10028288	superfamily	243086	684	729	4.80E-07	48.9106	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#9150 - 	CGI_10028288	superfamily	243029	301	341	0.00243192	38.1005	cl02422	HRM superfamily	N	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#9150 - 	CGI_10028288	superfamily	199168	89	112	0.00309512	37.3312	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#9150 - 	CGI_10028288	superfamily	246925	24	102	0.007391	38.8758	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#9151 - 	CGI_10028289	superfamily	243072	611	763	5.83E-14	70.4902	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9151 - 	CGI_10028289	superfamily	243072	335	402	8.23E-11	60.8602	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9151 - 	CGI_10028289	superfamily	243072	538	652	1.67E-07	50.845	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9151 - 	CGI_10028289	superfamily	209898	100	122	0.000167821	40.4646	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#9151 - 	CGI_10028289	superfamily	209898	77	97	0.00122943	38.1534	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#9152 - 	CGI_10028290	superfamily	218520	22	187	4.68E-59	186.715	cl05007	EBP superfamily	 - 	 - 	"Emopamil binding protein; Emopamil binding protein (EBP) is as a gene that encodes a non-glycosylated type I integral membrane protein of endoplasmic reticulum and shows high level expression in epithelial tissues. The EBP protein has emopamil binding domains, including the sterol acceptor site and the catalytic centre, which show Delta8-Delta7 sterol isomerase activity. Human sterol isomerase, a homologue of mouse EBP, is suggested not only to play a role in cholesterol biosynthesis, but also to affect lipoprotein internalisation. In humans, mutations of EBP are known to cause the genetic disorder of X-linked dominant chondrodysplasia punctata (CDPX2). This syndrome of humans is lethal in most males, and affected females display asymmetric hyperkeratotic skin and skeletal abnormalities."
Q#9153 - 	CGI_10028291	superfamily	247723	127	202	5.29E-43	146.762	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9153 - 	CGI_10028291	superfamily	247723	212	282	4.14E-40	138.94	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9155 - 	CGI_10028293	superfamily	241832	47	173	1.50E-59	197.528	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9155 - 	CGI_10028293	superfamily	110440	462	488	0.00320249	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9160 - 	CGI_10028298	superfamily	243179	97	165	1.26E-10	56.9725	cl02781	tetraspanin_LEL superfamily	C	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#9161 - 	CGI_10028299	superfamily	245206	1	111	8.65E-20	81.1332	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#9162 - 	CGI_10028300	superfamily	243077	9	54	1.65E-07	42.9177	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#9163 - 	CGI_10028301	superfamily	243092	286	388	0.0025535	38.8552	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9164 - 	CGI_10028302	superfamily	219110	1	63	2.59E-37	120.485	cl05913	RAMP4 superfamily	 - 	 - 	"Ribosome associated membrane protein RAMP4; This family consists of several ribosome associated membrane protein RAMP4 (or SERP1) sequences. Stabilisation of membrane proteins in response to stress involves the concerted action of a rescue unit in the ER membrane comprised of SERP1/RAMP4, other components of the translocon, and molecular chaperones in the ER."
Q#9165 - 	CGI_10028303	superfamily	245864	55	147	1.25E-19	83.4818	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9166 - 	CGI_10028304	superfamily	245864	4	411	2.18E-106	324.617	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9167 - 	CGI_10028305	superfamily	245864	4	389	2.63E-92	288.408	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9168 - 	CGI_10028306	superfamily	245864	26	477	6.47E-117	354.277	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9169 - 	CGI_10028307	superfamily	245864	41	241	8.44E-61	199.812	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9170 - 	CGI_10028308	superfamily	245864	26	96	1.18E-12	63.0662	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9171 - 	CGI_10028309	superfamily	245864	26	478	5.53E-101	313.061	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9172 - 	CGI_10028310	superfamily	245864	1	349	1.54E-72	234.48	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9173 - 	CGI_10028311	superfamily	245864	26	382	1.80E-78	252.199	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9174 - 	CGI_10028312	superfamily	241691	772	884	0.00132635	39.4176	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#9174 - 	CGI_10028312	superfamily	241565	59	128	0.00920671	35.429	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#9175 - 	CGI_10028313	superfamily	245864	26	474	1.98E-112	342.721	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9176 - 	CGI_10028314	superfamily	219570	5	454	1.51E-73	247.09	cl06694	CENP-I superfamily	 - 	 - 	"Mis6; Mis6 is an essential centromere connector protein acting during G1-S phase of the cell cycle. Mis6 is thought to be required for recruiting CENP-A, the centromere- specific histone H3 variant, an important event for centromere function and chromosome segregation during mitosis."
Q#9177 - 	CGI_10028315	superfamily	245201	3	234	4.80E-05	41.8386	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9178 - 	CGI_10028316	superfamily	245201	26	266	2.95E-07	48.7721	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9179 - 	CGI_10004654	superfamily	245201	23	211	2.64E-37	135.827	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9179 - 	CGI_10004654	superfamily	240618	295	383	1.07E-17	77.6744	cl18927	UBL_TBK1_like superfamily	 - 	 - 	"Ubiquitin-Like Domain Of Human Tbk1 and similar proteins; This family contains ubiquitin-like domain (UBL) found in TANK-binding kinase 1 (TBK1) and similar proteins. TBK1 regulates factors such as IRF3 and IRF7, promoting antiviral activity in the interferon signaling pathways. In addition to the central UBL, these proteins have an N-terminal kinase domain and a C-terminal elongated helical domain. The ubiquitin-like domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the IFN pathway."
Q#9181 - 	CGI_10004656	superfamily	245201	1171	1309	9.17E-23	99.2333	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9181 - 	CGI_10004656	superfamily	248099	52	128	2.90E-23	96.6246	cl17545	Bromo_TP superfamily	 - 	 - 	Bromodomain associated; This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold.
Q#9181 - 	CGI_10004656	superfamily	247999	1032	1077	1.90E-13	67.6221	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#9182 - 	CGI_10004657	superfamily	247724	19	180	3.33E-100	289.329	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9186 - 	CGI_10004661	superfamily	241574	358	556	1.01E-68	224.002	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9187 - 	CGI_10002369	superfamily	241600	1	169	2.36E-54	173.581	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#9188 - 	CGI_10002370	superfamily	241600	47	230	2.82E-61	195.152	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#9193 - 	CGI_10014193	superfamily	241733	1	65	5.42E-42	133.48	cl00259	Sm_like superfamily	N	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#9195 - 	CGI_10014195	superfamily	243034	1085	1178	8.42E-09	54.6936	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9195 - 	CGI_10014195	superfamily	243034	1202	1284	5.07E-06	46.2192	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9195 - 	CGI_10014195	superfamily	243034	836	945	0.00150912	38.5152	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9196 - 	CGI_10014196	superfamily	248458	84	448	4.96E-08	53.4717	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9197 - 	CGI_10014198	superfamily	216809	161	252	2.13E-16	71.835	cl03397	DUF108 superfamily	 - 	 - 	Domain of unknown function DUF108; This family has no known function. It is found to compose the complete protein in archaebacteria and a single domain in a large C. elegans protein.
Q#9197 - 	CGI_10014198	superfamily	217564	8	113	6.85E-12	60.0414	cl18420	NAD_binding_3 superfamily	 - 	 - 	"Homoserine dehydrogenase, NAD binding domain; This domain adopts a Rossmann NAD binding fold. The C-terminal domain of homoserine dehydrogenase contributes a single helix to this structural domain, which is not included in the Pfam model."
Q#9198 - 	CGI_10014199	superfamily	221749	1002	1056	5.73E-08	51.5849	cl15061	Gryzun-like superfamily	 - 	 - 	"Gryzun, putative Golgi trafficking; Members of this family are involved in Golgi trafficking."
Q#9199 - 	CGI_10014200	superfamily	243141	101	206	7.59E-22	88.1422	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#9200 - 	CGI_10014201	superfamily	241547	84	313	2.66E-88	277.242	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#9200 - 	CGI_10014201	superfamily	241547	375	626	9.58E-99	305.392	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#9201 - 	CGI_10014202	superfamily	245864	43	375	4.78E-62	209.442	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9201 - 	CGI_10014202	superfamily	245864	375	427	0.000409123	41.1098	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9202 - 	CGI_10014203	superfamily	245864	8	74	1.22E-22	90.4154	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9203 - 	CGI_10014204	superfamily	217311	1	328	2.32E-94	295.014	cl18402	DUF229 superfamily	N	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#9205 - 	CGI_10014206	superfamily	241564	1	47	3.22E-14	62.2831	cl00035	BIR superfamily	N	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#9206 - 	CGI_10014207	superfamily	245231	1	241	9.85E-71	221.626	cl10019	PurM-like superfamily	N	 - 	"AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain."
Q#9207 - 	CGI_10014208	superfamily	241782	69	453	1.16E-51	179.459	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#9208 - 	CGI_10014209	superfamily	243066	29	123	1.08E-20	86.9025	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#9208 - 	CGI_10014209	superfamily	198867	133	240	3.17E-17	76.9964	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#9209 - 	CGI_10014210	superfamily	221288	374	771	3.38E-138	417.502	cl14982	DUF3402 superfamily	 - 	 - 	Domain of unknown function (DUF3402); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 350 to 473 amino acids in length. This domain is found associated with pfam07923.
Q#9209 - 	CGI_10014210	superfamily	219645	22	311	3.55E-66	222.958	cl06798	N1221 superfamily	 - 	 - 	N1221-like protein; The sequences featured in this family are similar to a hypothetical protein product of ORF N1221 in the CPT1-SPC98 intergenic region of the yeast genome. This encodes an acidic polypeptide with several possible transmembrane regions.
Q#9210 - 	CGI_10014211	superfamily	243175	80	197	2.02E-58	182.063	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#9210 - 	CGI_10014211	superfamily	241832	1	72	4.09E-34	118.258	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9211 - 	CGI_10014212	superfamily	243175	58	178	3.93E-59	188.997	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#9211 - 	CGI_10014212	superfamily	241832	2	52	1.54E-20	84.36	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9213 - 	CGI_10014214	superfamily	245201	533	673	7.41E-06	47.325	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9213 - 	CGI_10014214	superfamily	245201	397	467	9.38E-06	47.1546	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9213 - 	CGI_10014214	superfamily	245716	10	33	1.87E-05	42.9307	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#9213 - 	CGI_10014214	superfamily	245201	623	749	5.68E-05	44.3598	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9214 - 	CGI_10004811	superfamily	241566	170	219	1.96E-15	71.3691	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#9214 - 	CGI_10004811	superfamily	241566	98	147	7.70E-14	67.1319	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#9214 - 	CGI_10004811	superfamily	245201	298	616	0	523.972	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9217 - 	CGI_10004814	superfamily	218676	12	371	1.36E-27	112.041	cl14911	Peptidase_M13_N superfamily	 - 	 - 	"Peptidase family M13; M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk."
Q#9219 - 	CGI_10004816	superfamily	218676	290	627	2.55E-22	98.9447	cl14911	Peptidase_M13_N superfamily	 - 	 - 	"Peptidase family M13; M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk."
Q#9219 - 	CGI_10004816	superfamily	246723	788	914	6.62E-09	58.0835	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#9219 - 	CGI_10004816	superfamily	246723	13	46	0.00775565	38.4383	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#9221 - 	CGI_10004207	superfamily	245225	487	780	3.40E-31	127.102	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#9221 - 	CGI_10004207	superfamily	247905	321	437	6.58E-10	58.7885	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#9221 - 	CGI_10004207	superfamily	245225	944	1395	1.56E-67	237.141	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#9221 - 	CGI_10004207	superfamily	242406	52	163	3.16E-11	62.9941	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#9222 - 	CGI_10004208	superfamily	245819	760	936	5.61E-64	215.136	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#9222 - 	CGI_10004208	superfamily	245225	11	306	1.62E-79	266.889	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#9222 - 	CGI_10004208	superfamily	245201	450	684	6.90E-34	132.275	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9222 - 	CGI_10004208	superfamily	219526	692	746	7.68E-05	43.7619	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#9223 - 	CGI_10004209	superfamily	241574	197	323	3.15E-18	82.6337	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9223 - 	CGI_10004209	superfamily	241574	39	165	6.09E-18	81.8633	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9224 - 	CGI_10004210	superfamily	241574	114	286	6.06E-72	226.313	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9226 - 	CGI_10009863	superfamily	247684	17	322	7.51E-72	232.938	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9226 - 	CGI_10009863	superfamily	241547	344	396	7.54E-16	75.0119	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#9227 - 	CGI_10009864	superfamily	241547	153	201	3.67E-10	58.5788	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#9227 - 	CGI_10009864	superfamily	241832	269	358	1.40E-07	48.8438	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9227 - 	CGI_10009864	superfamily	241547	189	236	4.82E-07	49.334	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#9232 - 	CGI_10006159	superfamily	241580	76	151	6.21E-37	127.285	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#9238 - 	CGI_10006165	superfamily	246723	21	117	8.47E-31	120.361	cl14813	GluZincin superfamily	NC	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#9238 - 	CGI_10006165	superfamily	246723	118	183	5.07E-22	94.9379	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#9239 - 	CGI_10006166	superfamily	217740	197	427	2.95E-72	229.17	cl18427	Scramblase superfamily	 - 	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#9239 - 	CGI_10006166	superfamily	222429	6	85	1.81E-22	90.3776	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#9240 - 	CGI_10006167	superfamily	217740	46	276	3.90E-82	249.201	cl18427	Scramblase superfamily	 - 	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#9241 - 	CGI_10006168	superfamily	246908	167	245	4.52E-15	72.8734	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#9241 - 	CGI_10006168	superfamily	128469	1145	1238	5.40E-14	70.562	cl17971	VPS9 superfamily	 - 	 - 	Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
Q#9241 - 	CGI_10006168	superfamily	241645	1264	1332	6.28E-11	60.74	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#9242 - 	CGI_10017479	superfamily	245213	14	49	9.64E-11	55.3354	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9242 - 	CGI_10017479	superfamily	243061	136	230	1.07E-41	140.17	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#9242 - 	CGI_10017479	superfamily	245847	55	119	1.49E-06	45.6254	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#9243 - 	CGI_10017480	superfamily	243112	14	37	1.45E-08	49.9419	cl02620	YDG_SRA superfamily	N	 - 	"YDG/SRA domain; The function of this domain is unknown, it contains a conserved motif YDG after which it has been named."
Q#9245 - 	CGI_10017482	superfamily	242443	45	361	1.89E-67	216.825	cl01342	Peptidase_A22B superfamily	 - 	 - 	"Signal peptide peptidase; The members of this family are membrane proteins. In some proteins this region is found associated with pfam02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with pfam01080."
Q#9248 - 	CGI_10017485	superfamily	248360	12	204	1.19E-68	212.135	cl17806	DER1 superfamily	 - 	 - 	"Der1-like family; The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localised to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.)."
Q#9249 - 	CGI_10017486	superfamily	241644	4	170	4.47E-49	157.749	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#9250 - 	CGI_10017487	superfamily	243066	23	122	1.52E-15	71.8797	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#9250 - 	CGI_10017487	superfamily	198867	131	235	9.97E-13	63.8996	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#9251 - 	CGI_10017488	superfamily	247792	16	67	8.79E-08	49.7516	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9251 - 	CGI_10017488	superfamily	241563	165	196	0.000582272	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9253 - 	CGI_10017490	superfamily	247723	44	136	1.86E-38	140.511	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9253 - 	CGI_10017490	superfamily	243091	1264	1385	2.41E-37	138.621	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#9253 - 	CGI_10017490	superfamily	214703	1385	1401	9.16E-06	44.7036	cl02636	PostSET superfamily	 - 	 - 	Cysteine-rich motif following a subset of SET domains; Cysteine-rich motif following a subset of SET domains.  
Q#9254 - 	CGI_10017491	superfamily	247856	233	294	2.61E-06	46.7721	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9254 - 	CGI_10017491	superfamily	247856	270	346	0.000134006	41.7645	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9254 - 	CGI_10017491	superfamily	243082	763	941	9.31E-21	94.2647	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9254 - 	CGI_10017491	superfamily	243082	1425	1488	8.59E-16	78.0982	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9254 - 	CGI_10017491	superfamily	245879	536	601	8.44E-11	60.5639	cl12116	DUSP superfamily	N	 - 	DUSP domain; The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Q#9254 - 	CGI_10017491	superfamily	243082	1276	1361	5.56E-08	53.8306	cl02553	Peptidase_C19 superfamily	NC	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9254 - 	CGI_10017491	superfamily	245879	395	442	2.25E-05	44.2714	cl12116	DUSP superfamily	C	 - 	DUSP domain; The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Q#9256 - 	CGI_10017493	superfamily	245213	39	74	4.18E-05	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9256 - 	CGI_10017493	superfamily	245213	76	111	6.28E-05	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9257 - 	CGI_10017494	superfamily	247725	24	134	3.81E-68	207.911	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9258 - 	CGI_10017495	superfamily	245226	526	693	2.00E-21	92.3636	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9259 - 	CGI_10017496	superfamily	243058	534	601	0.00024382	40.3756	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#9259 - 	CGI_10017496	superfamily	248054	104	156	2.96E-09	54.4004	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#9261 - 	CGI_10017498	superfamily	242418	351	532	1.82E-31	118.858	cl01298	Glyco_transf_25 superfamily	 - 	 - 	"Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of Neisseria gonorrhoeae and Lic2A of Haemophilus influenzae. M. catarrhalis Lgt2 catalyzes the addition of galactose (Gal) to the growing chain of LOS on the cell surface. N. gonorrhoeae LgtB and LgtE link Gal-beta(1,4)  to GlcNAc (N-acetylglucosamine) and Glc (glucose), respectively. The genes encoding LgtB and LgtE are two genes of a five gene locus involved in the synthesis of gonococcal LOS. LgtE is believed to perform the first step in LOS biosynthesis."
Q#9261 - 	CGI_10017498	superfamily	245596	47	166	0.000147855	42.2757	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#9263 - 	CGI_10017501	superfamily	247725	84	175	7.57E-06	42.3464	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9265 - 	CGI_10017503	superfamily	243050	54	106	4.10E-21	80.7757	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#9266 - 	CGI_10017504	superfamily	247792	43	88	3.75E-08	50.522	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9268 - 	CGI_10017506	superfamily	243092	101	437	3.41E-83	261.501	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9268 - 	CGI_10017506	superfamily	219730	10	71	1.19E-17	77.5607	cl06962	NLE superfamily	 - 	 - 	NLE (NUC135) domain; This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated yeast protein YTM1.
Q#9270 - 	CGI_10017508	superfamily	241825	52	150	5.75E-20	81.0471	cl00379	Ribosomal_L18_L5e superfamily	 - 	 - 	"Ribosomal L18/L5e:  L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified."
Q#9271 - 	CGI_10017509	superfamily	241547	231	508	2.65E-71	234.87	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#9272 - 	CGI_10017510	superfamily	202894	126	193	1.65E-20	81.8834	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#9273 - 	CGI_10017511	superfamily	248289	22	82	7.00E-07	47.5108	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#9276 - 	CGI_10017514	superfamily	151060	262	310	1.47E-24	94.926	cl11140	SR-25 superfamily	C	 - 	"Nuclear RNA-splicing-associated protein; SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway."
Q#9276 - 	CGI_10017514	superfamily	243703	7	84	1.55E-09	53.7726	cl04309	RNAP_Rpb7_N_like superfamily	 - 	 - 	"RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex."
Q#9282 - 	CGI_10005549	superfamily	193607	90	221	1.66E-75	227.07	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#9282 - 	CGI_10005549	superfamily	247792	43	81	3.60E-08	48.2108	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9283 - 	CGI_10005550	superfamily	241589	427	549	1.13E-34	126.98	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#9286 - 	CGI_10003017	superfamily	192389	14	199	1.23E-46	160.954	cl10781	SNAPc_SNAP43 superfamily	 - 	 - 	"Small nuclear RNA activating complex (SNAPc), subunit SNAP43; Members of this family are part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. They bind to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Furthermore, they also recruit TBP and BRF2 to the U6 snRNA TATA box."
Q#9287 - 	CGI_10003019	superfamily	244859	46	270	1.53E-15	74.12	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#9289 - 	CGI_10003083	superfamily	247905	203	336	4.85E-15	71.8852	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#9289 - 	CGI_10003083	superfamily	221155	406	510	1.61E-06	46.592	cl13152	RIG-I_C-RD superfamily	 - 	 - 	"C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity."
Q#9290 - 	CGI_10003085	superfamily	243040	22	144	4.94E-58	184.869	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#9291 - 	CGI_10003086	superfamily	244897	91	385	1.29E-25	105.261	cl08298	PTZ00007 superfamily	 - 	 - 	(NAP-L) nucleosome assembly protein -L; Provisional
Q#9294 - 	CGI_10006717	superfamily	219542	18	124	2.09E-40	143.151	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#9294 - 	CGI_10006717	superfamily	215896	141	322	5.83E-18	81.1872	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#9295 - 	CGI_10006718	superfamily	241832	7	79	4.22E-16	70.2704	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9295 - 	CGI_10006718	superfamily	243175	90	214	2.76E-13	63.0254	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#9296 - 	CGI_10006719	superfamily	247724	131	333	8.08E-07	48.2216	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9297 - 	CGI_10006720	superfamily	245201	18	189	4.48E-17	75.6508	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9298 - 	CGI_10006721	superfamily	245226	1134	1307	5.46E-96	305.695	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9298 - 	CGI_10006721	superfamily	243082	543	627	1.28E-27	114.532	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9298 - 	CGI_10006721	superfamily	243082	1005	1063	1.13E-05	47.5072	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9298 - 	CGI_10006721	superfamily	243082	810	888	3.64E-05	45.5812	cl02553	Peptidase_C19 superfamily	NC	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9298 - 	CGI_10006721	superfamily	243092	242	347	0.000217639	43.4776	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9300 - 	CGI_10006723	superfamily	219502	364	610	6.63E-50	173.399	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#9300 - 	CGI_10006723	superfamily	201962	182	253	3.06E-16	74.7196	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#9300 - 	CGI_10006723	superfamily	219507	264	359	3.41E-13	66.4939	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#9302 - 	CGI_10006725	superfamily	248097	130	240	7.39E-14	67.6754	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9302 - 	CGI_10006725	superfamily	248097	268	378	1.15E-10	58.4306	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9303 - 	CGI_10006726	superfamily	248097	99	234	1.31E-19	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9304 - 	CGI_10006727	superfamily	241599	204	255	1.04E-10	58.4089	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#9304 - 	CGI_10006727	superfamily	202226	100	188	2.25E-11	60.7698	cl08348	CUT superfamily	 - 	 - 	"CUT domain; The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein ."
Q#9305 - 	CGI_10006728	superfamily	205121	463	487	2.38E-06	45.958	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#9307 - 	CGI_10019525	superfamily	243092	37	78	2.15E-07	46.9444	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9308 - 	CGI_10019526	superfamily	243092	268	584	1.91E-18	85.4644	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9308 - 	CGI_10019526	superfamily	243092	1	341	2.33E-08	55.0336	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9310 - 	CGI_10019528	superfamily	243073	225	266	1.16E-08	49.7761	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#9310 - 	CGI_10019528	superfamily	246908	105	188	1.65E-16	71.8475	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#9311 - 	CGI_10019529	superfamily	243072	34	193	1.00E-31	116.714	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9311 - 	CGI_10019529	superfamily	243073	320	355	6.06E-08	48.6205	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#9312 - 	CGI_10019530	superfamily	243072	294	419	1.20E-42	155.234	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9312 - 	CGI_10019530	superfamily	243072	492	617	3.81E-41	150.612	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9312 - 	CGI_10019530	superfamily	243072	562	683	5.30E-41	150.227	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9312 - 	CGI_10019530	superfamily	243072	657	782	9.14E-41	149.841	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9312 - 	CGI_10019530	superfamily	243072	66	191	2.47E-40	148.301	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9312 - 	CGI_10019530	superfamily	243072	393	518	3.36E-40	147.915	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9312 - 	CGI_10019530	superfamily	243072	228	353	4.23E-40	147.915	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9312 - 	CGI_10019530	superfamily	194336	1221	1325	1.67E-26	107.822	cl02517	ZU5 superfamily	 - 	 - 	ZU5 domain; Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
Q#9312 - 	CGI_10019530	superfamily	246680	1714	1795	2.40E-19	86.1856	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#9314 - 	CGI_10019532	superfamily	247919	58	204	0.00385706	40.7366	cl17365	TrkH superfamily	C	 - 	Cation transport protein; This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilising ATP in the process. TrkH a member of the family from E. coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in E. coli.
Q#9316 - 	CGI_10019534	superfamily	241568	107	144	2.64E-06	44.7612	cl00043	CCP superfamily	C	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9316 - 	CGI_10019534	superfamily	241568	170	218	8.76E-06	43.2204	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9316 - 	CGI_10019534	superfamily	241568	244	283	0.000658836	37.4424	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9316 - 	CGI_10019534	superfamily	241568	42	82	0.00660425	34.3608	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9323 - 	CGI_10019541	superfamily	241628	18	170	7.45E-23	97.7932	cl00130	PseudoU_synth superfamily	C	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#9323 - 	CGI_10019541	superfamily	243090	292	405	3.11E-26	105.62	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#9323 - 	CGI_10019541	superfamily	198670	978	1057	6.02E-20	86.5121	cl02426	DIX superfamily	 - 	 - 	DIX domain; The DIX domain is present in Dishevelled and axin. This domain is involved in homo- and hetero-oligomerisation. It is involved in the homo- oligomerisation of mouse axin. The axin DIX domain also interacts with the dishevelled DIX domain. The DIX domain has also been called the DAX domain.
Q#9323 - 	CGI_10019541	superfamily	211424	171	271	2.00E-05	43.9616	cl16934	Axin_TNKS_binding superfamily	 - 	 - 	"Tankyrase binding N-terminal segment of axin; This N-terminal region of axin mediates interactions with the ankyrin-repeat clusters 2 and 3 of tankyrase, which controls the turnover of axin via poly-ADP-ribosylation. Axin functions as a negative regulator of the WNT signaling pathway."
Q#9323 - 	CGI_10019541	superfamily	220035	632	675	0.00249652	37.0907	cl07441	Axin_b-cat_bind superfamily	 - 	 - 	Axin beta-catenin binding domain; This domain is found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex. It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin.
Q#9324 - 	CGI_10019542	superfamily	247856	35	90	5.37E-08	46.3869	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9324 - 	CGI_10019542	superfamily	247856	66	124	6.43E-08	46.0017	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9324 - 	CGI_10019542	superfamily	247856	1	60	6.93E-08	46.0017	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9325 - 	CGI_10019543	superfamily	242611	204	467	1.56E-161	477.406	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#9325 - 	CGI_10019543	superfamily	245606	585	806	2.66E-37	138.808	cl11410	TPP_enzyme_PYR superfamily	 - 	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#9326 - 	CGI_10019544	superfamily	247683	330	385	8.05E-20	85.4516	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#9326 - 	CGI_10019544	superfamily	248022	642	1020	7.49E-68	233.324	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#9326 - 	CGI_10019544	superfamily	245835	5	242	4.38E-51	180.254	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#9327 - 	CGI_10019545	superfamily	216686	143	334	3.94E-48	163.263	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#9328 - 	CGI_10019546	superfamily	213147	405	523	1.77E-31	120.433	cl17040	ADDz superfamily	 - 	 - 	"ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain; The ADDz zinc finger domain is present in the chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2 type transcription factor protein. The Dnmt3 family includes two active DNA methyltransferases, Dnmt3a and -3b, and one regulatory factor Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif."
Q#9328 - 	CGI_10019546	superfamily	238192	549	814	3.48E-15	75.3494	cl18939	Cyt_C5_DNA_methylase superfamily	 - 	 - 	"Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability."
Q#9328 - 	CGI_10019546	superfamily	243083	236	323	1.18E-07	50.4452	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#9331 - 	CGI_10019549	superfamily	241564	17	74	2.01E-18	72.2983	cl00035	BIR superfamily	C	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#9332 - 	CGI_10019550	superfamily	222150	138	163	0.000197814	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9332 - 	CGI_10019550	superfamily	222150	342	366	0.000293849	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9332 - 	CGI_10019550	superfamily	222150	111	135	0.00166708	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9332 - 	CGI_10019550	superfamily	222150	313	337	0.00236958	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9334 - 	CGI_10019552	superfamily	245210	4	403	7.52E-102	337.223	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#9334 - 	CGI_10019552	superfamily	243109	2505	2692	2.70E-81	268.701	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#9334 - 	CGI_10019552	superfamily	245206	1868	2086	4.51E-75	260.844	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#9334 - 	CGI_10019552	superfamily	247637	1569	1841	2.99E-34	136.16	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#9334 - 	CGI_10019552	superfamily	244888	490	798	1.53E-77	263.118	cl08282	Acyl_transf_1 superfamily	 - 	 - 	Acyl transferase domain; Acyl transferase domain.  
Q#9334 - 	CGI_10019552	superfamily	245206	1327	1535	2.40E-15	80.1856	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#9334 - 	CGI_10019552	superfamily	214837	857	1009	2.53E-08	54.925	cl11739	PKS_DH superfamily	 - 	 - 	Dehydratase domain in polyketide synthase (PKS) enzymes; Dehydratase domain in polyketide synthase (PKS) enzymes.  
Q#9334 - 	CGI_10019552	superfamily	245209	2102	2171	1.41E-07	51.8673	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#9335 - 	CGI_10019553	superfamily	245835	169	383	2.44E-144	413.259	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#9335 - 	CGI_10019553	superfamily	241622	46	122	4.44E-15	70.2882	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#9338 - 	CGI_10019557	superfamily	243033	417	535	6.53E-05	41.9202	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#9339 - 	CGI_10019558	superfamily	238191	25	501	4.40E-117	356.257	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9340 - 	CGI_10019559	superfamily	238191	543	1019	2.72E-104	337.382	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9340 - 	CGI_10019559	superfamily	238191	45	512	6.41E-101	328.137	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9341 - 	CGI_10019560	superfamily	238191	1	110	5.30E-10	55.8012	cl18907	Esterase_lipase superfamily	N	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9342 - 	CGI_10019561	superfamily	247057	776	837	3.39E-16	74.8232	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#9344 - 	CGI_10009108	superfamily	110440	113	140	1.10E-05	42.3949	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9347 - 	CGI_10009111	superfamily	246669	157	281	9.33E-86	261.816	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#9347 - 	CGI_10009111	superfamily	246669	385	483	7.77E-56	184.527	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#9347 - 	CGI_10009111	superfamily	246669	292	372	6.52E-41	144.081	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#9348 - 	CGI_10009112	superfamily	241594	508	837	5.57E-119	368.431	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#9348 - 	CGI_10009112	superfamily	243072	56	181	3.75E-38	139.441	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9349 - 	CGI_10009113	superfamily	243040	29	150	2.74E-84	260.472	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#9356 - 	CGI_10009137	superfamily	245814	58	119	4.13E-06	44.0171	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9356 - 	CGI_10009137	superfamily	245814	257	309	1.33E-05	42.4763	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9362 - 	CGI_10009143	superfamily	217473	96	319	1.46E-28	115.925	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#9364 - 	CGI_10004288	superfamily	191867	3	179	1.99E-102	309.114	cl06740	FTCD_N superfamily	 - 	 - 	"Formiminotransferase domain, N-terminal subdomain; The formiminotransferase (FT) domain of formiminotransferase- cyclodeaminase (FTCD) forms a homodimer, and each protomer comprises two subdomains. The N-terminal subdomain is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains."
Q#9364 - 	CGI_10004288	superfamily	202490	181	335	6.40E-70	223.657	cl03808	FTCD superfamily	 - 	 - 	Formiminotransferase domain; Formiminotransferase domain.  
Q#9364 - 	CGI_10004288	superfamily	242449	387	523	4.60E-45	157.724	cl01350	FTCD_C superfamily	N	 - 	Formiminotransferase-cyclodeaminase; Members of this family are thought to be Formiminotransferase- cyclodeaminase enzymes EC:4.3.1.4. This domain is found in the C-terminus of the bifunctional animal members of the family.
Q#9365 - 	CGI_10004289	superfamily	243083	270	351	2.40E-33	122.897	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#9365 - 	CGI_10004289	superfamily	243084	154	256	5.48E-14	68.9463	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#9366 - 	CGI_10004290	superfamily	248458	369	540	6.35E-09	56.9385	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9366 - 	CGI_10004290	superfamily	248458	94	240	9.84E-06	46.5381	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9368 - 	CGI_10007524	superfamily	243540	47	271	1.65E-22	92.696	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#9370 - 	CGI_10005864	superfamily	247755	2053	2277	3.97E-110	352.192	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#9370 - 	CGI_10005864	superfamily	247755	1026	1245	6.40E-105	337.17	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#9370 - 	CGI_10005864	superfamily	243092	56	292	1.30E-28	118.977	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9373 - 	CGI_10005867	superfamily	245820	27	451	0	555.72	cl11970	PriL superfamily	 - 	 - 	"Archaeal/eukaryotic core primase: Large subunit, PriL; Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. The DNA replication machinery of archaeal organisms contains only the core primase, a simpler arrangement compared to eukaryotes. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL, such as the stabilization of PriS, involvement in the initiation of synthesis, the improvement of primase processivity, and the determination of product size."
Q#9375 - 	CGI_10005869	superfamily	245814	24	101	2.15E-05	40.9355	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9375 - 	CGI_10005869	superfamily	245814	120	204	0.000366049	37.5772	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9376 - 	CGI_10005870	superfamily	243034	448	541	5.48E-09	54.3084	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9376 - 	CGI_10005870	superfamily	243034	165	264	2.32E-08	52.7676	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9377 - 	CGI_10005871	superfamily	241645	3	84	3.14E-06	40.1941	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#9378 - 	CGI_10005872	superfamily	243082	132	217	9.29E-18	79.3528	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9378 - 	CGI_10005872	superfamily	243082	84	100	0.00108047	38.2331	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9379 - 	CGI_10005873	superfamily	243082	23	121	2.37E-15	73.861	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9382 - 	CGI_10008035	superfamily	216239	37	371	9.25E-103	310.777	cl18361	IRK superfamily	 - 	 - 	Inward rectifier potassium channel; Inward rectifier potassium channel.  
Q#9383 - 	CGI_10008036	superfamily	216239	23	322	3.61E-90	279.576	cl18361	IRK superfamily	 - 	 - 	Inward rectifier potassium channel; Inward rectifier potassium channel.  
Q#9384 - 	CGI_10008037	superfamily	216239	1	295	2.20E-103	310.007	cl18361	IRK superfamily	 - 	 - 	Inward rectifier potassium channel; Inward rectifier potassium channel.  
Q#9385 - 	CGI_10008038	superfamily	241571	670	783	5.51E-23	96.7126	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#9385 - 	CGI_10008038	superfamily	241609	791	864	1.60E-16	77.0331	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#9385 - 	CGI_10008038	superfamily	241568	1124	1181	5.69E-06	45.5316	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9385 - 	CGI_10008038	superfamily	243035	985	1093	1.09E-05	45.3034	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9385 - 	CGI_10008038	superfamily	241568	919	972	0.000274005	40.524	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9385 - 	CGI_10008038	superfamily	241583	240	398	3.31E-28	113.82	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#9388 - 	CGI_10008041	superfamily	241629	45	158	6.86E-09	54.0632	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#9388 - 	CGI_10008041	superfamily	241629	426	539	5.56E-05	41.8202	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#9389 - 	CGI_10008042	superfamily	247755	88	322	1.39E-79	254.013	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#9389 - 	CGI_10008042	superfamily	247789	426	638	3.31E-36	135.464	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#9390 - 	CGI_10008043	superfamily	248312	8	119	1.48E-06	44.2665	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#9392 - 	CGI_10008045	superfamily	247905	22	69	8.76E-11	59.9441	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#9393 - 	CGI_10000389	superfamily	243064	21	135	3.57E-23	89.3402	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#9395 - 	CGI_10002469	superfamily	241574	213	420	6.50E-84	266.374	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9395 - 	CGI_10002469	superfamily	241574	458	629	4.63E-16	77.2409	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9396 - 	CGI_10002470	superfamily	220611	16	64	0.00746028	31.3611	cl10864	Laps superfamily	NC	 - 	Learning-associated protein; This is a family of 121-amino acid secretory proteins. Laps functions in the regulation of neuronal cell adhesion and/or movement and synapse attachment. Laps binds to the ApC/EBP (Aplysia CCAAT/enhancer binding protein) promoter and activates the transcription of ApC/EBP mRNA.
Q#9398 - 	CGI_10006809	superfamily	245213	46	81	3.78E-09	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9398 - 	CGI_10006809	superfamily	245213	8	43	4.79E-09	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9398 - 	CGI_10006809	superfamily	245213	84	119	8.89E-09	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9398 - 	CGI_10006809	superfamily	245847	125	269	1.86E-18	79.1377	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#9399 - 	CGI_10006810	superfamily	225950	4	55	0.00155182	34.4781	cl18731	COG3416 superfamily	N	 - 	Uncharacterized protein conserved in bacteria [Function unknown]
Q#9401 - 	CGI_10006812	superfamily	246918	216	262	4.13E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9401 - 	CGI_10006812	superfamily	246918	104	150	1.42E-10	57.5967	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9401 - 	CGI_10006812	superfamily	246918	160	211	3.44E-09	53.3595	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9401 - 	CGI_10006812	superfamily	246918	272	323	1.23E-08	51.8187	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9401 - 	CGI_10006812	superfamily	246918	380	429	1.07E-07	49.1223	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9401 - 	CGI_10006812	superfamily	243119	437	481	0.000174335	39.7245	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#9401 - 	CGI_10006812	superfamily	246918	328	369	0.00060684	38.3367	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9405 - 	CGI_10006816	superfamily	227412	1	136	1.47E-21	86.3685	cl18811	YIP1 superfamily	N	 - 	"Rab GTPase interacting factor, Golgi membrane protein [Intracellular trafficking and secretion]"
Q#9408 - 	CGI_10006819	superfamily	241750	2	156	1.53E-31	114.593	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#9412 - 	CGI_10004267	superfamily	247684	5	432	8.12E-88	276.081	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9416 - 	CGI_10004271	superfamily	241563	61	96	0.00107099	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9418 - 	CGI_10004914	superfamily	241550	180	436	3.14E-68	218.202	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#9418 - 	CGI_10004914	superfamily	243647	67	153	1.45E-23	93.85	cl04104	Arg_tRNA_synt_N superfamily	 - 	 - 	"Arginyl tRNA synthetase N terminal domain; This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition."
Q#9419 - 	CGI_10004915	superfamily	245839	59	223	1.52E-31	114.234	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#9420 - 	CGI_10004916	superfamily	220622	31	174	8.54E-68	207.76	cl10879	Mesd superfamily	 - 	 - 	"Chaperone for wingless signalling and trafficking of LDL receptor; Mesd is a family of highly conserved proteins found from nematodes to humans. The final C-terminal residues, KEDL, are the endoplasmic reticulum retention sequence as it is an ER protein specifically required for the intracellular trafficking of members of the low-density lipoprotein family of receptors (LDLRs). The N- and C-terminal sequences are predicted to adopt a random coil conformation, with the exception of an isolated predicted helix within the N-terminal region, The central folded domain flanked by natively unstructured regions is the necessary structure for facilitating maturation of LRP6 (Low-Density Lipoprotein Receptor-Related Protein 6 Maturation)."
Q#9421 - 	CGI_10004917	superfamily	247723	232	347	1.17E-49	163.987	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9426 - 	CGI_10010703	superfamily	222150	400	425	0.00225775	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9427 - 	CGI_10010704	superfamily	222150	380	405	0.000906793	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9427 - 	CGI_10010704	superfamily	222150	353	376	0.00122031	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9428 - 	CGI_10010705	superfamily	246680	11	89	5.67E-16	70.3084	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#9429 - 	CGI_10010706	superfamily	247683	427	488	1.35E-26	105.835	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#9429 - 	CGI_10010706	superfamily	241622	328	407	2.15E-17	79.9182	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#9429 - 	CGI_10010706	superfamily	241622	1	75	3.14E-16	76.4514	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#9429 - 	CGI_10010706	superfamily	241622	90	163	3.35E-06	46.7911	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#9429 - 	CGI_10010706	superfamily	194336	1391	1494	1.15E-47	167.423	cl02517	ZU5 superfamily	 - 	 - 	ZU5 domain; Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
Q#9429 - 	CGI_10010706	superfamily	247744	537	705	1.94E-26	108.919	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#9430 - 	CGI_10010707	superfamily	243051	649	803	1.98E-25	103.997	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#9430 - 	CGI_10010707	superfamily	245213	608	645	4.37E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9430 - 	CGI_10010707	superfamily	245213	569	603	0.000147353	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9430 - 	CGI_10010707	superfamily	245213	489	524	0.000152315	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9430 - 	CGI_10010707	superfamily	245213	244	281	0.00447582	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9431 - 	CGI_10010708	superfamily	243051	675	782	3.53E-20	88.5889	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#9431 - 	CGI_10010708	superfamily	245213	593	630	6.88E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9431 - 	CGI_10010708	superfamily	245213	467	505	4.13E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9431 - 	CGI_10010708	superfamily	245213	508	546	0.000265466	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9431 - 	CGI_10010708	superfamily	245213	549	587	0.00027688	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9431 - 	CGI_10010708	superfamily	241583	1	161	1.39E-42	153.111	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#9431 - 	CGI_10010708	superfamily	241571	209	324	0.000432195	39.7031	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#9432 - 	CGI_10010709	superfamily	243107	6	32	0.000366359	37.5246	cl02611	G-patch superfamily	N	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#9433 - 	CGI_10010710	superfamily	243097	76	306	1.52E-93	284.955	cl02572	PIPKc superfamily	C	 - 	"Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs."
Q#9438 - 	CGI_10009776	superfamily	215647	49	289	1.43E-12	64.9372	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#9442 - 	CGI_10009780	superfamily	215647	187	427	9.10E-09	54.5369	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#9443 - 	CGI_10009781	superfamily	247724	5	117	3.35E-25	96.6831	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9445 - 	CGI_10006602	superfamily	219619	5	83	1.88E-10	54.1359	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#9446 - 	CGI_10006603	superfamily	219619	73	129	1.40E-12	62.2251	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#9446 - 	CGI_10006603	superfamily	219619	180	206	4.10E-07	46.8172	cl18518	Ion_trans_2 superfamily	NC	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#9447 - 	CGI_10006604	superfamily	219619	76	129	1.15E-13	65.3067	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#9447 - 	CGI_10006604	superfamily	219619	179	240	2.20E-09	53.3655	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#9448 - 	CGI_10006605	superfamily	241567	37	196	4.68E-11	60.7918	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#9448 - 	CGI_10006605	superfamily	241567	274	365	1.77E-05	44.1284	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#9449 - 	CGI_10006606	superfamily	243097	1	349	2.50E-94	287.356	cl02572	PIPKc superfamily	 - 	 - 	"Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs."
Q#9450 - 	CGI_10007272	superfamily	241607	436	486	1.63E-18	80.4261	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#9452 - 	CGI_10007274	superfamily	207662	261	333	1.69E-42	144.125	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#9454 - 	CGI_10007276	superfamily	243134	207	333	7.59E-19	83.8528	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#9454 - 	CGI_10007276	superfamily	243134	371	450	1.39E-09	56.5036	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#9454 - 	CGI_10007276	superfamily	243134	13	147	5.32E-09	54.9628	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#9454 - 	CGI_10007276	superfamily	243134	655	734	1.86E-05	43.792	cl02663	Fasciclin superfamily	N	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#9462 - 	CGI_10017262	superfamily	241984	1	197	1.65E-41	142.01	cl00615	Membrane-FADS-like superfamily	N	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#9463 - 	CGI_10017263	superfamily	243176	1	494	0	884.32	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#9464 - 	CGI_10017264	superfamily	241889	122	267	3.48E-56	184.741	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#9465 - 	CGI_10017265	superfamily	243555	20	207	1.68E-13	68.1866	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#9468 - 	CGI_10017268	superfamily	248012	102	201	3.42E-24	94.952	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#9469 - 	CGI_10017269	superfamily	248012	2	84	2.90E-07	43.8013	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#9471 - 	CGI_10017271	superfamily	245814	3	65	3.92E-08	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9472 - 	CGI_10017272	superfamily	245814	80	123	0.00554724	33.6167	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9473 - 	CGI_10017273	superfamily	241607	35	75	5.89E-11	54.1982	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#9474 - 	CGI_10017274	superfamily	241624	335	470	7.56E-36	133.606	cl00120	PP2Cc superfamily	N	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#9479 - 	CGI_10017279	superfamily	207724	175	234	6.65E-12	59.9367	cl02772	BSD superfamily	 - 	 - 	BSD domain; This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function.
Q#9483 - 	CGI_10017283	superfamily	245815	25	503	0	834.738	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#9483 - 	CGI_10017283	superfamily	245815	565	731	4.78E-24	105.086	cl11961	ALDH-SF superfamily	C	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#9484 - 	CGI_10017284	superfamily	241616	10	43	0.000180166	38.7804	cl00109	MADS superfamily	C	 - 	"MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers.  Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals.  Also found in fungi."
Q#9484 - 	CGI_10017284	superfamily	247999	265	319	0.00229944	35.544	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#9489 - 	CGI_10005130	superfamily	247742	5	413	0	741.081	cl17188	enolase_like superfamily	 - 	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#9490 - 	CGI_10000748	superfamily	248019	332	444	6.30E-15	72.3169	cl17465	DAGK_cat superfamily	C	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#9491 - 	CGI_10003415	superfamily	247042	32	428	1.28E-74	242.622	cl15693	Sema superfamily	 - 	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#9491 - 	CGI_10003415	superfamily	247042	426	492	0.00134794	39.6215	cl15693	Sema superfamily	N	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#9492 - 	CGI_10003416	superfamily	247746	130	213	0.0062628	35.697	cl17192	ATP-synt_B superfamily	N	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#9493 - 	CGI_10003417	superfamily	247684	7	383	0	766.119	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9494 - 	CGI_10015220	superfamily	241599	101	170	6.43E-05	40.3045	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#9494 - 	CGI_10015220	superfamily	243092	248	384	0.00305355	37.6996	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9495 - 	CGI_10015221	superfamily	211426	65	166	3.53E-37	135.536	cl16936	SATB1_N superfamily	 - 	 - 	"N-terminal domain of SATB1 and similar proteins; SATB1, the special AT-rich sequence-binding protein 1, is involved in organizing chromosomal loci into distinct loops, creating a "loopscape" that has a direct bearing on gene expression. This N-terminal domain, which may be involved in various interactions with chromatin proteins, resembles a ubiquitin domain and has been shown to form tetramers, a function critical to SATB1-DNA interactions. The related Drosophila homeobox gene defective proventriculus (dve) plays a key role in the functional specification during endoderm development."
Q#9495 - 	CGI_10015221	superfamily	241599	708	779	1.35E-07	49.5493	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#9495 - 	CGI_10015221	superfamily	241599	276	342	2.42E-07	48.7789	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#9496 - 	CGI_10015222	superfamily	247743	213	380	4.94E-29	111.084	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#9497 - 	CGI_10015223	superfamily	248030	244	736	5.08E-93	302.37	cl17476	Glyco_transf_7C superfamily	 - 	 - 	"N-terminal domain of galactosyltransferase; This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalyzed reaction."
Q#9498 - 	CGI_10015224	superfamily	247792	30	95	4.76E-06	43.9736	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9498 - 	CGI_10015224	superfamily	241563	128	168	3.48E-05	41.504	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9498 - 	CGI_10015224	superfamily	247797	220	287	0.000445032	40.4861	cl17243	PRK13975 superfamily	NC	 - 	thymidylate kinase; Provisional
Q#9499 - 	CGI_10015225	superfamily	247723	1	20	0.00188498	36.2264	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9500 - 	CGI_10015226	superfamily	241584	709	792	9.67E-16	74.8403	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	816	888	1.00E-12	65.9807	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	426	513	9.04E-10	57.1211	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	892	979	2.82E-09	55.9655	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	346	421	3.43E-09	55.5803	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	534	608	5.65E-09	54.8099	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	627	703	3.05E-07	49.8023	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	993	1077	2.23E-05	44.0243	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9500 - 	CGI_10015226	superfamily	241584	235	327	0.000127163	41.7131	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9503 - 	CGI_10015229	superfamily	246722	1	121	2.43E-54	190.131	cl14812	PIN_SF superfamily	C	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#9503 - 	CGI_10015229	superfamily	246722	595	713	1.53E-42	156.619	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#9503 - 	CGI_10015229	superfamily	246724	720	809	5.54E-31	118.507	cl14815	H3TH_StructSpec-5'-nucleases superfamily	 - 	 - 	"H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases."
Q#9503 - 	CGI_10015229	superfamily	246722	793	848	2.12E-08	54.9262	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#9504 - 	CGI_10015230	superfamily	241628	79	261	2.10E-121	356.186	cl00130	PseudoU_synth superfamily	 - 	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#9504 - 	CGI_10015230	superfamily	203846	39	97	8.82E-33	118.998	cl06897	DKCLD superfamily	 - 	 - 	DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins.
Q#9504 - 	CGI_10015230	superfamily	241977	288	361	1.82E-22	91.3862	cl00607	PUA superfamily	 - 	 - 	"PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain."
Q#9505 - 	CGI_10015231	superfamily	241572	47	100	2.47E-08	52.2409	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#9505 - 	CGI_10015231	superfamily	241572	155	207	0.00278342	36.8329	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#9507 - 	CGI_10015233	superfamily	241563	60	97	1.82E-06	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9507 - 	CGI_10015233	superfamily	128778	102	214	2.42E-05	43.0223	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#9507 - 	CGI_10015233	superfamily	110440	485	511	0.00461564	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9508 - 	CGI_10015234	superfamily	220617	23	134	4.95E-06	45.1325	cl10871	DUF2371 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2371); This is a family of proteins conserved from nematodes to humans. The function is not known.
Q#9511 - 	CGI_10015237	superfamily	243179	107	202	5.02E-08	50.5807	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#9513 - 	CGI_10015239	superfamily	247725	354	465	6.26E-65	217.139	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9513 - 	CGI_10015239	superfamily	215882	272	379	1.36E-28	113.145	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#9513 - 	CGI_10015239	superfamily	220215	190	266	1.13E-21	91.903	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#9513 - 	CGI_10015239	superfamily	220215	42	118	1.13E-21	91.903	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#9513 - 	CGI_10015239	superfamily	147837	1426	1537	1.47E-09	57.6121	cl05461	4_1_CTD superfamily	 - 	 - 	"4.1 protein C-terminal domain (CTD); At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates."
Q#9513 - 	CGI_10015239	superfamily	192138	478	512	1.02E-06	47.9988	cl07378	FA superfamily	C	 - 	"FERM adjacent (FA); This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates."
Q#9515 - 	CGI_10015241	superfamily	247801	47	170	1.37E-58	193.231	cl17247	CoA_trans superfamily	C	 - 	Coenzyme A transferase; Coenzyme A transferase.  
Q#9515 - 	CGI_10015241	superfamily	241634	236	329	0.00277444	36.8786	cl00143	SynN superfamily	C	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#9516 - 	CGI_10015242	superfamily	241642	214	272	2.35E-09	52.4978	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#9516 - 	CGI_10015242	superfamily	241634	40	171	1.79E-10	57.2942	cl00143	SynN superfamily	 - 	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#9517 - 	CGI_10015243	superfamily	247801	136	342	3.76E-97	289.573	cl17247	CoA_trans superfamily	 - 	 - 	Coenzyme A transferase; Coenzyme A transferase.  
Q#9517 - 	CGI_10015243	superfamily	247801	23	107	3.48E-25	101.168	cl17247	CoA_trans superfamily	N	 - 	Coenzyme A transferase; Coenzyme A transferase.  
Q#9518 - 	CGI_10015244	superfamily	215859	124	266	0.000391382	39.8923	cl18347	Peptidase_S9 superfamily	C	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#9521 - 	CGI_10015247	superfamily	243072	71	204	4.54E-31	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9522 - 	CGI_10015248	superfamily	244964	172	250	3.22E-13	63.0218	cl08458	CobW_C superfamily	 - 	 - 	"Cobalamin synthesis protein cobW C-terminal domain; This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family."
Q#9522 - 	CGI_10015248	superfamily	247757	85	116	0.00186388	36.8297	cl17203	Fer4_NifH superfamily	N	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#9523 - 	CGI_10002335	superfamily	242934	1	142	1.58E-42	143.086	cl02219	Bap31 superfamily	 - 	 - 	"B-cell receptor-associated protein 31-like; Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31."
Q#9524 - 	CGI_10002336	superfamily	247916	18	68	1.19E-07	48.9183	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#9525 - 	CGI_10012175	superfamily	216686	3	152	1.46E-33	120.12	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#9526 - 	CGI_10012176	superfamily	245235	3613	3688	2.45E-44	170.474	cl10023	POLBc superfamily	C	 - 	"DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y).  Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis."
Q#9526 - 	CGI_10012176	superfamily	245226	3476	3583	8.16E-43	159.708	cl10012	DnaQ_like_exo superfamily	NC	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9526 - 	CGI_10012176	superfamily	245226	3332	3386	4.22E-17	83.8233	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9528 - 	CGI_10012178	superfamily	149701	287	329	4.01E-12	60.3077	cl07373	Integrin_b_cyt superfamily	 - 	 - 	"Integrin beta cytoplasmic domain; Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion. Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit. Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity. This domain corresponds to the cytoplasmic domain of the beta subunit."
Q#9528 - 	CGI_10012178	superfamily	219669	202	262	0.00188703	35.8316	cl06832	Integrin_B_tail superfamily	 - 	 - 	Integrin beta tail domain; This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
Q#9529 - 	CGI_10012179	superfamily	248247	1	277	5.04E-72	244.436	cl17693	Integrin_beta superfamily	N	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#9529 - 	CGI_10012179	superfamily	248247	636	871	3.55E-58	205.146	cl17693	Integrin_beta superfamily	C	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#9529 - 	CGI_10012179	superfamily	149701	569	605	1.13E-08	52.6037	cl07373	Integrin_b_cyt superfamily	 - 	 - 	"Integrin beta cytoplasmic domain; Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion. Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit. Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity. This domain corresponds to the cytoplasmic domain of the beta subunit."
Q#9530 - 	CGI_10012180	superfamily	248247	9	298	8.37E-74	242.895	cl17693	Integrin_beta superfamily	N	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#9531 - 	CGI_10012181	superfamily	248247	34	154	5.18E-28	106.92	cl17693	Integrin_beta superfamily	C	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#9533 - 	CGI_10012183	superfamily	247856	130	157	0.00342012	34.878	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9535 - 	CGI_10003639	superfamily	241554	44	246	1.90E-15	71.7154	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#9537 - 	CGI_10004868	superfamily	241874	31	593	0	576.053	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#9538 - 	CGI_10004869	superfamily	241594	162	321	3.76E-06	46.404	cl00077	HECTc superfamily	C	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#9540 - 	CGI_10004871	superfamily	217414	513	636	1.13E-05	46.554	cl03927	Otopetrin superfamily	N	 - 	"Protein of unknown function, DUF270; Protein of unknown function, DUF270.  "
Q#9542 - 	CGI_10004873	superfamily	246918	232	263	6.56E-05	40.2627	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9544 - 	CGI_10003481	superfamily	247724	5	166	2.51E-130	366.5	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9546 - 	CGI_10003483	superfamily	241563	97	134	0.000201953	39.1928	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9547 - 	CGI_10003484	superfamily	241563	70	110	0.00116731	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9547 - 	CGI_10003484	superfamily	110440	487	514	0.00137741	37.0021	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9547 - 	CGI_10003484	superfamily	217316	118	198	0.00163264	37.2208	cl03832	DUF234 superfamily	 - 	 - 	Archaea bacterial proteins of unknown function; Archaea bacterial proteins of unknown function.  
Q#9547 - 	CGI_10003484	superfamily	110440	529	556	0.00935534	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9549 - 	CGI_10007903	superfamily	247757	20	153	6.43E-58	181.685	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#9551 - 	CGI_10007905	superfamily	241584	71	131	2.39E-09	50.1875	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9553 - 	CGI_10007907	superfamily	245599	254	432	2.66E-39	140.436	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#9553 - 	CGI_10007907	superfamily	207662	70	163	1.25E-43	149.518	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#9554 - 	CGI_10007908	superfamily	243290	133	273	1.70E-45	151.512	cl03075	GrpE superfamily	 - 	 - 	"GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent."
Q#9559 - 	CGI_10007913	superfamily	243175	79	150	7.75E-21	83.4936	cl02776	GST_C_family superfamily	C	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#9560 - 	CGI_10007914	superfamily	247792	209	251	5.36E-11	56.3	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9560 - 	CGI_10007914	superfamily	218247	37	173	5.27E-21	87.8171	cl04727	Pex2_Pex12 superfamily	N	 - 	"Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain."
Q#9566 - 	CGI_10007940	superfamily	189857	5	124	2.50E-38	128.522	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#9567 - 	CGI_10007941	superfamily	189857	5	124	2.84E-38	128.137	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#9568 - 	CGI_10007942	superfamily	189857	5	124	1.16E-38	129.292	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#9570 - 	CGI_10007944	superfamily	219502	399	642	1.74E-73	237.728	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#9570 - 	CGI_10007944	superfamily	201962	215	287	6.41E-22	90.898	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#9570 - 	CGI_10007944	superfamily	219507	296	394	2.80E-13	66.8791	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#9571 - 	CGI_10007945	superfamily	110440	462	489	0.00524988	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9573 - 	CGI_10007947	superfamily	241563	63	103	0.0024083	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9575 - 	CGI_10007949	superfamily	216686	227	392	2.76E-26	104.712	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#9576 - 	CGI_10007950	superfamily	247724	311	517	4.60E-92	281.891	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9576 - 	CGI_10007950	superfamily	243092	15	306	2.68E-34	130.533	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9578 - 	CGI_10023516	superfamily	241563	81	120	2.85E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9578 - 	CGI_10023516	superfamily	110440	505	531	8.10E-05	40.4689	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9579 - 	CGI_10023517	superfamily	110440	381	405	0.000161946	39.3133	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9580 - 	CGI_10023518	superfamily	241584	118	194	1.12E-12	61.7435	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9580 - 	CGI_10023518	superfamily	241584	7	113	2.00E-05	41.3279	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#9581 - 	CGI_10023519	superfamily	217915	272	777	1.89E-133	413.44	cl14957	Spc97_Spc98 superfamily	 - 	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#9583 - 	CGI_10023521	superfamily	245596	8	257	2.00E-105	318.436	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#9584 - 	CGI_10023522	superfamily	241832	164	253	3.10E-53	178.456	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9584 - 	CGI_10023522	superfamily	241832	266	355	2.47E-51	173.448	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9584 - 	CGI_10023522	superfamily	241832	42	138	5.01E-41	145.107	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9584 - 	CGI_10023522	superfamily	243082	558	694	4.47E-21	92.9314	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9584 - 	CGI_10023522	superfamily	243046	361	540	3.01E-30	121.641	cl02460	Transferrin superfamily	C	 - 	Transferrin; Transferrin.  
Q#9585 - 	CGI_10023523	superfamily	243352	58	349	1.94E-114	336.489	cl03224	Porin3 superfamily	 - 	 - 	"Eukaryotic porin family that forms channels in the mitochondrial outer membrane; The porin family 3 contains two sub-families that play vital roles in the mitochondrial outer membrane, a translocase for unfolded pre-proteins (Tom40) and the voltage-dependent anion channel (VDAC) that regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane."
Q#9586 - 	CGI_10023524	superfamily	245456	581	812	7.90E-110	337.666	cl10970	AP_MHD_Cterm superfamily	 - 	 - 	"C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15."
Q#9586 - 	CGI_10023524	superfamily	242876	72	193	0.00154635	38.4893	cl02092	Clat_adaptor_s superfamily	 - 	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#9588 - 	CGI_10023526	superfamily	243095	301	489	7.93E-100	321.76	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#9588 - 	CGI_10023526	superfamily	247683	194	247	1.18E-29	115.239	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#9588 - 	CGI_10023526	superfamily	243088	59	172	5.75E-31	120.675	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#9589 - 	CGI_10023527	superfamily	247866	51	268	6.01E-32	119.094	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#9592 - 	CGI_10023530	superfamily	247903	12	199	6.91E-54	173.252	cl17349	Peptidase_M54 superfamily	 - 	 - 	"Peptidase family M54, also called archaemetzincins or archaelysins; Peptidase M54 (archaemetzincin or archaelysin) is a zinc-dependent aminopeptidase that contains the consensus zinc-binding sequence HEXXHXXGXXH/D and a conserved Met residue at the active site, and is thus classified as a metzincin. Archaemetzincins, first identified in archaea, are also found in bacteria and eukaryotes, including two human members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1 is mainly found in the liver and heart while AMZ2 is primarily expressed in testis and heart; both have been reported to degrade synthetic substrates and peptides. The Peptidase M54 family contains an extended metzincin concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that a second zinc ion is bound to four cysteines, thus resembling a zinc finger. Phylogenetic analysis of this family reveals a complex evolutionary process involving a series of lateral gene transfer, gene loss and genetic duplication events."
Q#9593 - 	CGI_10023531	superfamily	241644	1	86	5.22E-32	110.37	cl00154	UBCc superfamily	C	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#9594 - 	CGI_10023532	superfamily	248458	36	214	5.71E-20	90.8361	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9594 - 	CGI_10023532	superfamily	248458	467	657	4.06E-11	63.8721	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9595 - 	CGI_10023533	superfamily	247755	8	175	2.85E-32	122.506	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#9595 - 	CGI_10023533	superfamily	247789	428	565	5.30E-11	61.1206	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#9596 - 	CGI_10023534	superfamily	207662	76	158	3.25E-47	157.963	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#9596 - 	CGI_10023534	superfamily	245599	232	413	4.52E-38	138.124	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#9597 - 	CGI_10023535	superfamily	241799	8	225	1.17E-100	294.38	cl00339	SugarP_isomerase superfamily	 - 	 - 	"SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway."
Q#9598 - 	CGI_10023536	superfamily	222150	595	619	6.45E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#9599 - 	CGI_10023537	superfamily	243072	395	544	5.56E-16	77.4238	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9599 - 	CGI_10023537	superfamily	243072	521	612	6.65E-06	46.6078	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9602 - 	CGI_10023540	superfamily	217293	30	109	7.37E-13	60.7243	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#9603 - 	CGI_10023541	superfamily	219425	38	156	5.14E-17	72.5742	cl06494	Hydrolase_2 superfamily	 - 	 - 	"Cell Wall Hydrolase; These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance B. subtilis sleB is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex. A similar role is carried out by the partially redundant B. subtilis cwlJ. It is not clear whether these enzymes are amidases or peptidases."
Q#9604 - 	CGI_10023542	superfamily	219425	24	129	1.47E-09	51.3883	cl06494	Hydrolase_2 superfamily	 - 	 - 	"Cell Wall Hydrolase; These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance B. subtilis sleB is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex. A similar role is carried out by the partially redundant B. subtilis cwlJ. It is not clear whether these enzymes are amidases or peptidases."
Q#9607 - 	CGI_10023546	superfamily	243035	10	75	1.58E-10	53.0773	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9609 - 	CGI_10023548	superfamily	202203	223	292	8.44E-24	96.8685	cl03534	E2F_TDP superfamily	 - 	 - 	"E2F/DP family winged-helix DNA-binding domain; This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins."
Q#9609 - 	CGI_10023548	superfamily	202203	355	421	4.00E-12	63.3561	cl03534	E2F_TDP superfamily	C	 - 	"E2F/DP family winged-helix DNA-binding domain; This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins."
Q#9611 - 	CGI_10023550	superfamily	241559	3	101	3.56E-16	71.1879	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#9613 - 	CGI_10023552	superfamily	247743	502	581	1.60E-05	45.5999	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#9613 - 	CGI_10023552	superfamily	192053	1965	2041	5.82E-34	128.045	cl18175	COQ9 superfamily	 - 	 - 	COQ9; COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q. It may either catalyze a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role.
Q#9613 - 	CGI_10023552	superfamily	219908	1539	1706	1.61E-09	61.7241	cl07251	Kinetochor_Ybp2 superfamily	N	 - 	"Uncharacterized protein family, YAP/Alf4/glomulin; This entry contains a number of protein families with apparently unrelated functions. These include the YAP binding proteins of yeasts. These are stress response and redox homeostasis proteins, induced by hydrogen peroxide or induced in response to alkylating agent methyl methanesulphonate (MMS). The family includes Aberrant root formation protein 4 (Alf4) of Arabidopsis thaliana (Mouse-ear cress), which is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation. The family includes glomulin (FAP68), which is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12."
Q#9616 - 	CGI_10001435	superfamily	248097	7	73	3.21E-06	40.3262	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9619 - 	CGI_10005170	superfamily	241600	46	173	1.48E-58	184.366	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#9623 - 	CGI_10011782	superfamily	245201	21	300	0	569.621	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9626 - 	CGI_10011785	superfamily	245212	77	146	0.00186683	35.7723	cl09940	S4 superfamily	NC	 - 	"S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site;  Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes."
Q#9628 - 	CGI_10011787	superfamily	191378	22	115	0.000425029	36.7172	cl05416	PSP94 superfamily	 - 	 - 	"Beta-microseminoprotein (PSP-94); This family consists of the mammalian specific protein beta-microseminoprotein. Prostatic secretory protein of 94 amino acids (PSP94), also called beta-microseminoprotein, is a small, nonglycosylated protein, rich in cysteine residues. It was first isolated as a major protein from human seminal plasma. The exact function of this protein is unknown."
Q#9629 - 	CGI_10011788	superfamily	215648	304	554	1.10E-48	171.625	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#9629 - 	CGI_10011788	superfamily	245225	1	206	2.86E-28	117.729	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#9629 - 	CGI_10011788	superfamily	219467	224	273	1.18E-12	64.2767	cl08456	NCD3G superfamily	 - 	 - 	"Nine Cysteines Domain of family 3 GPCR; This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins."
Q#9634 - 	CGI_10011794	superfamily	241568	914	967	8.40E-07	47.8428	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9634 - 	CGI_10011794	superfamily	243032	257	428	2.63E-06	49.1271	cl02427	Pumilio superfamily	C	 - 	"Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats."
Q#9634 - 	CGI_10011794	superfamily	243032	361	555	8.72E-06	47.5863	cl02427	Pumilio superfamily	C	 - 	"Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats."
Q#9637 - 	CGI_10022134	superfamily	241583	137	274	3.54E-10	57.581	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#9637 - 	CGI_10022134	superfamily	241571	323	390	0.000174647	39.7031	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#9638 - 	CGI_10022135	superfamily	245206	5	254	6.16E-67	211.537	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#9639 - 	CGI_10022136	superfamily	241571	85	182	1.92E-10	56.6518	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#9640 - 	CGI_10022137	superfamily	241571	78	194	6.88E-09	52.7998	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#9642 - 	CGI_10022139	superfamily	247725	670	791	1.42E-22	94.3615	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9643 - 	CGI_10022140	superfamily	243072	168	294	2.09E-37	136.745	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9643 - 	CGI_10022140	superfamily	243072	30	160	1.61E-21	91.6762	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9645 - 	CGI_10022142	superfamily	242395	105	378	1.19E-77	244.147	cl01255	nadF superfamily	 - 	 - 	NAD kinase [Coenzyme metabolism]
Q#9646 - 	CGI_10022143	superfamily	201673	159	677	1.13E-101	324.915	cl18217	Glyco_hydro_39 superfamily	 - 	 - 	Glycosyl hydrolases family 39; Glycosyl hydrolases family 39.  
Q#9649 - 	CGI_10022146	superfamily	220396	24	141	3.56E-27	103.012	cl14975	DUF2349 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2349); Members of this family of uncharacterized novel proteins have no known function.
Q#9650 - 	CGI_10022147	superfamily	241740	24	124	1.78E-41	135.932	cl00269	cytidine_deaminase-like superfamily	 - 	 - 	"Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes.  All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate."
Q#9651 - 	CGI_10022148	superfamily	227891	197	531	6.58E-35	136.173	cl15889	COG5604 superfamily	C	 - 	Uncharacterized conserved protein [Function unknown]
Q#9653 - 	CGI_10022150	superfamily	227891	4	143	1.45E-17	81.8596	cl15889	COG5604 superfamily	N	 - 	Uncharacterized conserved protein [Function unknown]
Q#9654 - 	CGI_10022151	superfamily	241563	99	135	0.000262316	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9655 - 	CGI_10022152	superfamily	248313	33	129	0.00618626	33.7438	cl17759	EamA superfamily	N	 - 	EamA-like transporter family; This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.
Q#9656 - 	CGI_10022153	superfamily	220735	402	1023	0	631.607	cl15660	Ufd2P_core superfamily	 - 	 - 	"Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity."
Q#9656 - 	CGI_10022153	superfamily	248098	1038	1107	1.59E-27	108.15	cl17544	U-box superfamily	 - 	 - 	U-box domain; This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
Q#9657 - 	CGI_10022154	superfamily	247742	62	414	0	606.787	cl17188	enolase_like superfamily	 - 	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#9657 - 	CGI_10022154	superfamily	149077	881	989	3.87E-31	119.652	cl06719	TMC superfamily	 - 	 - 	"TMC domain; These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters."
Q#9658 - 	CGI_10022155	superfamily	245835	18	217	6.65E-91	270.713	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#9659 - 	CGI_10022156	superfamily	214507	221	260	0.000283309	38.5652	cl15307	LRRCT superfamily	C	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#9659 - 	CGI_10022156	superfamily	246925	36	142	0.00278006	38.1054	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#9660 - 	CGI_10022157	superfamily	247725	1	96	4.71E-49	165.861	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9660 - 	CGI_10022157	superfamily	243072	390	507	1.25E-24	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9660 - 	CGI_10022157	superfamily	243047	144	257	7.66E-53	177.042	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#9662 - 	CGI_10022159	superfamily	206077	230	269	9.47E-14	64.5664	cl18287	AA_permease_C superfamily	C	 - 	C-terminus of AA_permease; This is the C-terminus of AA-permease enzymes that is not captured by the models pfam00324 and pfam13520.
Q#9664 - 	CGI_10022161	superfamily	238076	187	292	1.17E-53	184.545	cl18938	PAX superfamily	 - 	 - 	Paired Box domain
Q#9665 - 	CGI_10022162	superfamily	245201	273	601	0	674.998	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9665 - 	CGI_10022162	superfamily	243157	59	141	6.16E-42	145.952	cl02720	PB1 superfamily	 - 	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#9665 - 	CGI_10022162	superfamily	241566	174	223	8.85E-15	69.4431	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#9666 - 	CGI_10022163	superfamily	144634	32	267	1.20E-153	432.422	cl03106	F_actin_cap_B superfamily	 - 	 - 	"F-actin capping protein, beta subunit; F-actin capping protein, beta subunit.  "
Q#9667 - 	CGI_10022164	superfamily	246680	17	83	5.72E-08	49.8928	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#9669 - 	CGI_10022166	superfamily	248458	47	260	7.70E-18	84.6729	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9669 - 	CGI_10022166	superfamily	248458	312	470	1.55E-10	62.3313	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9669 - 	CGI_10022166	superfamily	241583	628	701	4.62E-19	86.471	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#9669 - 	CGI_10022166	superfamily	241583	703	741	8.38E-09	54.8847	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#9669 - 	CGI_10022166	superfamily	247097	849	884	1.55E-06	46.2901	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#9669 - 	CGI_10022166	superfamily	247097	808	842	1.95E-05	43.1369	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#9672 - 	CGI_10022169	superfamily	241832	4	43	3.79E-15	66.8036	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9672 - 	CGI_10022169	superfamily	243175	54	140	5.09E-07	44.5358	cl02776	GST_C_family superfamily	C	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#9672 - 	CGI_10022169	superfamily	243175	115	175	0.00120194	36.1415	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#9673 - 	CGI_10022170	superfamily	238191	106	179	0.000983298	39.6228	cl18907	Esterase_lipase superfamily	NC	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#9677 - 	CGI_10022174	superfamily	245612	197	674	0	622.795	cl11426	Amidase superfamily	 - 	 - 	Amidase; Amidase.  
Q#9679 - 	CGI_10002112	superfamily	203401	19	129	7.88E-28	100.453	cl05607	Med22 superfamily	 - 	 - 	"Surfeit locus protein 5 subunit 22 of Mediator complex; This family consists of several eukaryotic Surfeit locus protein 5 (SURF5) sequences. The human Surfeit locus has been mapped on chromosome 9q34.1. The locus includes six tightly clustered housekeeping genes (Surf1-6), and the gene organisation is similar in human, mouse and chicken Surfeit locus. The Med22 subunit of Mediator complex is part of the essential core head region."
Q#9680 - 	CGI_10002257	superfamily	241573	1582	1835	2.05E-74	253.408	cl00051	CysPc superfamily	N	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#9680 - 	CGI_10002257	superfamily	241653	1986	2108	4.98E-28	113.229	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#9680 - 	CGI_10002257	superfamily	241573	1453	1581	1.53E-23	103.945	cl00051	CysPc superfamily	C	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#9680 - 	CGI_10002257	superfamily	241764	1301	1375	3.85E-22	93.9103	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#9680 - 	CGI_10002257	superfamily	241764	1218	1286	2.08E-08	53.7516	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#9680 - 	CGI_10002257	superfamily	241653	1866	1974	7.85E-06	46.5896	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#9680 - 	CGI_10002257	superfamily	241563	60	102	0.000731963	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9683 - 	CGI_10002592	superfamily	247856	643	685	0.00628957	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9685 - 	CGI_10002594	superfamily	247684	7	382	0	769.586	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9689 - 	CGI_10002652	superfamily	245864	2	380	2.98E-89	279.934	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9690 - 	CGI_10002325	superfamily	243035	150	263	1.71E-06	44.9182	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9690 - 	CGI_10002325	superfamily	241568	20	76	4.28E-06	42.8352	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9690 - 	CGI_10002325	superfamily	241568	78	132	0.000303858	37.4424	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#9691 - 	CGI_10002326	superfamily	217293	33	239	3.05E-45	158.18	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#9691 - 	CGI_10002326	superfamily	202474	246	329	1.61E-16	77.6941	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#9693 - 	CGI_10002921	superfamily	247792	192	240	5.75E-10	55.9148	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9693 - 	CGI_10002921	superfamily	245201	430	686	3.82E-112	341.608	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9693 - 	CGI_10002921	superfamily	246908	305	404	1.93E-41	146.188	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#9694 - 	CGI_10002922	superfamily	241594	1528	1940	1.25E-103	338	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#9694 - 	CGI_10002922	superfamily	207713	675	737	3.20E-19	85.0637	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#9697 - 	CGI_10026644	superfamily	245213	32	66	8.52E-06	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9697 - 	CGI_10026644	superfamily	245814	101	162	0.00324271	34.3871	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9698 - 	CGI_10026645	superfamily	247804	56	108	1.50E-19	83.8981	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#9698 - 	CGI_10026645	superfamily	247804	11	54	1.89E-10	57.5854	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#9699 - 	CGI_10026646	superfamily	243072	238	346	4.52E-28	110.551	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9699 - 	CGI_10026646	superfamily	243072	27	145	2.04E-22	94.3726	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9699 - 	CGI_10026646	superfamily	243072	91	231	6.70E-18	81.2758	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9699 - 	CGI_10026646	superfamily	217473	605	744	0.00201954	39.6558	cl03978	Mab-21 superfamily	NC	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#9700 - 	CGI_10026647	superfamily	243072	1221	1348	3.26E-27	109.395	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9700 - 	CGI_10026647	superfamily	243072	644	759	1.37E-26	107.469	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9700 - 	CGI_10026647	superfamily	243072	767	882	2.74E-25	104.003	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9700 - 	CGI_10026647	superfamily	243072	1154	1283	2.40E-24	100.921	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9700 - 	CGI_10026647	superfamily	243072	1091	1214	4.96E-22	94.3726	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9700 - 	CGI_10026647	superfamily	243072	1018	1147	2.98E-21	92.0614	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9700 - 	CGI_10026647	superfamily	243072	832	978	8.78E-17	78.9646	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9700 - 	CGI_10026647	superfamily	243072	993	1021	2.48E-05	43.3116	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9702 - 	CGI_10026649	superfamily	243054	319	511	5.21E-20	91.3531	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9702 - 	CGI_10026649	superfamily	241559	15	119	6.33E-19	85.4403	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#9702 - 	CGI_10026649	superfamily	241559	137	239	1.18E-18	84.6699	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#9702 - 	CGI_10026649	superfamily	243054	888	1101	9.18E-17	81.7231	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9702 - 	CGI_10026649	superfamily	243054	778	992	4.39E-12	66.7004	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9702 - 	CGI_10026649	superfamily	243054	1008	1199	1.48E-11	65.1596	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9702 - 	CGI_10026649	superfamily	243054	1887	2091	1.00E-08	56.3	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9702 - 	CGI_10026649	superfamily	243054	513	621	2.51E-06	49.3664	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9702 - 	CGI_10026649	superfamily	243054	1640	1733	0.00173685	39.2353	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9702 - 	CGI_10026649	superfamily	243054	1317	1511	0.00625813	38.966	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9703 - 	CGI_10026650	superfamily	241760	1475	1523	1.70E-31	119.768	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#9703 - 	CGI_10026650	superfamily	243054	539	716	2.41E-16	80.1823	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9703 - 	CGI_10026650	superfamily	243054	125	310	3.04E-12	67.0855	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9703 - 	CGI_10026650	superfamily	243054	27	199	6.78E-12	65.93	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9703 - 	CGI_10026650	superfamily	241647	1223	1249	3.81E-07	49.0634	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#9703 - 	CGI_10026650	superfamily	149946	1375	1466	9.27E-45	158.972	cl07621	efhand_2 superfamily	 - 	 - 	"EF-hand; Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding."
Q#9703 - 	CGI_10026650	superfamily	243054	917	1160	2.90E-05	45.8996	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9703 - 	CGI_10026650	superfamily	243054	334	610	0.000125158	43.9736	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#9704 - 	CGI_10026651	superfamily	245814	77	143	9.14E-06	41.1491	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9705 - 	CGI_10026652	superfamily	247723	102	177	1.33E-53	169.596	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9707 - 	CGI_10026654	superfamily	247905	5	128	2.64E-33	118.88	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#9710 - 	CGI_10026657	superfamily	247941	21	165	7.00E-09	51.1825	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#9711 - 	CGI_10026658	superfamily	220608	42	157	2.12E-21	90.8282	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#9713 - 	CGI_10026660	superfamily	247805	107	199	8.26E-05	40.3203	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#9714 - 	CGI_10026662	superfamily	247684	10	124	2.95E-41	144.411	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9716 - 	CGI_10026664	superfamily	247684	59	554	0	878.986	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9717 - 	CGI_10026665	superfamily	198738	426	509	6.42E-51	170.194	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#9717 - 	CGI_10026665	superfamily	247057	145	213	3.17E-29	110.151	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#9720 - 	CGI_10026668	superfamily	216554	246	374	3.00E-22	92.1573	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#9721 - 	CGI_10026669	superfamily	217062	213	457	1.05E-40	147.416	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#9723 - 	CGI_10026671	superfamily	241679	163	511	8.09E-152	472.646	cl00199	SO_family_Moco superfamily	 - 	 - 	"Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Assimilatory NRs catalyze the reduction of nitrate to nitrite which is subsequently converted to NH4+ by nitrite reductase. Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate."
Q#9723 - 	CGI_10026671	superfamily	241578	834	1011	1.92E-48	172.785	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#9723 - 	CGI_10026671	superfamily	217293	1382	1575	1.33E-33	131.216	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#9723 - 	CGI_10026671	superfamily	242849	65	139	1.52E-17	80.3256	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#9723 - 	CGI_10026671	superfamily	202474	1582	1635	7.84E-07	50.7301	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#9726 - 	CGI_10026674	superfamily	217685	290	431	3.22E-35	129.762	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#9726 - 	CGI_10026674	superfamily	216290	152	273	4.09E-20	86.5733	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#9727 - 	CGI_10026675	superfamily	221329	23	167	2.43E-30	110.951	cl13389	DUF3456 superfamily	 - 	 - 	"TLR4 regulator and MIR-interacting MSAP; This family of proteins, found from plants to humans, is PRAT4 (A and B), a Protein Associated with Toll-like receptor 4. The Toll family of receptors - TLRs - plays an essential role in innate recognition of microbial products, the first line of defence against bacterial infection. PRAT4A influences the subcellular distribution and the strength of TLR responses and alters the relative activity of each TLR. PRAT4B regulates TLR4 trafficking to the cell surface and the extent of its expression there. TLR4 recognizes lipopolysaccharide (LPS), one of the most immuno-stimulatory glycolipids constituting the outer membrane of the Gram-negative bacteria. This family has also been described as a SAP-like MIR-interacting protein family."
Q#9728 - 	CGI_10026676	superfamily	241748	2	203	3.45E-101	295.556	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#9729 - 	CGI_10026677	superfamily	243051	20	172	1.13E-38	131.346	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#9730 - 	CGI_10026678	superfamily	243051	311	463	9.55E-37	132.887	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#9730 - 	CGI_10026678	superfamily	243051	151	301	2.41E-27	106.693	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#9732 - 	CGI_10026680	superfamily	245230	139	565	1.79E-117	359.75	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#9732 - 	CGI_10026680	superfamily	220832	1	103	1.13E-33	123.634	cl10534	Misat_Myo_SegII superfamily	 - 	 - 	"Misato Segment II myosin-like domain; The misato protein contains three distinct, conserved domains, segments I, II and III. Segments I and III are common to Tubulins pfam00091, but segment II aligns with myosin heavy chain sequences from D. melanogaster (PIR C35815), rabbit (SP P04460), and human (PIR S12458). Segment II of misato is a major contributor to its greater length compared with the various tubulins. The most significant sequence similarities to this 54-amino acid region are from a motif found in the heavy chains of myosins from different organisms. A comparison of segment II with the vertebrate myosin heavy chains reveals that it is homologous to a myosin peptide in the hinge region linking the S2 and LMM domains. Segment II also contains heptad repeats which are characteristic of the myosin tail alpha-helical coiled-coils."
Q#9733 - 	CGI_10026681	superfamily	241645	70	145	5.18E-46	149.25	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#9733 - 	CGI_10026681	superfamily	241645	146	221	5.18E-46	149.25	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#9733 - 	CGI_10026681	superfamily	241645	1	69	5.36E-40	133.842	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#9734 - 	CGI_10026682	superfamily	217305	8	76	9.58E-15	64.566	cl03807	TBCA superfamily	C	 - 	Tubulin binding cofactor A; Tubulin binding cofactor A.  
Q#9735 - 	CGI_10026683	superfamily	244539	1289	1470	9.49E-47	169.022	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#9735 - 	CGI_10026683	superfamily	247856	871	932	8.18E-09	54.4761	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9735 - 	CGI_10026683	superfamily	246664	40	641	0	741.424	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#9735 - 	CGI_10026683	superfamily	242267	1101	1248	2.30E-06	47.67	cl01043	Ferric_reduct superfamily	 - 	 - 	"Ferric reductase like transmembrane component; This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease."
Q#9741 - 	CGI_10026689	superfamily	245814	75	141	4.91E-06	45.1727	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9741 - 	CGI_10026689	superfamily	245201	384	662	8.99E-167	482.329	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9741 - 	CGI_10026689	superfamily	245814	163	243	9.84E-21	87.8331	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9743 - 	CGI_10026691	superfamily	216987	22	101	0.00328193	34.4469	cl18386	GDNF superfamily	 - 	 - 	"GDNF/GAS1 domain; This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity."
Q#9744 - 	CGI_10026692	superfamily	193358	4	79	8.97E-15	68.3222	cl15143	TORC_M superfamily	N	 - 	"Transducer of regulated CREB activity middle domain; This family includes the region between the N and C terminus of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding). Although the C- and N- terminal domains of these proteins have been well characterized, no functional role has been assigned to the central region, yet."
Q#9745 - 	CGI_10026693	superfamily	221830	3	66	6.13E-20	80.5355	cl15142	TORC_N superfamily	 - 	 - 	"Transducer of regulated CREB activity, N terminus; This family includes the N terminal region of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding). The proteins display a highly conserved predicted N-terminal coiled-coil domain and an invariant sequence matching a protein kinase A (PKA) phosphorylation consensus sequence (RKXS). The coiled-coil structure interacts with the bZIP domain of CREB. This interaction may occur via ionic bonds because it is disrupted under high-salt conditions. In addition to CREB-binding, the N-terminal region plays a role in the tetramer formation of TORCs, but the physiological function of the multimeric complex has not been clarified yet."
Q#9745 - 	CGI_10026693	superfamily	193358	158	215	0.00637774	34.8099	cl15143	TORC_M superfamily	C	 - 	"Transducer of regulated CREB activity middle domain; This family includes the region between the N and C terminus of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding). Although the C- and N- terminal domains of these proteins have been well characterized, no functional role has been assigned to the central region, yet."
Q#9746 - 	CGI_10026694	superfamily	247723	121	177	1.84E-23	93.5937	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9746 - 	CGI_10026694	superfamily	247723	388	465	5.67E-21	86.9366	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9746 - 	CGI_10026694	superfamily	247723	16	47	3.06E-09	53.5791	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9748 - 	CGI_10026696	superfamily	243034	177	259	1.00E-05	42.7524	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9749 - 	CGI_10026697	superfamily	110440	353	379	0.00177121	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9749 - 	CGI_10026697	superfamily	110440	312	338	0.00219954	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#9750 - 	CGI_10026698	superfamily	241611	112	291	2.05E-14	72.6863	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#9750 - 	CGI_10026698	superfamily	215647	659	815	1.72E-12	66.8632	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#9751 - 	CGI_10026699	superfamily	242847	427	489	3.14E-30	112.384	cl02038	Elf1 superfamily	 - 	 - 	Transcription elongation factor Elf1 like; This family of short proteins contains a putative zinc binding domain with four conserved cysteines. ELF1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae.
Q#9751 - 	CGI_10026699	superfamily	243091	62	104	0.00237508	36.7013	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#9752 - 	CGI_10026700	superfamily	243072	21	135	4.75E-23	94.3726	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9753 - 	CGI_10026701	superfamily	241563	104	141	5.76E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9753 - 	CGI_10026701	superfamily	243092	353	485	0.000971205	40.0108	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9755 - 	CGI_10026703	superfamily	241647	20	50	1.39E-08	50.9894	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#9755 - 	CGI_10026703	superfamily	243076	331	405	1.93E-19	82.2648	cl02539	BAG superfamily	 - 	 - 	BAG domain; Domain present in Hsp70 regulators.
Q#9768 - 	CGI_10021742	superfamily	248097	15	138	6.57E-25	93.4838	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9771 - 	CGI_10021745	superfamily	247755	31	164	4.18E-40	148.127	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#9774 - 	CGI_10021748	superfamily	241563	117	150	2.94E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9774 - 	CGI_10021748	superfamily	189332	346	414	0.000391405	41.5337	cl14874	Luminal_IRE1_like superfamily	NC	 - 	"The Luminal domain, a dimerization domain, of Inositol-requiring protein 1-like proteins; The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), eukaryotic translation Initiation Factor 2-Alpha Kinase 3  (EIF2AK3), and similar proteins. IRE1 and EIF2AK3 are serine/threonine protein kinases (STKs) and are type I transmembrane proteins that are localized in the endoplasmic reticulum (ER). They are kinase receptors that are activated through the release of BiP, a chaperone bound to their luminal domains under unstressed conditions. This results in dimerization through their luminal domains, allowing trans-autophosphorylation of their kinase domains and activation. They play roles in the signaling of the unfolded protein response (UPR), which is activated when protein misfolding is detected in the ER in order to decrease the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), contains an endoribonuclease domain in its cytoplasmic side and acts as an ER stress sensor. It is the oldest and most conserved component of the UPR in eukaryotes. Its activation results in the cleavage of its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans, promoting a splicing event that enables translation into a transcription factor which activates the UPR. EIF2AK3, also called PKR-like Endoplasmic Reticulum Kinase (PERK), phosphorylates the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. It functions as the central regulator of translational control during the UPR pathway. In addition to the eIF-2 alpha subunit, EIF2AK3 also phosphorylates Nrf2, a leucine zipper transcription factor which regulates cellular redox status and promotes cell survival during the UPR."
Q#9777 - 	CGI_10021751	superfamily	241599	65	114	3.66E-22	87.2988	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#9777 - 	CGI_10021751	superfamily	146451	260	279	0.00197939	35.0275	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#9778 - 	CGI_10021752	superfamily	215859	71	195	8.32E-06	45.2851	cl18347	Peptidase_S9 superfamily	 - 	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#9779 - 	CGI_10021753	superfamily	192485	28	69	2.11E-11	56.5994	cl10906	DUF2039 superfamily	N	 - 	Uncharacterized conserved protein (DUF2039); This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Q#9780 - 	CGI_10021754	superfamily	245202	67	131	4.13E-15	66.063	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#9781 - 	CGI_10021755	superfamily	241611	51	202	0.000139956	40.8348	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#9782 - 	CGI_10021756	superfamily	241546	742	863	5.33E-43	154.741	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#9782 - 	CGI_10021756	superfamily	243086	632	674	5.84E-12	63.1629	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#9782 - 	CGI_10021756	superfamily	242057	1450	1562	0.00138094	41.0713	cl00734	Bac_export_1 superfamily	NC	 - 	"Bacterial export proteins, family 1; This family includes the following members; FliR, MopE, SsaT, YopT, Hrp, HrcT and SpaR All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways."
Q#9783 - 	CGI_10021757	superfamily	241546	1096	1218	2.00E-43	156.667	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#9783 - 	CGI_10021757	superfamily	243086	984	1027	2.02E-11	62.0073	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#9784 - 	CGI_10021758	superfamily	245213	526	566	5.90E-08	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9784 - 	CGI_10021758	superfamily	245213	408	446	4.65E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9784 - 	CGI_10021758	superfamily	245213	447	478	1.34E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9784 - 	CGI_10021758	superfamily	245213	633	665	1.81E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9784 - 	CGI_10021758	superfamily	245213	487	525	9.16E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9784 - 	CGI_10021758	superfamily	245213	567	601	2.49E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9784 - 	CGI_10021758	superfamily	245213	788	821	0.000860574	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9784 - 	CGI_10021758	superfamily	243060	684	745	2.48E-05	43.5216	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#9784 - 	CGI_10021758	superfamily	193419	372	407	0.00637436	35.8309	cl15186	EGF_MSP1_1 superfamily	 - 	 - 	MSP1 EGF domain 1; This EGF-like domain is found at the C-terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is left attached to the surface of the invading parasite.
Q#9785 - 	CGI_10021759	superfamily	243060	13	116	3.12E-15	73.182	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#9786 - 	CGI_10021760	superfamily	243082	98	399	1.78E-156	467.138	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9787 - 	CGI_10021761	superfamily	241631	65	245	4.32E-88	267.166	cl00136	Sec7 superfamily	 - 	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#9787 - 	CGI_10021761	superfamily	247725	260	379	3.61E-60	192.907	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9788 - 	CGI_10021762	superfamily	245201	104	339	5.29E-67	225.536	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9789 - 	CGI_10021763	superfamily	243092	160	483	5.17E-20	88.9312	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9790 - 	CGI_10021764	superfamily	241563	73	113	1.46E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9797 - 	CGI_10021771	superfamily	241750	527	577	0.000383131	41.8743	cl00281	metallo-dependent_hydrolases superfamily	C	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#9799 - 	CGI_10021773	superfamily	243190	23	96	4.11E-28	98.5342	cl02794	Cyt_c_Oxidase_VIb superfamily	 - 	 - 	"Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex."
Q#9802 - 	CGI_10003643	superfamily	243035	185	303	2.52E-28	106.55	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9802 - 	CGI_10003643	superfamily	243035	44	140	3.19E-21	86.5197	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9806 - 	CGI_10010578	superfamily	217598	457	590	2.40E-43	154.164	cl04130	KCNQ_channel superfamily	N	 - 	KCNQ voltage-gated potassium channel; This family matches to the C-terminal tail of KCNQ type potassium channels.
Q#9806 - 	CGI_10010578	superfamily	219619	250	324	6.35E-16	73.3959	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#9807 - 	CGI_10010579	superfamily	248054	238	304	0.00100305	38.4375	cl17500	NAD_binding_8 superfamily	NC	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#9808 - 	CGI_10010580	superfamily	218493	344	477	2.12E-39	140.185	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#9808 - 	CGI_10010580	superfamily	248054	161	227	0.00336471	37.6671	cl17500	NAD_binding_8 superfamily	NC	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#9810 - 	CGI_10010582	superfamily	248458	38	225	1.41E-17	82.7469	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9810 - 	CGI_10010582	superfamily	248458	303	502	2.40E-12	66.9537	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9812 - 	CGI_10010584	superfamily	247683	187	237	8.46E-12	60.9395	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#9812 - 	CGI_10010584	superfamily	247683	54	103	4.08E-08	50.5391	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#9812 - 	CGI_10010584	superfamily	247683	532	583	0.000208645	39.3683	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#9815 - 	CGI_10010587	superfamily	241763	144	358	9.00E-114	332.666	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#9815 - 	CGI_10010587	superfamily	244586	56	116	2.93E-12	61.1055	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#9816 - 	CGI_10010588	superfamily	241763	167	381	5.04E-103	306.088	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#9816 - 	CGI_10010588	superfamily	244586	79	139	2.28E-09	53.0163	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#9817 - 	CGI_10010589	superfamily	245814	368	435	0.00351	37.0997	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#9818 - 	CGI_10002783	superfamily	243072	154	283	1.62E-19	84.7426	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9818 - 	CGI_10002783	superfamily	243072	293	420	3.09E-16	75.4978	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9818 - 	CGI_10002783	superfamily	243072	362	496	3.14E-15	72.4162	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9822 - 	CGI_10011654	superfamily	243092	489	791	9.78E-25	105.495	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#9823 - 	CGI_10011655	superfamily	245864	13	202	2.01E-50	171.692	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#9824 - 	CGI_10011656	superfamily	247684	7	399	6.89E-95	297.652	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9826 - 	CGI_10011658	superfamily	217293	39	203	1.77E-36	133.912	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#9826 - 	CGI_10011658	superfamily	202474	240	437	3.49E-33	125.074	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#9827 - 	CGI_10011659	superfamily	202474	111	194	2.85E-30	113.903	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#9827 - 	CGI_10011659	superfamily	202474	192	252	0.00907646	35.3221	cl08379	Neur_chan_memb superfamily	N	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#9828 - 	CGI_10008217	superfamily	241733	24	109	2.39E-58	177.008	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#9831 - 	CGI_10008220	superfamily	248097	93	221	9.13E-18	76.1498	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9832 - 	CGI_10008221	superfamily	247792	24	75	5.12E-06	44.3588	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9832 - 	CGI_10008221	superfamily	241563	177	215	0.00214975	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9833 - 	CGI_10008222	superfamily	216033	65	156	3.70E-12	60.4252	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#9834 - 	CGI_10008223	superfamily	246925	311	463	4.06E-06	48.891	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#9834 - 	CGI_10008223	superfamily	246925	808	928	0.000387858	42.7278	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#9834 - 	CGI_10008223	superfamily	246925	595	689	0.00199227	40.4166	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#9834 - 	CGI_10008223	superfamily	246925	137	321	0.0049669	39.261	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#9835 - 	CGI_10008224	superfamily	248458	313	487	5.63E-11	62.7165	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9835 - 	CGI_10008224	superfamily	248458	71	220	3.31E-07	50.7753	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#9836 - 	CGI_10008225	superfamily	244363	74	164	8.64E-36	124.079	cl06336	Commd superfamily	N	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#9837 - 	CGI_10008226	superfamily	241610	1	53	5.49E-12	54.9486	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#9838 - 	CGI_10008227	superfamily	241610	2	53	8.21E-15	61.8822	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#9841 - 	CGI_10008230	superfamily	241563	75	115	5.70E-07	47.0888	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9843 - 	CGI_10008233	superfamily	177822	28	114	4.61E-05	39.9033	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#9845 - 	CGI_10008235	superfamily	177822	43	277	1.54E-18	82.6605	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#9847 - 	CGI_10003846	superfamily	222429	6	58	2.95E-07	42.6128	cl18676	Myb_DNA-bind_5 superfamily	C	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#9851 - 	CGI_10003850	superfamily	241867	120	336	1.37E-24	99.1236	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#9852 - 	CGI_10003302	superfamily	241600	3	207	5.84E-69	212.101	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#9853 - 	CGI_10003303	superfamily	241600	15	232	1.98E-58	186.292	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#9854 - 	CGI_10003304	superfamily	241600	9	177	2.85E-49	160.484	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#9855 - 	CGI_10015615	superfamily	245201	19	282	1.97E-130	387.624	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#9856 - 	CGI_10015616	superfamily	241574	48	186	5.51E-45	147.755	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9857 - 	CGI_10015617	superfamily	219152	12	364	1.61E-104	316.491	cl18495	PIG-U superfamily	 - 	 - 	"GPI transamidase subunit PIG-U; Many eukaryotic proteins are anchored to the cell surface via glycosylphosphatidylinositol (GPI), which is posttranslationally attached to the carboxyl-terminus by GPI transamidase. The mammalian GPI transamidase is a complex of at least four subunits, GPI8, GAA1, PIG-S, and PIG-T. PIG-U is thought to represent a fifth subunit in this complex and may be involved in the recognition of either the GPI attachment signal or the lipid portion of GPI."
Q#9858 - 	CGI_10015618	superfamily	247740	11	257	5.30E-87	269.749	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#9858 - 	CGI_10015618	superfamily	241575	374	434	0.00130389	37.2519	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#9859 - 	CGI_10015619	superfamily	241637	705	742	0.00257525	36.9027	cl00146	TFIIS_I superfamily	N	 - 	N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Q#9860 - 	CGI_10015620	superfamily	243072	165	284	1.20E-38	141.752	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#9862 - 	CGI_10015622	superfamily	241596	78	117	5.05E-07	42.5863	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#9865 - 	CGI_10015625	superfamily	248097	1	98	3.25E-12	58.4306	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9866 - 	CGI_10015626	superfamily	241574	78	270	1.43E-74	238.254	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9866 - 	CGI_10015626	superfamily	241574	334	520	6.00E-15	73.3889	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#9867 - 	CGI_10015627	superfamily	243035	33	148	3.14E-24	91.9125	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9868 - 	CGI_10006479	superfamily	247856	159	221	1.00E-22	87.9885	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9868 - 	CGI_10006479	superfamily	247856	86	148	3.29E-21	83.7513	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9869 - 	CGI_10006480	superfamily	247856	17	79	1.07E-08	48.3129	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9869 - 	CGI_10006480	superfamily	247856	63	119	8.50E-08	45.6165	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9870 - 	CGI_10006481	superfamily	247856	384	445	8.90E-18	77.5881	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9870 - 	CGI_10006481	superfamily	247856	255	314	1.28E-17	77.2029	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9870 - 	CGI_10006481	superfamily	247856	182	243	6.07E-17	75.2769	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9870 - 	CGI_10006481	superfamily	247856	37	98	2.25E-10	56.4021	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9870 - 	CGI_10006481	superfamily	247856	311	373	2.75E-07	47.5425	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9870 - 	CGI_10006481	superfamily	247856	109	153	0.000218933	39.0681	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	298	360	5.86E-19	82.2105	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	225	287	1.49E-18	81.0549	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	579	641	1.49E-18	81.0549	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	427	489	2.10E-18	80.6697	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	354	416	2.30E-18	80.6697	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	652	708	3.38E-16	74.5065	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	483	538	5.32E-11	59.4837	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	73	134	4.27E-09	53.7057	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	150	212	1.49E-06	46.3869	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9871 - 	CGI_10006482	superfamily	247856	517	567	0.00574827	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9872 - 	CGI_10006483	superfamily	247856	128	183	1.25E-18	77.2029	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9872 - 	CGI_10006483	superfamily	247856	53	153	1.09E-07	47.1573	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#9873 - 	CGI_10006484	superfamily	241623	538	885	1.73E-178	522.557	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#9873 - 	CGI_10006484	superfamily	246669	27	185	1.53E-73	239.458	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#9873 - 	CGI_10006484	superfamily	241742	282	501	6.85E-57	193.316	cl00271	PI3Ka superfamily	 - 	 - 	"Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture."
Q#9874 - 	CGI_10006485	superfamily	245841	44	426	4.09E-129	391.063	cl12025	PolY superfamily	 - 	 - 	"Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions.  Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases.  Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria.  In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion.  Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention."
Q#9876 - 	CGI_10006487	superfamily	241645	12	90	2.81E-33	119.366	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#9876 - 	CGI_10006487	superfamily	244906	119	166	7.39E-23	89.8919	cl08315	CAP_GLY superfamily	N	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#9877 - 	CGI_10006488	superfamily	241644	4620	4780	1.69E-31	124.237	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#9877 - 	CGI_10006488	superfamily	241564	235	307	6.43E-25	102.729	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#9877 - 	CGI_10006488	superfamily	221546	3503	3690	1.06E-37	143.209	cl13752	DUF3643 superfamily	 - 	 - 	Protein of unknown function (DUF3643); This family of proteins is found in eukaryotes. Proteins in this family are typically between 217 and 4852 amino acids in length. There is a conserved TLA sequence motif.
Q#9878 - 	CGI_10011071	superfamily	199168	52	75	0.000361447	34.2496	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#9881 - 	CGI_10011074	superfamily	243035	639	750	2.06E-09	56.0889	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9881 - 	CGI_10011074	superfamily	243035	371	482	2.94E-07	49.5406	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9881 - 	CGI_10011074	superfamily	243061	504	587	0.000262451	40.1427	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#9882 - 	CGI_10011075	superfamily	221370	1	95	2.30E-05	40.4325	cl13441	DUF3497 superfamily	N	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#9883 - 	CGI_10011076	superfamily	247804	98	141	1.34E-08	51.8074	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#9883 - 	CGI_10011076	superfamily	203011	461	538	3.79E-16	74.1657	cl04515	SWIRM superfamily	 - 	 - 	SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
Q#9884 - 	CGI_10011077	superfamily	244859	7	234	1.69E-14	70.2681	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#9886 - 	CGI_10005027	superfamily	248097	138	265	3.84E-20	83.4686	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9888 - 	CGI_10005029	superfamily	248097	194	321	8.20E-21	85.7798	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9889 - 	CGI_10005030	superfamily	248097	43	92	2.34E-12	58.4306	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9890 - 	CGI_10005031	superfamily	248097	197	324	2.98E-19	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9891 - 	CGI_10005032	superfamily	248097	35	149	8.03E-17	72.683	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9892 - 	CGI_10005033	superfamily	243082	160	526	2.09E-151	439.5	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#9892 - 	CGI_10005033	superfamily	245220	46	107	1.98E-10	57.0294	cl09957	zf-UBP superfamily	 - 	 - 	Zn-finger in ubiquitin-hydrolases and other protein; Zn-finger in ubiquitin-hydrolases and other protein.  
Q#9893 - 	CGI_10005034	superfamily	245206	97	229	9.60E-41	141.955	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#9893 - 	CGI_10005034	superfamily	245206	32	81	2.13E-15	71.8483	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#9895 - 	CGI_10005036	superfamily	199166	244	416	3.05E-17	79.6788	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#9895 - 	CGI_10005036	superfamily	199166	162	316	1.24E-13	68.8932	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#9896 - 	CGI_10005037	superfamily	219782	41	105	4.62E-17	73.1378	cl07050	RNA_pol_Rbc25 superfamily	N	 - 	"RNA polymerase III subunit Rpc25; Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III."
Q#9898 - 	CGI_10018604	superfamily	217897	95	282	4.60E-73	224.824	cl04402	APG5 superfamily	 - 	 - 	Autophagy protein Apg5; Apg5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway.
Q#9900 - 	CGI_10018606	superfamily	243078	4	123	6.02E-34	128.099	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#9900 - 	CGI_10018606	superfamily	247723	433	509	2.45E-29	113.589	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9901 - 	CGI_10018607	superfamily	242559	30	371	0	538.054	cl01529	GH99_GH71_like superfamily	 - 	 - 	"Glycoside hydrolase families 71, 99, and related domains; This superfamily of glycoside hydrolases contains families GH71 and GH99 (following the CAZY nomenclature), as well as other members with undefined function and specificity."
Q#9903 - 	CGI_10018609	superfamily	243035	109	157	1.28E-12	61.0766	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9905 - 	CGI_10018611	superfamily	247805	28	73	5.06E-07	45.3279	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#9907 - 	CGI_10018613	superfamily	116971	118	172	0.00710713	35.0114	cl07131	Ly49 superfamily	NC	 - 	"Ly49-like protein, N-terminal region; The sequences making up this family are annotated as, or are similar to, Ly49 receptors. These are type II transmembrane receptors expressed by mouse natural killer (NK) cells. They are classified as being activating (e.g.Ly49D and H) or inhibitory (e.g. Ly49A and G), depending on their effect on NK cell function. They are members of the C-type lectin receptor superfamily, and in fact in many family members this region is found immediately N-terminal to a lectin C-type domain (pfam00059)."
Q#9908 - 	CGI_10018614	superfamily	243034	5	97	2.35E-19	80.5019	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#9908 - 	CGI_10018614	superfamily	248098	202	274	2.85E-36	125.484	cl17544	U-box superfamily	 - 	 - 	U-box domain; This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
Q#9908 - 	CGI_10018614	superfamily	244881	76	124	0.00668451	36.0434	cl08267	ISOPREN_C2_like superfamily	C	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#9909 - 	CGI_10018615	superfamily	222269	1	178	7.97E-39	142.462	cl18657	Cupin_8 superfamily	N	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#9912 - 	CGI_10018618	superfamily	247725	396	494	1.56E-44	159.413	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9912 - 	CGI_10018618	superfamily	247725	12	146	8.46E-58	198.796	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#9912 - 	CGI_10018618	superfamily	243591	821	933	0.0070539	38.6154	cl03951	CDC37_N superfamily	N	 - 	Cdc37 N terminal kinase binding; Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domain corresponds to the N terminal domain which binds predominantly to protein kinases and is found N terminal to the Hsp (Heat shocked protein) 90-binding domain pfam08565. Expression of a construct consisting of only the N-terminal domain of Saccharomyces pombe Cdc37 results in cellular viability. This indicates that interactions with the cochaperone Hsp90 may not be essential for Cdc37 function.
Q#9913 - 	CGI_10018619	superfamily	190261	426	499	4.51E-27	106.479	cl03504	RFX_DNA_binding superfamily	 - 	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#9913 - 	CGI_10018619	superfamily	218683	7	97	3.25E-26	104.596	cl05307	DUF814 superfamily	 - 	 - 	"Domain of unknown function (DUF814); This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from B. subtilis yloA, where the N-terminal region is involved in this activity. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important."
Q#9913 - 	CGI_10018619	superfamily	218161	308	385	0.00723495	36.8889	cl04612	RFX1_trans_act superfamily	NC	 - 	"RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation."
Q#9913 - 	CGI_10018619	superfamily	206361	157	193	0.0090491	35.7627	cl16696	DUF4315 superfamily	C	 - 	Domain of unknown function (DUF4315); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length.
Q#9914 - 	CGI_10018620	superfamily	241622	292	360	4.66E-15	72.5994	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#9914 - 	CGI_10018620	superfamily	241622	14	78	1.79E-08	53.0781	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#9914 - 	CGI_10018620	superfamily	241622	81	135	7.58E-07	48.3319	cl00117	PDZ superfamily	C	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#9914 - 	CGI_10018620	superfamily	143751	398	473	4.75E-10	57.8286	cl11968	harmonin_N_like superfamily	 - 	 - 	"N-terminal protein-binding module of harmonin and similar domains; This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected."
Q#9914 - 	CGI_10018620	superfamily	143751	183	258	2.00E-07	50.0076	cl11968	harmonin_N_like superfamily	 - 	 - 	"N-terminal protein-binding module of harmonin and similar domains; This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected."
Q#9915 - 	CGI_10018621	superfamily	247792	14	62	3.33E-07	48.2108	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9915 - 	CGI_10018621	superfamily	241563	159	195	2.82E-05	42.2744	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9915 - 	CGI_10018621	superfamily	241563	261	300	7.61E-07	47.0888	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9915 - 	CGI_10018621	superfamily	128778	311	432	1.50E-06	47.2595	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#9916 - 	CGI_10018622	superfamily	247907	1094	1239	1.89E-12	67.058	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#9916 - 	CGI_10018622	superfamily	247907	918	1056	2.71E-10	60.1245	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#9916 - 	CGI_10018622	superfamily	246918	652	702	6.72E-15	71.8491	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9916 - 	CGI_10018622	superfamily	246918	604	647	3.79E-10	57.9819	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9916 - 	CGI_10018622	superfamily	246918	283	333	8.50E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9916 - 	CGI_10018622	superfamily	246918	710	752	1.57E-05	44.4999	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9916 - 	CGI_10018622	superfamily	246918	447	501	2.43E-05	43.7295	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9916 - 	CGI_10018622	superfamily	246918	504	556	0.000520002	39.8775	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9919 - 	CGI_10018625	superfamily	241680	3	211	3.90E-31	115.086	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#9920 - 	CGI_10018626	superfamily	241680	23	191	2.38E-31	114.658	cl00200	MIP superfamily	N	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#9921 - 	CGI_10018627	superfamily	241680	166	319	1.32E-26	108.11	cl00200	MIP superfamily	N	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#9921 - 	CGI_10018627	superfamily	241680	24	169	3.46E-20	89.6202	cl00200	MIP superfamily	C	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#9921 - 	CGI_10018627	superfamily	241680	434	595	6.70E-15	73.4848	cl00200	MIP superfamily	C	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#9922 - 	CGI_10018628	superfamily	241680	17	231	2.21E-29	110.421	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#9923 - 	CGI_10018629	superfamily	247755	500	726	4.37E-98	317.139	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#9923 - 	CGI_10018629	superfamily	247755	1278	1497	6.71E-89	290.946	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#9923 - 	CGI_10018629	superfamily	246918	1679	1710	3.51E-10	58.7523	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#9924 - 	CGI_10018630	superfamily	245226	12	36	0.00303335	36.1083	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9925 - 	CGI_10018631	superfamily	245226	13	86	2.56E-06	46.1235	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9927 - 	CGI_10018633	superfamily	245213	110	143	0.000267142	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9928 - 	CGI_10018634	superfamily	248264	1	50	0.00407526	32.209	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#9929 - 	CGI_10005388	superfamily	243050	4	57	5.05E-24	86.856	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#9930 - 	CGI_10005389	superfamily	220695	55	184	0.000140764	41.7955	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#9931 - 	CGI_10005390	superfamily	241637	444	512	1.47E-10	58.0886	cl00146	TFIIS_I superfamily	 - 	 - 	N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Q#9931 - 	CGI_10005390	superfamily	243263	4	137	1.39E-16	81.3002	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#9932 - 	CGI_10005391	superfamily	243859	34	119	8.99E-11	54.2582	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#9933 - 	CGI_10005392	superfamily	241564	1	66	2.67E-32	115.826	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#9933 - 	CGI_10005392	superfamily	247792	278	317	1.86E-05	41.2772	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9934 - 	CGI_10005393	superfamily	241564	305	370	2.03E-32	119.678	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#9934 - 	CGI_10005393	superfamily	241564	74	141	1.23E-16	75.3799	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#9934 - 	CGI_10005393	superfamily	247792	582	621	4.53E-06	44.3588	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9937 - 	CGI_10004088	superfamily	216399	47	276	1.69E-102	302.337	cl03142	Cyto_heme_lyase superfamily	 - 	 - 	Cytochrome c/c1 heme lyase; Cytochrome c/c1 heme lyase.  
Q#9938 - 	CGI_10004089	superfamily	243074	125	170	1.09E-11	57.5165	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#9939 - 	CGI_10004090	superfamily	241832	48	98	3.06E-07	47.6665	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#9940 - 	CGI_10004091	superfamily	247723	393	487	8.78E-59	194.952	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9940 - 	CGI_10004091	superfamily	247723	576	645	2.04E-41	145.865	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9940 - 	CGI_10004091	superfamily	247723	689	763	4.46E-39	139.719	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9940 - 	CGI_10004091	superfamily	247723	281	361	6.77E-35	128.268	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9944 - 	CGI_10008131	superfamily	243035	5	80	1.01E-09	56.0889	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#9945 - 	CGI_10008132	superfamily	241563	60	102	0.000765905	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#9946 - 	CGI_10008133	superfamily	247684	2	152	1.04E-58	191.75	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#9947 - 	CGI_10006013	superfamily	141488	126	188	5.22E-16	69.8576	cl02524	GAS2 superfamily	 - 	 - 	Growth-Arrest-Specific Protein 2 Domain; Growth-Arrest-Specific Protein 2 Domain.  
Q#9947 - 	CGI_10006013	superfamily	241559	15	77	3.52E-06	43.4535	cl00030	CH superfamily	N	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#9948 - 	CGI_10006014	superfamily	203593	122	235	0.00896518	36.8946	cl18243	Mod_r superfamily	C	 - 	"Modifier of rudimentary (Mod(r)) protein; This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic, and both of these regions are represented in this family. Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB). The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37). The mammalian homologue of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors."
Q#9949 - 	CGI_10006015	superfamily	241559	8	113	2.38E-19	78.8919	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#9950 - 	CGI_10006016	superfamily	241559	46	134	1.37E-20	82.7439	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#9950 - 	CGI_10006016	superfamily	109460	162	186	0.00036683	36.2474	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#9956 - 	CGI_10008835	superfamily	204544	16	117	3.63E-31	117.031	cl11308	NAD-GH superfamily	C	 - 	"NAD-specific glutamate dehydrogenase; The members of this are annotated as being NAD-specific glutamate dehydrogenase encoded in antisense gene pair with DnaK-J. However, this could not be confirmed."
Q#9957 - 	CGI_10008836	superfamily	246487	135	245	1.83E-49	172.854	cl13749	eIF3G superfamily	 - 	 - 	"eIF3G domain found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3. eIF3 is a large multi-subunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. Besides, eIF-3G is one of the cytosolic targets; it interacts with mature apoptosis-inducing factor (AIF). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G; it plays an important role in the initiation phase of protein synthesis in yeast. It binds both mRNA and rRNA fragments due to an RNA recognition motif near its C-terminus."
Q#9957 - 	CGI_10008836	superfamily	247723	312	388	1.69E-47	165.791	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#9957 - 	CGI_10008836	superfamily	246722	879	978	1.43E-19	87.7009	cl14812	PIN_SF superfamily	C	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#9957 - 	CGI_10008836	superfamily	241647	408	438	0.000143814	40.9742	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#9959 - 	CGI_10008838	superfamily	244913	222	659	0	633.47	cl08327	Glyco_hydro_47 superfamily	 - 	 - 	"Glycosyl hydrolase family 47; Members of this family are alpha-mannosidases that catalyze the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2)."
Q#9968 - 	CGI_10007478	superfamily	192997	3	123	6.71E-27	104.201	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#9969 - 	CGI_10007479	superfamily	241754	607	947	0	602.346	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#9969 - 	CGI_10007479	superfamily	245213	319	355	4.12E-11	60.7282	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9969 - 	CGI_10007479	superfamily	245213	209	242	2.95E-08	52.2538	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#9969 - 	CGI_10007479	superfamily	222460	1503	1644	5.98E-08	52.901	cl16484	Microtub_bind superfamily	 - 	 - 	Kinesin-associated microtubule-binding; This domain binds to micotubules.
Q#9973 - 	CGI_10007483	superfamily	216401	12	285	3.20E-124	358.51	cl03143	F-actin_cap_A superfamily	 - 	 - 	F-actin capping protein alpha subunit; F-actin capping protein alpha subunit.  
Q#9976 - 	CGI_10007486	superfamily	245226	104	270	4.63E-19	82.3484	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#9977 - 	CGI_10007487	superfamily	129885	93	318	6.10E-56	183.71	cl17977	nst superfamily	 - 	 - 	"UDP-galactose transporter; The 10-12 TMS Nucleotide Sugar Transporters (TC 2.A.7.10)Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids."
Q#9978 - 	CGI_10007488	superfamily	129885	137	206	1.57E-21	88.9512	cl17977	nst superfamily	C	 - 	"UDP-galactose transporter; The 10-12 TMS Nucleotide Sugar Transporters (TC 2.A.7.10)Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids."
Q#9979 - 	CGI_10000852	superfamily	247792	68	113	1.88E-06	40.8261	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#9981 - 	CGI_10005162	superfamily	246723	108	403	1.19E-145	425.054	cl14813	GluZincin superfamily	C	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#9983 - 	CGI_10005164	superfamily	222478	387	422	0.000144844	39.8901	cl16506	zf-RVT superfamily	N	 - 	zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.
Q#9987 - 	CGI_10026865	superfamily	220692	64	377	1.59E-09	57.5993	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#9989 - 	CGI_10026867	superfamily	245815	10	488	0	880.529	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#9990 - 	CGI_10026868	superfamily	245815	11	485	0	885.152	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#9995 - 	CGI_10026873	superfamily	248097	14	121	9.40E-18	73.8386	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#9996 - 	CGI_10026874	superfamily	247724	38	315	3.86E-141	406.46	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#9996 - 	CGI_10026874	superfamily	247063	317	399	6.92E-54	175.456	cl15768	TGS superfamily	 - 	 - 	"The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role."
Q#9996 - 	CGI_10026874	superfamily	247803	3	62	0.000178119	40.5896	cl17249	YlqF_related_GTPase superfamily	N	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#9999 - 	CGI_10026877	superfamily	241600	1	202	6.93E-101	293.378	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10000 - 	CGI_10026878	superfamily	241600	1	164	1.24E-76	230.205	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10001 - 	CGI_10026879	superfamily	241600	348	554	1.09E-97	298.385	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10001 - 	CGI_10026879	superfamily	241600	163	303	3.96E-55	186.677	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10001 - 	CGI_10026879	superfamily	241600	34	129	1.58E-26	107.326	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10002 - 	CGI_10026880	superfamily	241600	1	169	2.67E-83	247.539	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10003 - 	CGI_10026881	superfamily	241600	1	173	5.00E-78	234.057	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10004 - 	CGI_10026882	superfamily	241600	7	199	4.11E-90	266.028	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10005 - 	CGI_10026883	superfamily	241600	1	206	1.03E-96	282.977	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10006 - 	CGI_10026884	superfamily	241600	1	159	4.88E-68	207.863	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10007 - 	CGI_10026885	superfamily	241600	1	113	1.67E-41	137.757	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10008 - 	CGI_10026886	superfamily	241600	34	212	6.57E-79	237.909	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10010 - 	CGI_10026888	superfamily	241845	150	318	3.80E-27	105.496	cl00407	tRNA_m1G_MT superfamily	 - 	 - 	"tRNA (Guanine-1)-methyltransferase; This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyzes the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA."
Q#10011 - 	CGI_10026889	superfamily	247757	35	224	3.78E-76	238.518	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#10011 - 	CGI_10026889	superfamily	247757	291	394	4.56E-54	180.738	cl17203	Fer4_NifH superfamily	N	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#10012 - 	CGI_10026890	superfamily	246713	142	279	5.47E-25	98.853	cl14786	ENDO3c superfamily	C	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#10012 - 	CGI_10026890	superfamily	219650	11	144	1.50E-21	88.0891	cl06806	OGG_N superfamily	 - 	 - 	"8-oxoguanine DNA glycosylase, N-terminal domain; The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (EC:3.2.2.23) and DNA lyase activity (EC:4.2.99.18). The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket."
Q#10014 - 	CGI_10026892	superfamily	241866	266	597	7.23E-174	499.6	cl00445	Iso_dh superfamily	 - 	 - 	Isocitrate/isopropylmalate dehydrogenase; Isocitrate/isopropylmalate dehydrogenase.  
Q#10014 - 	CGI_10026892	superfamily	242910	7	235	1.13E-93	295.345	cl02159	Peptidase_C13 superfamily	C	 - 	"Peptidase C13 family; Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterized as a 'haemoglobinase', but this term is probably incorrect. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed."
Q#10015 - 	CGI_10026893	superfamily	247744	673	845	4.15E-55	189.37	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#10015 - 	CGI_10026893	superfamily	247744	405	580	8.19E-41	149.309	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#10015 - 	CGI_10026893	superfamily	247744	146	301	1.08E-36	137.753	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#10016 - 	CGI_10026894	superfamily	247744	24	196	7.18E-66	203.622	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#10017 - 	CGI_10026895	superfamily	241584	534	605	9.24E-11	60.2027	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10017 - 	CGI_10026895	superfamily	241584	444	524	7.28E-10	57.5063	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10017 - 	CGI_10026895	superfamily	241584	355	439	2.76E-08	52.8839	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10017 - 	CGI_10026895	superfamily	243058	234	351	7.80E-05	42.6868	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#10018 - 	CGI_10026896	superfamily	247999	698	750	2.17E-09	55.1892	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#10018 - 	CGI_10026896	superfamily	243098	272	321	2.33E-06	46.1129	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#10018 - 	CGI_10026896	superfamily	243098	638	687	2.33E-06	46.1129	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#10018 - 	CGI_10026896	superfamily	247999	796	845	0.000164965	40.6582	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#10018 - 	CGI_10026896	superfamily	247999	332	381	0.000865078	38.6256	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#10019 - 	CGI_10026897	superfamily	243072	110	236	8.77E-35	129.426	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10019 - 	CGI_10026897	superfamily	243072	177	305	2.72E-34	127.885	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10019 - 	CGI_10026897	superfamily	245201	485	615	4.70E-32	124.656	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10019 - 	CGI_10026897	superfamily	243072	246	375	2.10E-31	119.796	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10019 - 	CGI_10026897	superfamily	243072	349	417	3.57E-11	61.2454	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10019 - 	CGI_10026897	superfamily	245201	637	674	0.00121547	40.2124	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10022 - 	CGI_10026900	superfamily	247856	13	93	5.88E-06	39.8385	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10023 - 	CGI_10026901	superfamily	220778	32	981	1.81E-60	225.146	cl11127	Nup188 superfamily	 - 	 - 	"Nucleoporin subcomplex protein binding to Pom34; This is one of the many peptides that make up the nucleoporin complex (NPC), and is found across eukaryotes. The Nup188 subcomplex (Nic96p-Nup188p-Nup192p-Pom152p) is one of at least six that make up the NPC, and as such is symmetrically localised on both faces of the NPC at the nuclear end, being integrally bound to the C-terminus of Pom34p."
Q#10024 - 	CGI_10026902	superfamily	241578	131	299	7.09E-35	128.66	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10025 - 	CGI_10026903	superfamily	243400	113	171	0.000769729	38.9613	cl03362	AICARFT_IMPCHas superfamily	NC	 - 	"AICARFT/IMPCHase bienzyme; This is a family of bifunctional enzymes catalyzing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalyzed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase EC:2.1.2.3 (AICARFT), this enzyme catalyzes the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate. This is catalyzed by a pair of C-terminal deaminase fold domains in the protein, where the active site is formed by the dimeric interface of two monomeric units. The last step is catalyzed by the N-terminal IMP (Inosine monophosphate) cyclohydrolase domain EC:3.5.4.10 (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP."
Q#10026 - 	CGI_10026904	superfamily	248097	14	117	7.11E-14	63.053	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10027 - 	CGI_10026905	superfamily	248097	51	170	8.01E-17	72.683	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10028 - 	CGI_10026906	superfamily	217738	105	234	1.40E-35	131.64	cl04267	Ndc80_HEC superfamily	 - 	 - 	HEC/Ndc80p family; Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle.
Q#10028 - 	CGI_10026906	superfamily	245313	281	414	0.00483048	36.7653	cl10488	FlaC_arch superfamily	 - 	 - 	"Flagella accessory protein C (FlaC); Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells)."
Q#10029 - 	CGI_10026907	superfamily	248097	68	171	9.52E-15	66.905	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10031 - 	CGI_10026909	superfamily	241596	44	98	2.16E-11	58.7647	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#10032 - 	CGI_10026910	superfamily	222150	289	313	0.000448219	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10034 - 	CGI_10026912	superfamily	243035	32	150	8.56E-29	103.468	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10035 - 	CGI_10026913	superfamily	243176	8	521	0	892.452	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#10038 - 	CGI_10026916	superfamily	246669	219	354	2.90E-71	220.753	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#10038 - 	CGI_10026916	superfamily	246669	87	211	1.23E-59	190.234	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#10039 - 	CGI_10026917	superfamily	245814	110	166	1.12E-05	42.9396	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10041 - 	CGI_10026919	superfamily	241546	1672	1793	7.68E-40	146.652	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#10041 - 	CGI_10026919	superfamily	245847	34	143	9.92E-06	46.5765	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10041 - 	CGI_10026919	superfamily	243086	1561	1595	0.00217494	38.5102	cl02559	GPS superfamily	C	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#10042 - 	CGI_10026920	superfamily	243051	795	966	2.69E-36	135.583	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10042 - 	CGI_10026920	superfamily	243051	378	529	1.08E-33	128.264	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10042 - 	CGI_10026920	superfamily	243051	623	783	2.91E-33	127.109	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10042 - 	CGI_10026920	superfamily	245814	553	609	3.75E-07	49.0247	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10042 - 	CGI_10026920	superfamily	245814	301	368	6.65E-10	56.994	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10043 - 	CGI_10026921	superfamily	243035	10	35	2.15E-05	37.6694	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10044 - 	CGI_10026922	superfamily	243035	24	120	3.07E-12	59.1506	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10046 - 	CGI_10026924	superfamily	246597	38	220	5.82E-56	181.006	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#10047 - 	CGI_10026925	superfamily	248458	30	391	4.17E-19	86.2137	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#10049 - 	CGI_10026927	superfamily	221174	99	254	2.52E-48	166.312	cl13199	Folliculin superfamily	 - 	 - 	"Vesicle coat protein involved in Golgi to plasma membrane transport; In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex. Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterized by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases."
Q#10050 - 	CGI_10026928	superfamily	246723	91	541	0	616.113	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#10054 - 	CGI_10009291	superfamily	177822	1	145	3.45E-07	48.7629	cl18088	PLN02164 superfamily	NC	 - 	sulfotransferase
Q#10055 - 	CGI_10009292	superfamily	177822	54	234	5.94E-12	63.4005	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#10060 - 	CGI_10009297	superfamily	247068	473	569	2.48E-25	102.392	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10060 - 	CGI_10009297	superfamily	247068	257	353	6.19E-20	86.9837	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10060 - 	CGI_10009297	superfamily	247068	578	676	1.13E-18	83.5169	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10060 - 	CGI_10009297	superfamily	247068	372	465	2.42E-16	76.5833	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10060 - 	CGI_10009297	superfamily	247068	167	249	8.80E-15	71.9609	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10060 - 	CGI_10009297	superfamily	247068	695	778	2.72E-12	64.6421	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10060 - 	CGI_10009297	superfamily	247068	63	139	0.000211863	41.145	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10061 - 	CGI_10009298	superfamily	247068	626	725	2.40E-22	94.3025	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10061 - 	CGI_10009298	superfamily	247068	522	618	3.34E-21	90.8357	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10061 - 	CGI_10009298	superfamily	247068	306	395	1.94E-19	85.8281	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10061 - 	CGI_10009298	superfamily	247068	198	298	4.76E-16	75.8129	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10061 - 	CGI_10009298	superfamily	247068	737	825	2.63E-15	73.8869	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10061 - 	CGI_10009298	superfamily	247068	418	514	9.27E-13	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10061 - 	CGI_10009298	superfamily	247068	76	188	1.65E-07	50.775	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10062 - 	CGI_10009300	superfamily	247068	571	666	1.48E-25	103.162	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10062 - 	CGI_10009300	superfamily	247068	674	769	1.01E-23	98.1545	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10062 - 	CGI_10009300	superfamily	247068	355	455	1.37E-21	91.9913	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10062 - 	CGI_10009300	superfamily	247068	470	563	5.12E-20	87.3689	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10062 - 	CGI_10009300	superfamily	247068	247	347	2.60E-16	76.5833	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10062 - 	CGI_10009300	superfamily	247068	789	872	3.53E-12	64.6421	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10062 - 	CGI_10009300	superfamily	247068	134	237	1.46E-09	56.9382	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10063 - 	CGI_10009301	superfamily	247068	462	557	1.47E-23	97.3841	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10063 - 	CGI_10009301	superfamily	247068	568	662	3.16E-20	87.7541	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10063 - 	CGI_10009301	superfamily	247068	243	341	6.69E-19	83.9021	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10063 - 	CGI_10009301	superfamily	247068	356	454	4.72E-17	78.5093	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10063 - 	CGI_10009301	superfamily	247068	131	233	4.88E-17	78.5093	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10063 - 	CGI_10009301	superfamily	247068	675	765	4.93E-14	69.6497	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10063 - 	CGI_10009301	superfamily	247068	17	91	3.24E-05	43.4562	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10064 - 	CGI_10002017	superfamily	247069	6	134	1.32E-30	109.012	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#10065 - 	CGI_10002018	superfamily	247069	107	252	2.58E-33	121.338	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#10065 - 	CGI_10002018	superfamily	247643	29	75	2.06E-10	55.2483	cl16919	CRAL_TRIO_N superfamily	 - 	 - 	"CRAL/TRIO, N-terminal domain; This all-alpha domain is found to the N-terminus of pfam00650."
Q#10067 - 	CGI_10010038	superfamily	241568	44	94	3.67E-06	44.7612	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10067 - 	CGI_10010038	superfamily	243035	114	175	5.86E-06	44.533	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10067 - 	CGI_10010038	superfamily	192535	185	480	1.67E-06	48.361	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#10068 - 	CGI_10010039	superfamily	248458	93	235	4.88E-14	71.5761	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#10069 - 	CGI_10010040	superfamily	247743	25	173	3.67E-17	78.3419	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#10069 - 	CGI_10010040	superfamily	216502	233	461	7.38E-68	218.23	cl03209	Peptidase_M41 superfamily	 - 	 - 	Peptidase family M41; Peptidase family M41.  
Q#10070 - 	CGI_10010041	superfamily	243072	88	197	3.82E-14	68.5642	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10071 - 	CGI_10010042	superfamily	201540	13	81	0.00569454	35.6021	cl16960	Troponin superfamily	N	 - 	"Troponin; Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin."
Q#10072 - 	CGI_10010043	superfamily	241563	18	50	0.000144706	39.2427	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10073 - 	CGI_10010044	superfamily	241563	18	50	0.00335444	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10074 - 	CGI_10010045	superfamily	247725	57	141	4.48E-09	49.6006	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10075 - 	CGI_10003219	superfamily	243034	23	103	9.09E-07	48.5304	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10075 - 	CGI_10003219	superfamily	243072	230	337	0.000625779	40.0595	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10075 - 	CGI_10003219	superfamily	243072	683	806	0.00126801	38.9039	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10078 - 	CGI_10006532	superfamily	246908	226	308	5.59E-07	46.6378	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#10078 - 	CGI_10006532	superfamily	247725	10	128	1.16E-06	45.8904	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10079 - 	CGI_10006533	superfamily	245835	287	509	2.09E-113	337.709	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#10079 - 	CGI_10006533	superfamily	243088	134	257	1.03E-57	188.942	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#10080 - 	CGI_10006534	superfamily	147027	53	96	5.42E-06	40.526	cl08423	Endosulfine superfamily	NC	 - 	cAMP-regulated phosphoprotein/endosulfine conserved region; Conserved region found in both cAMP-regulated phosphoprotein 19 (ARPP-19) and Alpha/Beta endosulfine. No function has yet been assigned to ARPP-19. Endosulfine is the endogenous ligand for the ATP-dependent potassium (K ATP) channels which occupy a key position in the control of insulin release from the pancreatic beta cell by coupling cell polarity to metabolism. In both cases the region occupies the majority of the protein.
Q#10081 - 	CGI_10006535	superfamily	241645	9	79	3.67E-38	134.903	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#10081 - 	CGI_10006535	superfamily	241643	536	573	1.32E-05	42.8315	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#10082 - 	CGI_10006536	superfamily	243092	163	410	3.51E-08	53.4928	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10084 - 	CGI_10006539	superfamily	245206	29	304	9.92E-134	383.74	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#10085 - 	CGI_10006540	superfamily	243099	90	195	2.71E-40	136.694	cl02575	Bcl-2_like superfamily	N	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#10087 - 	CGI_10006542	superfamily	243099	90	192	1.20E-37	129.375	cl02575	Bcl-2_like superfamily	N	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#10090 - 	CGI_10004183	superfamily	241766	53	328	1.74E-127	368.363	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#10093 - 	CGI_10004186	superfamily	216981	259	411	1.80E-12	64.4762	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#10096 - 	CGI_10014292	superfamily	241574	650	869	6.72E-109	336.865	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#10096 - 	CGI_10014292	superfamily	241584	191	225	0.00577196	35.9351	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10096 - 	CGI_10014292	superfamily	197431	453	513	0.000103913	42.7964	cl06408	UP_III_II superfamily	NC	 - 	"Uroplakin IIIb, IIIa and II; Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb,  UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains separating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers; six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis."
Q#10100 - 	CGI_10014296	superfamily	245201	30	230	1.84E-49	165.771	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10101 - 	CGI_10014297	superfamily	247068	521	619	1.75E-27	108.94	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	730	826	6.10E-27	107.399	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	835	934	2.63E-23	96.9989	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	631	723	9.88E-22	92.3765	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	943	1044	1.78E-20	88.5245	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	152	233	4.92E-16	75.8129	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	437	521	1.26E-15	74.6573	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	350	424	6.75E-10	57.7086	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	255	343	2.73E-07	50.0046	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10101 - 	CGI_10014297	superfamily	247068	42	143	0.000441524	39.9894	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10106 - 	CGI_10016183	superfamily	241574	179	284	7.19E-14	70.1729	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#10109 - 	CGI_10016186	superfamily	177822	48	283	1.70E-20	88.4385	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#10114 - 	CGI_10016191	superfamily	218802	201	228	0.00263243	35.8002	cl05462	DUF862 superfamily	N	 - 	"PPPDE putative peptidase domain; The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)."
Q#10115 - 	CGI_10016192	superfamily	203591	112	250	3.24E-37	135.962	cl06275	DUF1399 superfamily	 - 	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#10115 - 	CGI_10016192	superfamily	203591	42	115	0.000504022	39.2768	cl06275	DUF1399 superfamily	N	 - 	Protein of unknown function (DUF1399); This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.
Q#10117 - 	CGI_10016194	superfamily	247805	26	90	1.23E-05	47.6391	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10118 - 	CGI_10016195	superfamily	246669	17	90	1.02E-35	119.982	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#10119 - 	CGI_10016196	superfamily	241578	165	418	1.34E-111	331.644	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10119 - 	CGI_10016196	superfamily	246669	65	147	1.94E-47	160.039	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#10119 - 	CGI_10016196	superfamily	246669	17	45	1.52E-06	46.0234	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#10120 - 	CGI_10016197	superfamily	245814	38	128	5.25E-05	40.4587	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10121 - 	CGI_10016198	superfamily	110440	484	510	0.0068378	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10122 - 	CGI_10016199	superfamily	110440	393	419	0.00300846	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10123 - 	CGI_10016200	superfamily	241566	30	79	8.53E-17	69.4431	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#10124 - 	CGI_10016201	superfamily	246669	1	104	8.38E-59	189.395	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#10124 - 	CGI_10016201	superfamily	245201	145	342	4.14E-153	438.442	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10124 - 	CGI_10016201	superfamily	245201	343	385	1.97E-15	75.1992	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10125 - 	CGI_10016202	superfamily	241877	325	446	0.0050065	37.9942	cl00459	MIT_CorA-like superfamily	NC	 - 	"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport."
Q#10126 - 	CGI_10016203	superfamily	246680	48	123	2.63E-08	49.9364	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#10127 - 	CGI_10016204	superfamily	190308	66	178	7.55E-06	45.0023	cl18163	Fringe superfamily	C	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#10128 - 	CGI_10016205	superfamily	243072	784	916	5.05E-13	68.179	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10128 - 	CGI_10016205	superfamily	243072	470	613	8.46E-13	67.4086	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10128 - 	CGI_10016205	superfamily	243072	557	717	1.15E-09	58.1638	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10129 - 	CGI_10016206	superfamily	247724	141	341	3.40E-05	42.4436	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10130 - 	CGI_10025401	superfamily	215754	110	208	8.04E-22	87.694	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#10130 - 	CGI_10025401	superfamily	215754	4	100	3.17E-17	74.9824	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#10130 - 	CGI_10025401	superfamily	215754	207	278	9.93E-15	68.0488	cl02813	Mito_carr superfamily	C	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#10131 - 	CGI_10025402	superfamily	246712	54	244	1.53E-100	293.661	cl14785	FMT_C_like superfamily	 - 	 - 	"Carboxy-terminal domain of Formyltransferase and similar domains; This family represents the C-terminal domain of formyltransferase and similar proteins. This domain is found in a variety of enzymes with formyl transferase and alkyladenine DNA glycosylase activities. The proteins with formyltransferase function include methionyl-tRNA formyltransferase, ArnA, 10-formyltetrahydrofolate dehydrogenase and HypX proteins. Although most proteins with formyl transferase activity contain this C-terminal domain, prokaryotic glycinamide ribonucleotide transformylase (GART), a single domain protein, only contains the core catalytic domain. Thus, the C-terminal domain is not required for formyl transferase catalytic activity and may be involved in substrate binding. Some members of this family have shown nucleic acid binding capacity. The C-terminal domain of methionyl-tRNA formyltransferase is involved in tRNA binding. Alkyladenine DNA glycosylase is a distant member of this family with very low sequence similarity to other members. It catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site and shows ability to bind to DNA."
Q#10132 - 	CGI_10025403	superfamily	247724	63	295	1.98E-138	413.48	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10132 - 	CGI_10025403	superfamily	247063	289	361	7.33E-38	136.841	cl15768	TGS superfamily	 - 	 - 	"The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role."
Q#10132 - 	CGI_10025403	superfamily	217667	419	703	2.14E-49	180.262	cl12282	NPR3 superfamily	 - 	 - 	"Nitrogen Permease regulator of amino acid transport activity 3; This family, also known in yeasts as Rmd11, complexes with NPR2, pfam06218. This complex heterodimer is responsible for inactivating TORC1. an evolutionarily conserved protein complex that controls cell size via nutritional input signals, specifically, in response to amino acid starvation."
Q#10133 - 	CGI_10025404	superfamily	242383	8	172	8.48E-78	232.064	cl01240	CtaG_Cox11 superfamily	 - 	 - 	"Cytochrome c oxidase assembly protein CtaG/Cox11; Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein. In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre. Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units. The C terminal region of the protein is known to form a dimer. Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae. Met 224 is also thought to play a role in copper transfer or stabilising the copper site."
Q#10139 - 	CGI_10025410	superfamily	241669	17	137	3.93E-23	94.264	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#10139 - 	CGI_10025410	superfamily	241669	387	499	5.25E-22	91.1824	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#10139 - 	CGI_10025410	superfamily	241669	262	380	8.76E-22	90.7972	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#10139 - 	CGI_10025410	superfamily	241669	142	258	2.40E-16	75.3892	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#10140 - 	CGI_10025411	superfamily	222617	90	220	3.23E-35	126.616	cl16738	YHYH superfamily	 - 	 - 	"YHYH protein; This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif."
Q#10141 - 	CGI_10025412	superfamily	222617	46	176	3.91E-36	128.157	cl16738	YHYH superfamily	 - 	 - 	"YHYH protein; This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif."
Q#10142 - 	CGI_10025413	superfamily	243072	3	92	1.72E-20	86.6686	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10142 - 	CGI_10025413	superfamily	221304	152	424	7.90E-87	268.9	cl13359	GPCR_chapero_1 superfamily	 - 	 - 	"GPCR-chaperone; This domain, and the associated ANK family repeat pfam00023 domain, together act as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2."
Q#10143 - 	CGI_10025414	superfamily	221304	50	184	1.94E-43	147.947	cl13359	GPCR_chapero_1 superfamily	N	 - 	"GPCR-chaperone; This domain, and the associated ANK family repeat pfam00023 domain, together act as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2."
Q#10144 - 	CGI_10025415	superfamily	216152	1	177	1.06E-49	165.565	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#10145 - 	CGI_10025416	superfamily	247736	233	280	0.000179897	40.3369	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#10145 - 	CGI_10025416	superfamily	241752	586	691	1.84E-07	50.7919	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#10146 - 	CGI_10025417	superfamily	247856	68	129	3.87E-13	61.0245	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10146 - 	CGI_10025417	superfamily	247856	103	170	1.38E-11	56.7873	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10149 - 	CGI_10025420	superfamily	243062	278	362	2.35E-12	62.7478	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#10149 - 	CGI_10025420	superfamily	216062	55	227	1.13E-11	62.4554	cl02928	TGFb_propeptide superfamily	 - 	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#10150 - 	CGI_10025421	superfamily	243066	4	108	2.13E-27	106.162	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#10150 - 	CGI_10025421	superfamily	198867	117	214	1.51E-23	95.486	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#10150 - 	CGI_10025421	superfamily	243146	451	497	1.03E-11	60.753	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10150 - 	CGI_10025421	superfamily	243146	353	398	2.44E-11	59.5974	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10150 - 	CGI_10025421	superfamily	243146	412	462	3.22E-11	59.1091	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10150 - 	CGI_10025421	superfamily	243146	318	364	1.06E-09	54.8719	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10150 - 	CGI_10025421	superfamily	243146	264	317	1.65E-08	51.4051	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10150 - 	CGI_10025421	superfamily	243146	511	564	2.99E-08	50.6347	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10151 - 	CGI_10025422	superfamily	242181	2	332	4.74E-101	304.17	cl00900	Ldh_2 superfamily	 - 	 - 	"Malate/L-lactate dehydrogenase; This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyzes the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyzes the reactions: (S)-malate + NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively."
Q#10153 - 	CGI_10025424	superfamily	247723	160	244	7.78E-38	133.572	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10153 - 	CGI_10025424	superfamily	247723	9	85	7.12E-34	121.998	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10154 - 	CGI_10025425	superfamily	110440	354	379	0.00953086	33.5353	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10155 - 	CGI_10025426	superfamily	241613	164	198	4.07E-06	44.8902	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#10155 - 	CGI_10025426	superfamily	243051	16	87	1.42E-05	44.6489	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10155 - 	CGI_10025426	superfamily	246925	222	391	4.86E-05	44.6538	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#10155 - 	CGI_10025426	superfamily	220695	600	735	0.00655565	37.9435	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#10156 - 	CGI_10025427	superfamily	222090	51	239	1.52E-21	90.795	cl18636	Methyltransf_22 superfamily	 - 	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#10157 - 	CGI_10025428	superfamily	218405	981	1173	1.61E-45	164.977	cl18455	DUF676 superfamily	 - 	 - 	Putative serine esterase (DUF676); This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.
Q#10157 - 	CGI_10025428	superfamily	221557	179	242	6.50E-16	74.6206	cl13784	DUF3657 superfamily	 - 	 - 	"Protein of unknown function (DUF3657); This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam05057."
Q#10158 - 	CGI_10025429	superfamily	241563	16	47	0.00317877	33.6068	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10160 - 	CGI_10025431	superfamily	247723	336	413	1.11E-51	169.809	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10160 - 	CGI_10025431	superfamily	247723	186	264	1.75E-49	164.01	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10160 - 	CGI_10025431	superfamily	247723	85	176	1.95E-44	150.652	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10161 - 	CGI_10025432	superfamily	245595	176	436	5.54E-163	466.127	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#10162 - 	CGI_10025433	superfamily	199226	17	43	0.00184311	35.8732	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#10163 - 	CGI_10025434	superfamily	202841	95	162	4.00E-20	80.7276	cl08411	Autophagy_act_C superfamily	 - 	 - 	"Autophagocytosis associated protein, active-site domain; Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex."
Q#10164 - 	CGI_10025435	superfamily	241625	22	105	9.32E-09	49.1261	cl00123	PROF superfamily	C	 - 	"Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway."
Q#10165 - 	CGI_10025436	superfamily	219525	621	666	1.65E-05	43.1766	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10165 - 	CGI_10025436	superfamily	219525	497	553	0.00674119	35.4726	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10167 - 	CGI_10025438	superfamily	219525	422	470	4.80E-07	47.0285	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10167 - 	CGI_10025438	superfamily	219525	300	356	6.58E-07	46.6433	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10168 - 	CGI_10025439	superfamily	243061	2	83	8.86E-30	103.191	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10170 - 	CGI_10025441	superfamily	217293	635	839	2.13E-60	205.945	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10170 - 	CGI_10025441	superfamily	217293	225	427	3.21E-48	171.662	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10170 - 	CGI_10025441	superfamily	202474	434	626	1.09E-19	89.2501	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10170 - 	CGI_10025441	superfamily	202474	846	935	1.69E-14	73.4569	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10171 - 	CGI_10025442	superfamily	219824	1	33	2.71E-05	43.4985	cl07139	AA_permease_N superfamily	C	 - 	Amino acid permease N-terminal; This domain is found to the N-terminus of the amino acid permease domain (pfam00324) in metazoan Na-K-Cl cotransporters.
Q#10172 - 	CGI_10025443	superfamily	243092	568	785	1.06E-27	113.969	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10172 - 	CGI_10025443	superfamily	243092	4	223	3.23E-23	100.487	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10172 - 	CGI_10025443	superfamily	243092	542	585	0.00550101	35.7908	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10173 - 	CGI_10025444	superfamily	241832	13	147	3.37E-50	165.151	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#10173 - 	CGI_10025444	superfamily	241832	196	305	1.30E-19	82.0212	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#10173 - 	CGI_10025444	superfamily	241832	158	187	2.16E-06	44.9689	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#10174 - 	CGI_10025445	superfamily	241787	1	66	5.55E-25	89.5311	cl00326	Ribosomal_L23 superfamily	 - 	 - 	Ribosomal protein L23; Ribosomal protein L23.  
Q#10175 - 	CGI_10025446	superfamily	243992	5	59	1.03E-10	51.8058	cl05087	Complex1_LYR_1 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#10176 - 	CGI_10025447	superfamily	247755	1031	1251	1.67E-117	367.974	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#10176 - 	CGI_10025447	superfamily	247755	378	580	4.10E-106	335.593	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#10176 - 	CGI_10025447	superfamily	216049	62	334	2.44E-34	134.721	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#10176 - 	CGI_10025447	superfamily	216049	722	988	8.58E-34	132.795	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#10177 - 	CGI_10025448	superfamily	246681	5	131	2.56E-66	204.596	cl14643	SRPBCC superfamily	C	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#10178 - 	CGI_10025449	superfamily	248054	57	81	1.79E-05	42.8444	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#10182 - 	CGI_10000919	superfamily	248012	1	57	5.11E-18	73.4617	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10183 - 	CGI_10003490	superfamily	247684	9	182	2.94E-20	86.4887	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10184 - 	CGI_10003491	superfamily	247684	9	182	2.86E-20	86.4887	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10185 - 	CGI_10003492	superfamily	247684	9	182	1.36E-20	87.2591	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10186 - 	CGI_10011675	superfamily	245847	133	268	6.18E-05	42.4896	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10186 - 	CGI_10011675	superfamily	245847	560	620	0.00170388	38.2524	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10187 - 	CGI_10011676	superfamily	241574	579	724	6.70E-52	183.171	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#10187 - 	CGI_10011676	superfamily	241574	784	1006	1.56E-14	73.7741	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#10187 - 	CGI_10011676	superfamily	245847	33	161	2.03E-05	44.4156	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10188 - 	CGI_10011677	superfamily	221337	705	739	2.78E-05	43.0743	cl13401	DUF3471 superfamily	C	 - 	"Domain of unknown function (DUF3471); This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144."
Q#10188 - 	CGI_10011677	superfamily	221198	148	182	0.00718531	36.1193	cl13226	KfrA_N superfamily	N	 - 	"Plasmid replication region DNA-binding N-term; The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning."
Q#10189 - 	CGI_10011678	superfamily	247912	32	232	2.77E-30	115.676	cl17358	Beta-lactamase superfamily	C	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#10190 - 	CGI_10011679	superfamily	243096	61	150	2.76E-20	90.0496	cl02571	RhoGEF superfamily	N	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#10192 - 	CGI_10011681	superfamily	241874	12	424	0	577.705	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#10193 - 	CGI_10011682	superfamily	241874	10	177	1.00E-73	233.722	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#10194 - 	CGI_10011683	superfamily	241874	1	370	0	536.874	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#10195 - 	CGI_10011684	superfamily	241874	26	581	0	651.664	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#10197 - 	CGI_10011686	superfamily	245874	68	117	3.37E-07	46.6506	cl12111	TNFR superfamily	NC	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#10200 - 	CGI_10010073	superfamily	244560	1697	1820	1.62E-26	108.924	cl06954	BP28CT superfamily	N	 - 	BP28CT (NUC211) domain; This C terminal domain is found in BAP28-like nucleolar proteins.
Q#10200 - 	CGI_10010073	superfamily	204903	165	282	6.60E-21	91.4627	cl13787	U3snoRNP10 superfamily	 - 	 - 	"U3 small nucleolar RNA-associated protein 10; This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam08146. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA."
Q#10201 - 	CGI_10010074	superfamily	241622	269	338	9.53E-09	51.7987	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10201 - 	CGI_10010074	superfamily	243038	24	93	5.56E-18	77.2425	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#10201 - 	CGI_10010074	superfamily	243038	115	194	1.11E-16	74.0051	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#10202 - 	CGI_10010075	superfamily	247805	333	546	1.44E-78	253.176	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10202 - 	CGI_10010075	superfamily	247905	556	685	5.77E-41	146.999	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#10202 - 	CGI_10010075	superfamily	199156	261	275	7.34E-05	41.2857	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#10204 - 	CGI_10010077	superfamily	218284	43	99	3.65E-15	69.5907	cl04786	SOUL superfamily	C	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#10205 - 	CGI_10010078	superfamily	245814	265	334	0.000125138	40.1144	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10206 - 	CGI_10010079	superfamily	245814	198	276	9.99E-06	43.196	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10207 - 	CGI_10010080	superfamily	241584	464	557	0.000244222	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10207 - 	CGI_10010080	superfamily	245814	283	361	6.39E-06	44.3516	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10211 - 	CGI_10002309	superfamily	248097	124	199	4.29E-15	68.4458	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10211 - 	CGI_10002309	superfamily	248097	2	69	0.000179907	38.7854	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10212 - 	CGI_10002310	superfamily	245612	16	494	1.91E-176	507.733	cl11426	Amidase superfamily	 - 	 - 	Amidase; Amidase.  
Q#10213 - 	CGI_10002311	superfamily	247741	12	325	4.31E-172	492.904	cl17187	Aldolase_Class_I superfamily	 - 	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#10213 - 	CGI_10002311	superfamily	247741	328	554	1.98E-106	324.571	cl17187	Aldolase_Class_I superfamily	N	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#10214 - 	CGI_10004505	superfamily	241578	5	93	0.0016174	38.0414	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10219 - 	CGI_10004510	superfamily	217062	41	307	2.71E-43	151.268	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#10220 - 	CGI_10011704	superfamily	114037	98	186	0.00124914	37.6219	cl05042	BLYB superfamily	 - 	 - 	"Borrelia hemolysin accessory protein; This family consists of several borrelia hemolysin accessory proteins (BLYB). BLYB was thought to be an accessory protein, which was proposed to comprise a hemolysis system but it is now thought that BlyA and BlyB function instead as a prophage-encoded holin or holin-like system."
Q#10220 - 	CGI_10011704	superfamily	241563	8	52	0.00472852	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10220 - 	CGI_10011704	superfamily	241563	62	99	0.00858537	34.7624	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10223 - 	CGI_10011707	superfamily	242876	1	148	1.58E-53	168.358	cl02092	Clat_adaptor_s superfamily	 - 	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#10224 - 	CGI_10011708	superfamily	247724	34	347	0	554.059	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10226 - 	CGI_10011710	superfamily	243092	32	319	9.51E-67	213.351	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10229 - 	CGI_10011713	superfamily	207662	61	153	1.72E-59	196.216	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#10229 - 	CGI_10011713	superfamily	207662	257	349	1.72E-59	196.216	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#10229 - 	CGI_10011713	superfamily	245599	443	677	5.21E-78	251.131	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#10230 - 	CGI_10011714	superfamily	220647	47	165	3.76E-07	47.3224	cl18565	L_HGMIC_fpl superfamily	C	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#10231 - 	CGI_10011715	superfamily	243092	32	191	0.000359158	40.0108	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10232 - 	CGI_10011716	superfamily	241563	61	99	0.000961345	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10234 - 	CGI_10011718	superfamily	241609	32	106	8.07E-23	92.4411	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#10234 - 	CGI_10011718	superfamily	241609	191	274	1.16E-19	83.5815	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#10234 - 	CGI_10011718	superfamily	241613	410	440	2.69E-05	41.8086	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#10234 - 	CGI_10011718	superfamily	241609	112	187	5.46E-16	73.109	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#10234 - 	CGI_10011718	superfamily	243051	280	418	0.00659013	36.2018	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10236 - 	CGI_10011720	superfamily	243128	49	222	3.17E-10	56.9851	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#10237 - 	CGI_10011721	superfamily	222150	218	243	7.68E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10237 - 	CGI_10011721	superfamily	222150	593	617	3.50E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10237 - 	CGI_10011721	superfamily	222150	857	881	7.33E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10237 - 	CGI_10011721	superfamily	222150	1232	1257	0.000116076	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10237 - 	CGI_10011721	superfamily	222150	1205	1228	0.000264768	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10239 - 	CGI_10011723	superfamily	244594	508	608	6.58E-52	179.014	cl07053	Sin3_corepress superfamily	 - 	 - 	Sin3 family co-repressor; This domain is found on transcriptional regulators. It forms interactions with histone deacetylases.
Q#10239 - 	CGI_10011723	superfamily	202341	88	134	1.51E-16	75.9738	cl07842	PAH superfamily	 - 	 - 	"Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions."
Q#10239 - 	CGI_10011723	superfamily	202341	429	475	1.71E-10	58.6398	cl07842	PAH superfamily	 - 	 - 	"Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions."
Q#10239 - 	CGI_10011723	superfamily	202341	260	320	2.30E-10	58.2546	cl07842	PAH superfamily	 - 	 - 	"Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions."
Q#10240 - 	CGI_10011724	superfamily	147390	127	179	7.81E-16	69.2744	cl04970	XPA_C superfamily	 - 	 - 	XPA protein C-terminus; XPA protein C-terminus.  
Q#10240 - 	CGI_10011724	superfamily	189926	94	125	4.92E-09	50.8019	cl03148	XPA_N superfamily	 - 	 - 	XPA protein N-terminal; XPA protein N-terminal.  
Q#10241 - 	CGI_10001915	superfamily	247743	222	359	7.51E-23	95.6759	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#10241 - 	CGI_10001915	superfamily	216502	422	595	8.27E-66	216.689	cl03209	Peptidase_M41 superfamily	 - 	 - 	Peptidase family M41; Peptidase family M41.  
Q#10242 - 	CGI_10001918	superfamily	246940	64	243	3.32E-05	42.7058	cl15377	Radical_SAM superfamily	 - 	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#10243 - 	CGI_10001919	superfamily	247749	45	364	5.26E-164	472.842	cl17195	LDH_MDH_like superfamily	 - 	 - 	"NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others."
Q#10243 - 	CGI_10001919	superfamily	247827	394	561	5.49E-33	124	cl17273	Thioredoxin_4 superfamily	 - 	 - 	Thioredoxin; Thioredoxin.  
Q#10244 - 	CGI_10001922	superfamily	241852	3	383	1.78E-119	356.368	cl00416	CS_ACL-C_CCL superfamily	 - 	 - 	"Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. Some CS proteins function as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs catalyze an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA; they do this in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate CiCoA, and c) the hydrolysis of CiCoA to produce citrate and CoA. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. There are two types of CSs: type I CS and type II CSs.  Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site.  Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism.  In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL."
Q#10247 - 	CGI_10014855	superfamily	241573	26	288	5.47E-38	142.85	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#10247 - 	CGI_10014855	superfamily	241653	307	429	3.15E-11	61.5676	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#10251 - 	CGI_10014859	superfamily	242406	4	104	5.45E-16	70.6981	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#10253 - 	CGI_10014861	superfamily	241644	5	144	1.45E-58	181.632	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#10254 - 	CGI_10014862	superfamily	245201	177	449	1.04E-114	345.29	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10254 - 	CGI_10014862	superfamily	219525	26	70	2.01E-08	51.2657	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10256 - 	CGI_10014864	superfamily	243034	130	221	1.59E-15	73.9535	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10256 - 	CGI_10014864	superfamily	243034	688	789	1.28E-06	47.76	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10260 - 	CGI_10009872	superfamily	248097	39	162	8.23E-27	99.647	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10261 - 	CGI_10009873	superfamily	218200	2	278	1.55E-140	407.138	cl04660	Glyco_transf_54 superfamily	 - 	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#10262 - 	CGI_10009874	superfamily	247905	251	361	3.01E-24	100.39	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#10262 - 	CGI_10009874	superfamily	247805	35	171	8.17E-14	70.444	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10263 - 	CGI_10009875	superfamily	242274	41	276	1.18E-68	219.68	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#10264 - 	CGI_10009876	superfamily	242225	3	142	2.87E-78	230.853	cl00969	Ribosomal_S19e superfamily	 - 	 - 	Ribosomal protein S19e; Ribosomal protein S19e.  
Q#10265 - 	CGI_10026801	superfamily	243050	94	149	5.01E-18	78.1603	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#10265 - 	CGI_10026801	superfamily	243050	33	86	1.65E-11	59.7915	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#10266 - 	CGI_10026802	superfamily	241571	37	142	5.07E-18	80.149	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10266 - 	CGI_10026802	superfamily	243146	295	346	0.000314534	38.8095	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10266 - 	CGI_10026802	superfamily	243146	248	294	0.00142233	36.8835	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10266 - 	CGI_10026802	superfamily	243146	335	367	0.00734405	34.8951	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#10272 - 	CGI_10026808	superfamily	245213	569	602	0.00042364	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10272 - 	CGI_10026808	superfamily	205157	699	734	1.88E-06	45.9915	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#10272 - 	CGI_10026808	superfamily	241578	144	184	0.00119369	40.0608	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10272 - 	CGI_10026808	superfamily	241578	356	391	0.00842648	37.3644	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10273 - 	CGI_10026809	superfamily	245815	1	467	0	816.249	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#10273 - 	CGI_10026809	superfamily	245815	529	756	1.31E-34	137.442	cl11961	ALDH-SF superfamily	C	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#10274 - 	CGI_10026810	superfamily	241555	348	593	4.64E-126	375.353	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#10274 - 	CGI_10026810	superfamily	247757	70	310	2.40E-120	361.139	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#10275 - 	CGI_10026811	superfamily	245936	182	375	4.18E-69	217.803	cl12283	IPK superfamily	 - 	 - 	Inositol polyphosphate kinase; ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
Q#10276 - 	CGI_10026812	superfamily	243072	615	742	5.30E-31	120.566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	682	809	2.26E-30	119.025	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	353	483	3.58E-29	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	283	415	3.96E-29	115.173	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	221	339	1.44E-28	113.633	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	936	1093	5.55E-28	112.092	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	429	568	9.31E-25	102.462	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	749	911	5.55E-23	97.4542	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10276 - 	CGI_10026812	superfamily	243072	115	275	1.63E-21	93.217	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10277 - 	CGI_10026813	superfamily	241758	324	591	1.55E-34	131.773	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#10277 - 	CGI_10026813	superfamily	241780	1	148	2.26E-44	156.293	cl00319	Gn_AT_II superfamily	 - 	 - 	"Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate.  Asparagine synthetase B  synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the formation of the beta-lactam ring in the beta-lactamase inhibitor clavulanic acid. GltS synthesizes L-glutamate from 2-oxoglutarate and L-glutamine. These enzymes are generally dimers, but GPATase also exists as a homotetramer."
Q#10278 - 	CGI_10026814	superfamily	245201	67	318	1.34E-51	174.347	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10282 - 	CGI_10026818	superfamily	152471	610	771	4.43E-44	157.906	cl13471	DUF3522 superfamily	 - 	 - 	Protein of unknown function (DUF3522); This family of proteins is functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 220 to 787 amino acids in length.
Q#10283 - 	CGI_10026819	superfamily	218122	308	627	7.06E-90	284.875	cl04558	Choline_transpo superfamily	 - 	 - 	Plasma-membrane choline transporter; This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals.
Q#10285 - 	CGI_10026821	superfamily	247907	2888	3039	7.40E-40	148.335	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#10285 - 	CGI_10026821	superfamily	247907	3306	3448	9.21E-37	139.476	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#10285 - 	CGI_10026821	superfamily	247907	3480	3629	3.07E-29	117.519	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#10285 - 	CGI_10026821	superfamily	247907	2690	2856	2.41E-26	109.43	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#10285 - 	CGI_10026821	superfamily	247907	3065	3217	4.68E-25	105.578	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#10285 - 	CGI_10026821	superfamily	238012	546	593	2.77E-11	62.3718	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1376	1418	5.01E-11	61.6014	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	2029	2074	3.02E-10	59.2902	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1824	1867	3.09E-10	59.2902	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	497	541	6.18E-10	58.5198	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	636	678	7.38E-10	58.1346	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	450	494	3.04E-09	56.5938	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1467	1510	5.47E-09	55.8234	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	795	838	8.57E-09	55.053	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1514	1565	4.45E-08	53.127	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	2076	2120	5.20E-08	52.7418	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1981	2027	5.90E-08	52.7418	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	405	447	8.33E-08	52.3566	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	592	633	1.01E-07	51.9714	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	742	793	2.43E-07	50.8158	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1872	1927	1.94E-06	48.1194	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	276	317	1.41E-05	45.8082	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	683	740	1.53E-05	45.8082	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1422	1459	7.79E-05	43.497	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	335	392	0.000218782	42.3414	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	238012	1928	1980	0.000267733	41.9562	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#10285 - 	CGI_10026821	superfamily	243198	28	275	9.26E-83	275.393	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#10285 - 	CGI_10026821	superfamily	243080	1626	1750	2.47E-36	137.392	cl02548	Laminin_B superfamily	 - 	 - 	Laminin B (Domain IV); Laminin B (Domain IV).  
Q#10285 - 	CGI_10026821	superfamily	203372	2586	2716	1.05E-16	80.5951	cl05515	Laminin_II superfamily	 - 	 - 	"Laminin Domain II; It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure."
Q#10286 - 	CGI_10026822	superfamily	245814	336	395	6.11E-06	44.1088	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10286 - 	CGI_10026822	superfamily	245814	217	276	0.000541149	38.1568	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10290 - 	CGI_10026827	superfamily	221219	1	29	0.000348865	39.1539	cl13259	RRN7 superfamily	 - 	 - 	RNA polymerase I-specific transcription initiation factor Rrn7; Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter.
Q#10291 - 	CGI_10026828	superfamily	241983	12	350	6.18E-44	154.823	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#10292 - 	CGI_10026829	superfamily	243072	330	438	2.14E-18	83.587	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10292 - 	CGI_10026829	superfamily	243072	149	257	3.38E-18	83.2018	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10292 - 	CGI_10026829	superfamily	243072	468	570	9.93E-13	67.0234	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10292 - 	CGI_10026829	superfamily	243072	1	103	1.02E-10	60.8602	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10292 - 	CGI_10026829	superfamily	219953	1243	1305	7.21E-15	74.1423	cl07317	DUF1777 superfamily	N	 - 	Protein of unknown function (DUF1777); This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins.
Q#10292 - 	CGI_10026829	superfamily	217473	639	827	4.32E-07	51.9821	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#10293 - 	CGI_10026830	superfamily	248264	60	122	2.93E-13	62.2546	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#10295 - 	CGI_10026832	superfamily	246598	3	242	1.77E-138	392.867	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#10296 - 	CGI_10026833	superfamily	241563	166	201	4.23E-05	41.504	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10296 - 	CGI_10026833	superfamily	247792	36	82	0.00268375	36.2696	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10296 - 	CGI_10026833	superfamily	241563	105	152	0.000790538	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10297 - 	CGI_10026834	superfamily	245596	259	410	1.41E-10	62.9022	cl11394	Glyco_tranf_GTA_type superfamily	NC	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#10298 - 	CGI_10026835	superfamily	241568	804	858	5.69E-07	48.228	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10298 - 	CGI_10026835	superfamily	214531	160	203	1.99E-05	43.3593	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#10298 - 	CGI_10026835	superfamily	214531	204	246	3.71E-05	42.5889	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#10298 - 	CGI_10026835	superfamily	241578	495	533	0.0014306	40.0608	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10300 - 	CGI_10026837	superfamily	248013	26	71	3.32E-05	40.7103	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#10300 - 	CGI_10026837	superfamily	218713	223	335	1.16E-37	134.392	cl05332	MRG superfamily	C	 - 	"MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif."
Q#10301 - 	CGI_10026838	superfamily	247683	769	830	8.69E-36	131.381	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#10301 - 	CGI_10026838	superfamily	247744	895	1072	4.04E-34	129.189	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#10301 - 	CGI_10026838	superfamily	241622	672	750	8.84E-17	77.2218	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10301 - 	CGI_10026838	superfamily	241622	148	221	4.17E-13	66.8214	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10301 - 	CGI_10026838	superfamily	243136	541	595	0.00222134	37.4876	cl02672	L27 superfamily	 - 	 - 	L27 domain; The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.
Q#10302 - 	CGI_10026839	superfamily	241599	147	203	5.57E-20	81.906	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#10308 - 	CGI_10026845	superfamily	246918	119	173	6.30E-12	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10308 - 	CGI_10026845	superfamily	246918	64	116	2.38E-11	57.5967	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10310 - 	CGI_10026847	superfamily	247684	19	148	2.02E-12	60.6803	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10311 - 	CGI_10026848	superfamily	247684	1	186	3.05E-121	350.539	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10314 - 	CGI_10026851	superfamily	245596	210	427	7.12E-36	133.761	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#10315 - 	CGI_10026852	superfamily	192254	699	759	0.000510756	39.4955	cl07826	ATG_C superfamily	C	 - 	ATG C terminal domain; ATG2 (also known as Apg2) is a peripheral membrane protein. It functions in both cytoplasm to vacuole targeting and autophagy.
Q#10316 - 	CGI_10026853	superfamily	243062	237	337	4.98E-11	58.4413	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#10318 - 	CGI_10026855	superfamily	241564	159	221	2.77E-24	95.0251	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#10318 - 	CGI_10026855	superfamily	247792	369	407	0.000168786	38.966	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10320 - 	CGI_10026857	superfamily	241564	411	478	4.03E-28	107.737	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#10320 - 	CGI_10026857	superfamily	247792	582	621	0.000758836	37.8104	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10320 - 	CGI_10026857	superfamily	241564	216	277	1.03E-10	58.4495	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#10321 - 	CGI_10026858	superfamily	241564	281	335	1.01E-21	88.4767	cl00035	BIR superfamily	C	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#10321 - 	CGI_10026858	superfamily	247792	389	427	3.40E-05	41.2772	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10323 - 	CGI_10026860	superfamily	241564	17	84	1.02E-29	108.892	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#10323 - 	CGI_10026860	superfamily	247792	263	301	3.79E-05	40.5068	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10324 - 	CGI_10026861	superfamily	243051	386	540	3.34E-27	109.39	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10324 - 	CGI_10026861	superfamily	241571	238	314	7.00E-09	54.7258	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10324 - 	CGI_10026861	superfamily	245213	687	718	0.000165782	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10324 - 	CGI_10026861	superfamily	241583	1	174	6.29E-33	126.532	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#10324 - 	CGI_10026861	superfamily	243051	598	679	2.15E-13	68.9165	cl02479	MAM superfamily	NC	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10324 - 	CGI_10026861	superfamily	243051	727	839	1.03E-12	66.6325	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#10327 - 	CGI_10026864	superfamily	243066	95	190	2.23E-10	55.3896	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#10332 - 	CGI_10008196	superfamily	245205	14	70	2.82E-06	41.8397	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#10333 - 	CGI_10008197	superfamily	243061	20	112	3.32E-08	49.2626	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10335 - 	CGI_10008199	superfamily	220389	2	160	6.67E-71	216.112	cl10747	DUF2053 superfamily	 - 	 - 	Predicted membrane protein (DUF2053); This entry is of the conserved N-terminal 150 residues of proteins conserved from plants to humans. The function is unknown although some annotation suggests it to be a transmembrane protein.
Q#10337 - 	CGI_10008201	superfamily	241571	162	272	2.00E-15	75.9118	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10337 - 	CGI_10008201	superfamily	241571	439	544	1.15E-11	64.741	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10337 - 	CGI_10008201	superfamily	241571	335	429	9.06E-10	58.963	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10337 - 	CGI_10008201	superfamily	245213	1791	1827	6.96E-09	54.9502	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	241568	875	936	5.04E-08	52.8504	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10337 - 	CGI_10008201	superfamily	241568	611	665	4.31E-07	50.154	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10337 - 	CGI_10008201	superfamily	247907	2175	2322	4.35E-07	51.2649	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#10337 - 	CGI_10008201	superfamily	245213	1838	1873	9.63E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	245213	1707	1750	2.22E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	243035	49	119	8.15E-06	46.8442	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10337 - 	CGI_10008201	superfamily	241568	690	726	2.29E-05	44.7612	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10337 - 	CGI_10008201	superfamily	245213	2108	2143	3.30E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	245213	1955	1990	0.000310226	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	245213	1993	2028	0.000322538	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	245213	1916	1951	0.000344494	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	245213	823	852	0.000357091	41.083	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10337 - 	CGI_10008201	superfamily	241568	1275	1330	0.00378413	38.2128	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10337 - 	CGI_10008201	superfamily	219525	2671	2721	1.35E-07	51.2657	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10337 - 	CGI_10008201	superfamily	219525	2728	2775	5.37E-07	49.7249	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10337 - 	CGI_10008201	superfamily	219525	1606	1649	1.59E-06	48.1841	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10337 - 	CGI_10008201	superfamily	219525	1502	1547	1.08E-05	45.8729	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10337 - 	CGI_10008201	superfamily	111397	1129	1208	6.15E-05	43.8691	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#10337 - 	CGI_10008201	superfamily	219525	1554	1599	0.000108487	42.7914	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10339 - 	CGI_10007169	superfamily	245814	71	131	4.30E-07	46.7135	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10340 - 	CGI_10007170	superfamily	245814	264	315	0.0085316	34.7723	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10340 - 	CGI_10007170	superfamily	245814	326	411	8.32E-11	58.6708	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10340 - 	CGI_10007170	superfamily	245814	89	134	0.000196285	39.5332	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10341 - 	CGI_10007171	superfamily	241568	1089	1146	1.79E-09	56.7024	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10341 - 	CGI_10007171	superfamily	245213	1790	1825	1.55E-07	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10341 - 	CGI_10007171	superfamily	241568	1150	1207	9.55E-05	42.8352	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10341 - 	CGI_10007171	superfamily	245213	545	579	0.000191439	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10341 - 	CGI_10007171	superfamily	245213	1827	1863	0.000221725	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10341 - 	CGI_10007171	superfamily	245213	507	541	0.00814084	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10341 - 	CGI_10007171	superfamily	111397	1004	1084	2.87E-13	68.5218	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#10341 - 	CGI_10007171	superfamily	246918	1880	1923	4.51E-09	55.2855	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10341 - 	CGI_10007171	superfamily	246918	587	636	2.62E-08	53.3595	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10341 - 	CGI_10007171	superfamily	219525	793	838	3.54E-08	52.8065	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10341 - 	CGI_10007171	superfamily	219525	2146	2191	1.31E-07	50.8805	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10341 - 	CGI_10007171	superfamily	111397	1208	1292	1.94E-07	51.1879	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#10341 - 	CGI_10007171	superfamily	219525	1560	1607	5.67E-07	49.3397	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10341 - 	CGI_10007171	superfamily	219525	1522	1565	4.83E-06	46.2581	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10341 - 	CGI_10007171	superfamily	219525	400	446	1.55E-05	45.1026	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10341 - 	CGI_10007171	superfamily	219525	343	393	3.04E-05	43.947	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10342 - 	CGI_10007172	superfamily	245213	160	195	1.11E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10342 - 	CGI_10007172	superfamily	111397	197	277	2.55E-13	63.8994	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#10343 - 	CGI_10007173	superfamily	241568	172	233	6.11E-06	45.5316	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10343 - 	CGI_10007173	superfamily	241568	246	295	1.83E-05	43.9908	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10343 - 	CGI_10007173	superfamily	245213	835	866	0.000409015	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10343 - 	CGI_10007173	superfamily	245213	799	828	0.00687813	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10343 - 	CGI_10007173	superfamily	246918	874	927	1.30E-11	61.8339	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10343 - 	CGI_10007173	superfamily	111397	295	378	4.62E-09	55.0398	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#10343 - 	CGI_10007173	superfamily	219525	635	685	6.75E-08	50.8805	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10343 - 	CGI_10007173	superfamily	219525	1152	1197	3.16E-07	48.9545	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10343 - 	CGI_10007173	superfamily	219525	692	738	0.00035767	40.095	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10343 - 	CGI_10007173	superfamily	111397	87	167	0.00221351	37.7059	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#10344 - 	CGI_10007174	superfamily	245814	136	208	6.31E-05	40.9517	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10346 - 	CGI_10007176	superfamily	245814	223	309	5.83E-05	40.587	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10347 - 	CGI_10007177	superfamily	219525	25	70	4.42E-09	47.7989	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10357 - 	CGI_10016580	superfamily	110440	214	240	0.000760547	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10359 - 	CGI_10016582	superfamily	243035	4	74	1.21E-13	61.8669	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10360 - 	CGI_10016583	superfamily	243035	39	148	1.73E-18	76.8897	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10361 - 	CGI_10016584	superfamily	243035	32	161	1.42E-21	84.9789	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10362 - 	CGI_10016585	superfamily	247856	48	90	1.03E-09	55.2465	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10363 - 	CGI_10016586	superfamily	241600	299	346	2.19E-10	58.4059	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10364 - 	CGI_10016587	superfamily	241600	456	666	5.17E-95	294.533	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10365 - 	CGI_10016589	superfamily	243092	470	681	2.89E-10	60.4264	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10366 - 	CGI_10016590	superfamily	222412	142	172	0.000335975	36.1945	cl16432	Tnp_zf-ribbon_2 superfamily	 - 	 - 	DDE_Tnp_1-like zinc-ribbon; This zinc-ribbon domain is frequently found at the C-terminal of proteins derived from transposable elements.
Q#10367 - 	CGI_10016592	superfamily	245847	33	99	6.15E-15	66.4261	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10368 - 	CGI_10016593	superfamily	246664	17	266	4.55E-80	248.644	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#10375 - 	CGI_10002487	superfamily	246683	791	889	3.46E-51	183.09	cl14648	Aldose_epim superfamily	C	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#10375 - 	CGI_10002487	superfamily	243119	364	412	4.27E-05	42.4209	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#10375 - 	CGI_10002487	superfamily	243119	428	463	0.000455181	39.3494	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#10375 - 	CGI_10002487	superfamily	241611	644	733	0.00054097	40.0644	cl00102	PTX superfamily	N	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#10379 - 	CGI_10009583	superfamily	220695	55	182	3.59E-05	43.3363	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#10380 - 	CGI_10009584	superfamily	245603	1	66	2.74E-11	56.0612	cl11403	pepsin_retropepsin_like superfamily	 - 	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#10381 - 	CGI_10002791	superfamily	247724	88	107	0.00172271	35.3802	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10384 - 	CGI_10002877	superfamily	243082	13	157	6.09E-58	185.539	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#10387 - 	CGI_10002710	superfamily	245847	8	120	2.67E-13	62.1889	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10388 - 	CGI_10002711	superfamily	245847	191	237	0.00327445	35.6102	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10391 - 	CGI_10002714	superfamily	243091	101	156	0.000258691	37.6991	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#10393 - 	CGI_10003448	superfamily	243034	383	485	5.06E-17	77.8055	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10393 - 	CGI_10003448	superfamily	243092	21	197	2.06E-23	100.487	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10393 - 	CGI_10003448	superfamily	243092	524	624	4.53E-09	56.9596	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10396 - 	CGI_10011542	superfamily	219094	77	317	6.39E-07	48.8013	cl05875	Neogenin_C superfamily	N	 - 	"Neogenin C-terminus; This family represents the C-terminus of eukaryotic neogenin precursor proteins, which contains several potential phosphorylation sites. Neogenin is a member of the N-CAM family of cell adhesion molecules (and therefore contains multiple copies of pfam00047 and pfam00041) and is closely related to the DCC tumour suppressor gene product - these proteins may play an integral role in regulating differentiation programmes and/or cell migration events within many adult and embryonic tissues."
Q#10397 - 	CGI_10011543	superfamily	241584	730	818	3.77E-16	76.3811	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10397 - 	CGI_10011543	superfamily	241584	1136	1231	4.26E-16	75.9959	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10397 - 	CGI_10011543	superfamily	241584	825	918	4.26E-15	73.2995	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10397 - 	CGI_10011543	superfamily	241584	929	1019	3.54E-12	64.8251	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10397 - 	CGI_10011543	superfamily	241584	636	713	1.67E-08	53.6543	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10397 - 	CGI_10011543	superfamily	241584	1032	1128	2.80E-07	50.1875	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10397 - 	CGI_10011543	superfamily	247684	13	230	2.80E-57	205.204	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10397 - 	CGI_10011543	superfamily	245814	244	325	6.35E-16	75.5923	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10397 - 	CGI_10011543	superfamily	245814	546	615	1.31E-15	74.2267	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10397 - 	CGI_10011543	superfamily	245814	337	418	5.38E-12	63.9533	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10397 - 	CGI_10011543	superfamily	245814	439	526	7.96E-11	60.5968	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10398 - 	CGI_10011544	superfamily	247684	17	178	7.68E-45	153.972	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10399 - 	CGI_10011545	superfamily	243384	26	48	0.000126283	36.6474	cl03312	Flavokinase superfamily	C	 - 	Riboflavin kinase; This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism. This domain is thought to have kinase activity.
Q#10401 - 	CGI_10011547	superfamily	241984	60	150	8.15E-41	141.924	cl00615	Membrane-FADS-like superfamily	C	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#10401 - 	CGI_10011547	superfamily	241984	204	300	1.12E-30	114.96	cl00615	Membrane-FADS-like superfamily	N	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#10402 - 	CGI_10011548	superfamily	216966	11	196	1.21E-49	161.723	cl03523	HORMA superfamily	 - 	 - 	"HORMA domain; The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity."
Q#10403 - 	CGI_10011549	superfamily	241596	104	161	3.88E-14	63.7723	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#10404 - 	CGI_10011550	superfamily	241596	94	154	2.58E-15	68.7799	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#10405 - 	CGI_10003838	superfamily	247724	21	192	5.00E-111	319.348	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10406 - 	CGI_10003839	superfamily	213148	324	445	1.45E-28	113.924	cl17041	helicase_insert_domain superfamily	 - 	 - 	"helical domain inserted in SF2-type helicase domain in Hef-, MDA5- and FancM-like proteins; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex."
Q#10406 - 	CGI_10003839	superfamily	247905	458	603	6.40E-24	100.775	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#10406 - 	CGI_10003839	superfamily	247805	131	274	4.06E-21	93.1708	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10406 - 	CGI_10003839	superfamily	245342	2105	2185	1.56E-05	45.4175	cl10594	ERCC4 superfamily	 - 	 - 	ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Q#10407 - 	CGI_10003840	superfamily	190724	1136	1201	4.23E-09	55.1158	cl04231	Ribosomal_S5_C superfamily	 - 	 - 	"Ribosomal protein S5, C-terminal domain; Ribosomal protein S5, C-terminal domain.  "
Q#10407 - 	CGI_10003840	superfamily	144065	1066	1111	0.000373828	40.3465	cl02842	Ribosomal_S5 superfamily	 - 	 - 	"Ribosomal protein S5, N-terminal domain; Ribosomal protein S5, N-terminal domain.  "
Q#10408 - 	CGI_10003841	superfamily	241672	2	297	5.54E-119	347.23	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#10410 - 	CGI_10003843	superfamily	215859	44	145	0.00226396	35.6551	cl18347	Peptidase_S9 superfamily	N	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#10411 - 	CGI_10003221	superfamily	243035	49	146	1.57E-09	51.4666	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10412 - 	CGI_10003369	superfamily	243269	48	418	3.60E-67	222.552	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#10413 - 	CGI_10003370	superfamily	243072	3	75	4.23E-09	50.4598	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10414 - 	CGI_10004085	superfamily	149199	10	333	0	516.223	cl06843	DUF1693 superfamily	 - 	 - 	Domain of unknown function (DUF1693); This family contains many hypothetical proteins. It also includes four nematode prion-like proteins. This domain has been identified as part of the nucleotidyltransferase superfamily.
Q#10415 - 	CGI_10004086	superfamily	241578	850	951	0.000511307	41.123	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10416 - 	CGI_10003670	superfamily	247896	9	63	7.56E-14	66.1834	cl17342	Pyruvate_Kinase superfamily	N	 - 	"Pyruvate kinase (PK):  Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors.  Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state.  PK exists as several different isozymes, depending on organism and tissue type.  In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung.  PK forms a homotetramer, with each subunit containing three domains.  The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer."
Q#10417 - 	CGI_10003671	superfamily	247896	1	461	0	701.763	cl17342	Pyruvate_Kinase superfamily	 - 	 - 	"Pyruvate kinase (PK):  Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors.  Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state.  PK exists as several different isozymes, depending on organism and tissue type.  In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung.  PK forms a homotetramer, with each subunit containing three domains.  The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer."
Q#10421 - 	CGI_10006375	superfamily	247804	468	515	3.36E-08	50.2666	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#10421 - 	CGI_10006375	superfamily	243077	23	67	4.65E-06	44.4436	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#10423 - 	CGI_10006377	superfamily	248097	3	124	1.55E-13	62.2826	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10424 - 	CGI_10006378	superfamily	247057	24	105	1.16E-39	128.718	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#10425 - 	CGI_10006379	superfamily	247792	18	70	6.81E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10426 - 	CGI_10006380	superfamily	248097	1	71	0.000980196	34.163	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10427 - 	CGI_10006381	superfamily	247057	1085	1166	2.28E-38	139.504	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#10427 - 	CGI_10006381	superfamily	221437	819	932	3.40E-33	125.93	cl13561	DUF3588 superfamily	 - 	 - 	"Protein of unknown function (DUF3588); This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 866 amino acids in length, and the family is found in association with pfam02820. The exact function of this family is not known."
Q#10427 - 	CGI_10006381	superfamily	248259	352	449	3.17E-32	122.358	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#10427 - 	CGI_10006381	superfamily	248259	687	779	4.69E-23	96.1646	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#10427 - 	CGI_10006381	superfamily	248259	580	676	3.84E-20	87.6902	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#10427 - 	CGI_10006381	superfamily	248259	466	559	3.97E-20	87.6902	cl17705	MBT superfamily	 - 	 - 	"mbt repeat; The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function."
Q#10428 - 	CGI_10006382	superfamily	221559	103	225	5.57E-43	145.072	cl13789	DUF3661 superfamily	 - 	 - 	"Vaculolar membrane protein; This domain family is found in eukaryotes, and is typically between 123 and 138 amino acids in length."
Q#10432 - 	CGI_10006386	superfamily	246918	213	265	6.22E-12	61.0635	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10432 - 	CGI_10006386	superfamily	246918	270	323	4.13E-11	58.7523	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10432 - 	CGI_10006386	superfamily	246918	383	437	5.37E-07	46.8111	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10432 - 	CGI_10006386	superfamily	246918	156	207	1.88E-06	45.2703	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10435 - 	CGI_10005557	superfamily	245055	30	380	3.24E-101	316.437	cl09326	MATE_like superfamily	 - 	 - 	"Multidrug and toxic compound extrusion family and similar proteins; The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria."
Q#10435 - 	CGI_10005557	superfamily	245055	483	559	2.29E-05	45.6414	cl09326	MATE_like superfamily	NC	 - 	"Multidrug and toxic compound extrusion family and similar proteins; The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria."
Q#10436 - 	CGI_10005558	superfamily	245206	30	208	3.65E-39	139.353	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#10436 - 	CGI_10005558	superfamily	245206	206	329	5.30E-34	125.486	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#10439 - 	CGI_10005561	superfamily	241740	2	104	3.96E-37	123.991	cl00269	cytidine_deaminase-like superfamily	 - 	 - 	"Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes.  All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate."
Q#10442 - 	CGI_10005564	superfamily	247057	147	214	1.89E-40	134.452	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#10444 - 	CGI_10012005	superfamily	242203	32	204	3.54E-33	123.907	cl00935	Brix superfamily	 - 	 - 	Brix domain; Brix domain.  
Q#10446 - 	CGI_10012007	superfamily	241563	60	102	0.00020745	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10446 - 	CGI_10012007	superfamily	110440	490	516	0.00703075	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10448 - 	CGI_10012009	superfamily	245864	74	533	2.30E-103	330.78	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#10448 - 	CGI_10012009	superfamily	245864	541	888	1.08E-52	190.567	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#10449 - 	CGI_10012010	superfamily	241640	206	441	9.12E-91	277.62	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#10451 - 	CGI_10012012	superfamily	219237	53	150	3.90E-30	114.09	cl06140	PLA2G12 superfamily	N	 - 	Group XII secretory phospholipase A2 precursor (PLA2G12); This family consists of several group XII secretory phospholipase A2 precursor (PLA2G12) (EC:3.1.1.4) proteins. Group XII and group V PLA(2)s are thought to participate in helper T cell immune response through release of immediate second signals and generation of downstream eicosanoids.
Q#10451 - 	CGI_10012012	superfamily	219237	181	263	3.27E-26	102.919	cl06140	PLA2G12 superfamily	N	 - 	Group XII secretory phospholipase A2 precursor (PLA2G12); This family consists of several group XII secretory phospholipase A2 precursor (PLA2G12) (EC:3.1.1.4) proteins. Group XII and group V PLA(2)s are thought to participate in helper T cell immune response through release of immediate second signals and generation of downstream eicosanoids.
Q#10452 - 	CGI_10012013	superfamily	241563	60	102	6.71E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10452 - 	CGI_10012013	superfamily	110440	527	554	0.00392359	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10453 - 	CGI_10012014	superfamily	245864	25	445	5.12E-97	311.135	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#10453 - 	CGI_10012014	superfamily	243131	702	767	0.000301149	39.6463	cl02660	zf-TAZ superfamily	 - 	 - 	"TAZ zinc finger; The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC."
Q#10454 - 	CGI_10012015	superfamily	245201	78	244	1.45E-23	96.1517	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10455 - 	CGI_10012016	superfamily	244083	668	784	1.27E-28	111.573	cl05417	PLA2_like superfamily	 - 	 - 	"PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers."
Q#10455 - 	CGI_10012016	superfamily	241958	275	537	3.36E-88	285.949	cl00573	SDF superfamily	N	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#10455 - 	CGI_10012016	superfamily	241958	58	197	1.46E-26	111.839	cl00573	SDF superfamily	C	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#10456 - 	CGI_10012017	superfamily	247769	499	639	1.96E-07	50.4157	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#10456 - 	CGI_10012017	superfamily	242093	768	816	0.00926424	35.4661	cl00788	MttA_Hcf106 superfamily	N	 - 	mttA/Hcf106 family; Members of this protein family are involved in a sec independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts. Members of this family in E.coli are involved in export of redox proteins with a "twin arginine" leader motif.
Q#10458 - 	CGI_10012019	superfamily	244539	17	142	6.74E-18	82.88	cl06868	FNR_like superfamily	N	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#10458 - 	CGI_10012019	superfamily	247683	625	677	1.91E-16	74.7614	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#10458 - 	CGI_10012019	superfamily	202162	305	341	3.30E-14	67.8208	cl03489	HS1_rep superfamily	 - 	 - 	Repeat in HS1/Cortactin; The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.
Q#10458 - 	CGI_10012019	superfamily	202162	268	304	2.75E-13	65.5096	cl03489	HS1_rep superfamily	 - 	 - 	Repeat in HS1/Cortactin; The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.
Q#10458 - 	CGI_10012019	superfamily	202162	342	378	4.84E-13	64.7392	cl03489	HS1_rep superfamily	 - 	 - 	Repeat in HS1/Cortactin; The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.
Q#10458 - 	CGI_10012019	superfamily	202162	379	415	7.82E-12	61.2724	cl03489	HS1_rep superfamily	 - 	 - 	Repeat in HS1/Cortactin; The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.
Q#10458 - 	CGI_10012019	superfamily	202162	231	267	1.06E-10	57.8056	cl03489	HS1_rep superfamily	 - 	 - 	Repeat in HS1/Cortactin; The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.
Q#10458 - 	CGI_10012019	superfamily	202162	416	452	4.60E-10	56.2648	cl03489	HS1_rep superfamily	 - 	 - 	Repeat in HS1/Cortactin; The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.
Q#10460 - 	CGI_10007158	superfamily	241754	230	552	8.16E-170	511.804	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#10460 - 	CGI_10007158	superfamily	247057	33	75	7.21E-05	42.2844	cl15755	SAM_superfamily superfamily	C	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#10461 - 	CGI_10007159	superfamily	241563	51	87	7.23E-07	46.7036	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10461 - 	CGI_10007159	superfamily	110440	472	497	0.00387898	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10463 - 	CGI_10007161	superfamily	241563	388	428	7.69E-08	50.1704	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10463 - 	CGI_10007161	superfamily	128778	7	117	0.00586916	36.4739	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#10463 - 	CGI_10007161	superfamily	110440	808	833	0.00796654	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#10466 - 	CGI_10007165	superfamily	216981	157	334	2.66E-07	49.8386	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#10466 - 	CGI_10007165	superfamily	209366	769	791	2.21E-05	42.5734	cl11604	zf-A20 superfamily	 - 	 - 	A20-like zinc finger; The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation.
Q#10468 - 	CGI_10007167	superfamily	243058	326	421	5.79E-06	44.6128	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#10468 - 	CGI_10007167	superfamily	243058	160	276	3.32E-05	42.3016	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#10470 - 	CGI_10025805	superfamily	247068	563	658	2.23E-27	109.325	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	762	856	2.45E-18	83.1317	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	1106	1207	5.10E-16	76.5833	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	1339	1433	1.03E-14	72.7313	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	1215	1313	9.04E-14	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	1449	1571	1.26E-13	69.6497	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	996	1097	6.81E-12	64.2569	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	323	432	2.45E-11	62.7161	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	441	555	1.88E-10	60.0197	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	866	977	4.34E-09	56.1678	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	194	314	2.83E-08	53.8566	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	667	732	1.98E-06	48.0786	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	93	185	0.000156739	42.3006	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10470 - 	CGI_10025805	superfamily	247068	1592	1681	0.000771121	39.9724	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	1049	1148	3.38E-21	91.6061	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	721	818	5.58E-18	81.9761	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	1268	1367	1.14E-17	81.2057	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	949	1040	1.83E-17	80.8205	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	1156	1250	3.13E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	504	596	2.47E-14	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	388	495	3.55E-14	71.1905	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	1387	1463	6.89E-14	70.0349	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	618	712	1.39E-13	69.2645	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	58	145	5.31E-12	64.6421	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	276	378	4.11E-09	56.1678	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	828	939	1.03E-06	48.849	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10471 - 	CGI_10025806	superfamily	247068	155	262	4.47E-05	43.8414	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10472 - 	CGI_10025807	superfamily	247724	127	335	3.82E-136	399.358	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10472 - 	CGI_10025807	superfamily	243184	450	536	1.43E-46	159.33	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#10472 - 	CGI_10025807	superfamily	243185	358	444	1.11E-29	112.698	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#10473 - 	CGI_10025808	superfamily	241782	15	438	7.10E-98	302.18	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#10474 - 	CGI_10025809	superfamily	243050	452	504	8.56E-26	99.817	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#10474 - 	CGI_10025809	superfamily	241622	10	88	7.30E-17	75.681	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10474 - 	CGI_10025809	superfamily	243050	332	382	1.46E-22	90.9784	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#10474 - 	CGI_10025809	superfamily	243050	393	444	3.43E-18	78.6736	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#10475 - 	CGI_10025810	superfamily	241622	13	93	2.48E-20	83.385	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10475 - 	CGI_10025810	superfamily	243050	255	306	6.66E-21	83.9611	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#10475 - 	CGI_10025810	superfamily	128974	172	196	4.89E-08	48.368	cl00302	ZM superfamily	 - 	 - 	"ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules."
Q#10477 - 	CGI_10025812	superfamily	241640	629	856	2.04E-88	282.243	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#10477 - 	CGI_10025812	superfamily	241571	452	568	9.70E-30	115.202	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10477 - 	CGI_10025812	superfamily	241571	324	438	1.36E-29	114.817	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10477 - 	CGI_10025812	superfamily	241571	24	139	1.13E-26	106.343	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10477 - 	CGI_10025812	superfamily	241571	190	305	3.24E-25	102.105	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#10477 - 	CGI_10025812	superfamily	241613	575	609	5.96E-12	61.8389	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#10479 - 	CGI_10025814	superfamily	241599	51	89	3.89E-09	50.7049	cl00084	homeodomain superfamily	C	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#10482 - 	CGI_10025817	superfamily	241547	69	273	1.05E-71	223.699	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#10483 - 	CGI_10025818	superfamily	245201	1	321	0	634.229	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10484 - 	CGI_10025819	superfamily	245814	237	297	0.000345379	39.5799	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10484 - 	CGI_10025819	superfamily	245814	128	202	0.00102672	38.1759	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10484 - 	CGI_10025819	superfamily	245814	22	93	0.00250203	36.7145	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10485 - 	CGI_10025820	superfamily	216686	1	174	2.59E-39	135.914	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#10486 - 	CGI_10025821	superfamily	216686	121	307	7.86E-35	127.824	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#10487 - 	CGI_10025822	superfamily	220015	31	118	3.38E-19	77.3734	cl07407	RPA_C superfamily	 - 	 - 	"Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints."
Q#10488 - 	CGI_10025823	superfamily	247792	13	56	7.53E-08	50.1368	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10488 - 	CGI_10025823	superfamily	243035	713	779	3.45E-06	46.0738	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10489 - 	CGI_10025824	superfamily	242906	63	143	2.62E-25	96.5397	cl02153	TFIIE_beta_winged_helix superfamily	 - 	 - 	"TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity; Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional domains, an N-terminal serine-rich region, a central core domain exhibiting a winged-helix structure capable of binding double-stranded DNA, a leucine repeat, a sigma3 region, and a C-terminal domain containing two basic regions. The assembly of transcription preinitiation complex (PIC) includes the general transcription factors and RNA polymerase II (pol II) initiated by the binding of the TBP subunit of TFIID to the TATA box, followed by either the sequential assembly of other general transcription factors and pol II or a preassembled pol II holoenzyme pathway. TFIIE interacts directly with TFIIF, TFIIB, pol II, and promoter DNA. TFIIE recruits TFIIH and regulates its activities. TFIIE and TFIIH are also important for the transition from initiation to elongation."
Q#10491 - 	CGI_10025826	superfamily	247724	122	338	4.14E-12	65.6457	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10491 - 	CGI_10025826	superfamily	245201	719	913	0.00149818	39.9126	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10492 - 	CGI_10025827	superfamily	115057	1616	1952	7.36E-82	283.11	cl05724	BLVR superfamily	N	 - 	"Bovine leukaemia virus receptor (BLVR); This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown."
Q#10492 - 	CGI_10025827	superfamily	115057	988	1128	2.98E-38	152.142	cl05724	BLVR superfamily	N	 - 	"Bovine leukaemia virus receptor (BLVR); This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown."
Q#10492 - 	CGI_10025827	superfamily	115057	710	819	3.41E-18	89.3541	cl05724	BLVR superfamily	C	 - 	"Bovine leukaemia virus receptor (BLVR); This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown."
Q#10492 - 	CGI_10025827	superfamily	115057	1423	1532	3.41E-18	89.3541	cl05724	BLVR superfamily	C	 - 	"Bovine leukaemia virus receptor (BLVR); This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown."
Q#10494 - 	CGI_10025830	superfamily	241576	61	169	2.30E-22	93.2115	cl00055	MH1 superfamily	 - 	 - 	"N-terminal Mad Homology 1 (MH1) domain; The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure.  It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. Receptor-regulated SMAD proteins (R-SMADs, including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by phosphorylation by transforming growth factor (TGF)-beta type I receptors. The active R-SMAD associates with a common mediator SMAD (Co-SMAD or SMAD4) and other cofactors, which together translocate to the nucleus to regulate gene expression. The inhibitory or antagonistic SMADs (I-SMADs, including SMAD6 and SMAD7) negatively regulate TGF-beta signaling by competing with R-SMADs for type I receptor or Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a nuclear localization signal as well as DNA-binding activity. The activated R-SMAD/SMAD4 complex then binds with very low affinity to a DNA sequence CAGAC called SMAD-binding element (SBE) via the MH1 domain."
Q#10494 - 	CGI_10025830	superfamily	151076	2	40	8.15E-19	81.4988	cl11159	NfI_DNAbd_pre-N superfamily	 - 	 - 	"Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organisms. The N-terminal 200 residues contains the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication."
Q#10495 - 	CGI_10025831	superfamily	245201	528	717	2.12E-39	146.896	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10496 - 	CGI_10025832	superfamily	246925	168	283	1.60E-05	46.1946	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#10498 - 	CGI_10025834	superfamily	241563	60	100	0.00522369	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10499 - 	CGI_10025835	superfamily	221566	8	339	1.10E-121	377.458	cl13804	DUF3668 superfamily	 - 	 - 	Cep120 protein; This family includes the Cep120 protein which is associated with centriole structure and function.
Q#10500 - 	CGI_10025836	superfamily	245201	46	239	2.43E-32	122.345	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10501 - 	CGI_10025837	superfamily	245213	468	502	8.84E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10501 - 	CGI_10025837	superfamily	147730	889	1089	1.35E-123	379.834	cl05347	TSP_C superfamily	 - 	 - 	Thrombospondin C-terminal region; This region is found at the C-terminus of thrombospondin and related proteins.
Q#10501 - 	CGI_10025837	superfamily	202235	642	676	1.58E-09	55.4691	cl15981	TSP_3 superfamily	 - 	 - 	Thrombospondin type 3 repeat; The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
Q#10501 - 	CGI_10025837	superfamily	202235	763	799	4.48E-05	42.3723	cl15981	TSP_3 superfamily	 - 	 - 	Thrombospondin type 3 repeat; The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
Q#10501 - 	CGI_10025837	superfamily	202235	837	871	0.000699869	38.9055	cl15981	TSP_3 superfamily	 - 	 - 	Thrombospondin type 3 repeat; The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
Q#10501 - 	CGI_10025837	superfamily	152034	203	248	0.00140671	38.1041	cl13107	COMP superfamily	 - 	 - 	Cartilage oligomeric matrix protein; This family of proteins represents the five-stranded coiled-coil domain of cartilage oligomeric matrix protein (COMP). This region has a binding site between two internal rings formed by Leu37 and Thr40
Q#10501 - 	CGI_10025837	superfamily	205157	578	606	0.00271828	37.1319	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#10502 - 	CGI_10025838	superfamily	241572	153	242	2.21E-14	68.034	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#10502 - 	CGI_10025838	superfamily	241572	252	316	2.95E-06	44.9262	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#10503 - 	CGI_10025839	superfamily	245847	22	154	3.79E-32	114.757	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10506 - 	CGI_10025843	superfamily	199156	114	130	0.00830597	31.2705	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#10508 - 	CGI_10025845	superfamily	247805	33	181	6.66E-10	54.2656	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10510 - 	CGI_10025847	superfamily	243035	42	178	1.99E-26	105.394	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10510 - 	CGI_10025847	superfamily	243035	383	517	3.85E-26	104.239	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10510 - 	CGI_10025847	superfamily	243035	202	335	1.29E-25	103.083	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10511 - 	CGI_10025848	superfamily	243035	38	187	1.14E-24	94.9941	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10512 - 	CGI_10025849	superfamily	241645	5	116	3.98E-69	205.162	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#10513 - 	CGI_10025850	superfamily	247858	564	728	6.28E-22	93.6066	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#10515 - 	CGI_10025852	superfamily	245201	417	708	0	591.506	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10518 - 	CGI_10025856	superfamily	247755	617	835	8.73E-143	425.637	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#10518 - 	CGI_10025856	superfamily	248376	288	592	1.14E-52	186.075	cl17822	MutS_III superfamily	 - 	 - 	"MutS domain III; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in."
Q#10518 - 	CGI_10025856	superfamily	216613	7	118	3.58E-20	87.6292	cl03286	MutS_I superfamily	 - 	 - 	"MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in."
Q#10518 - 	CGI_10025856	superfamily	218486	141	267	9.78E-13	66.6157	cl04975	MutS_II superfamily	 - 	 - 	"MutS domain II; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam01624, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. This domain corresponds to domain II in Thermus aquaticus MutS as characterized in, and has similarity resembles RNAse-H-like domains (see pfam00075)."
Q#10519 - 	CGI_10025857	superfamily	218603	386	500	6.51E-07	51.4508	cl08440	Serendipity_A superfamily	NC	 - 	"Serendipity locus alpha protein (SRY-A); The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei. SRY-A is required for the cellularisation of the embryo and is involved in the localisation of the actin filaments just prior to and during plasma membrane invagination."
Q#10521 - 	CGI_10025859	superfamily	243088	1	73	2.97E-11	58.9605	cl02563	PX_domain superfamily	N	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#10524 - 	CGI_10016076	superfamily	247866	53	280	6.94E-20	85.9672	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#10525 - 	CGI_10016077	superfamily	241643	315	352	6.53E-08	48.9947	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#10525 - 	CGI_10016077	superfamily	241643	222	258	6.32E-06	43.2167	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#10525 - 	CGI_10016077	superfamily	241645	17	93	0.00456736	34.9354	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#10526 - 	CGI_10016078	superfamily	241754	18	338	2.22E-170	511.842	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#10526 - 	CGI_10016078	superfamily	243114	1135	1169	0.0013178	38.5453	cl02622	Pre-SET superfamily	N	 - 	Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.
Q#10527 - 	CGI_10016079	superfamily	217293	81	256	1.36E-47	163.187	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10527 - 	CGI_10016079	superfamily	202474	295	378	2.47E-29	113.518	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10530 - 	CGI_10016083	superfamily	241675	43	302	3.21E-136	389.349	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#10531 - 	CGI_10016084	superfamily	246938	6	183	1.01E-46	160.116	cl15371	NIF3 superfamily	C	 - 	"NIF3 (NGG1p interacting factor 3); This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown."
Q#10531 - 	CGI_10016084	superfamily	246938	193	320	2.19E-23	96.1725	cl15371	NIF3 superfamily	N	 - 	"NIF3 (NGG1p interacting factor 3); This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown."
Q#10532 - 	CGI_10016085	superfamily	243066	17	103	1.37E-24	94.9272	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#10533 - 	CGI_10016086	superfamily	243371	31	475	8.37E-99	317.028	cl03282	Pro_dh superfamily	 - 	 - 	Proline dehydrogenase; Proline dehydrogenase.  
Q#10533 - 	CGI_10016086	superfamily	243371	565	810	3.37E-73	248.077	cl03282	Pro_dh superfamily	N	 - 	Proline dehydrogenase; Proline dehydrogenase.  
Q#10538 - 	CGI_10016092	superfamily	248097	146	271	4.12E-15	69.2162	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10541 - 	CGI_10016095	superfamily	220808	19	130	2.48E-40	135.134	cl11187	MTP18 superfamily	 - 	 - 	Mitochondrial 18 KDa protein (MTP18); This family of proteins are mitochondrial 18KDa proteins that are often misannotated as carbonic anhydrases. It was shown that knockdown of MTP18 protein results in a cytochrome c release from mitochondria and consequently leads to apoptosis. Overexpression studies suggest that MTP18 is required for mitochondrial fission.
Q#10543 - 	CGI_10016097	superfamily	245205	455	621	1.33E-60	200.997	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#10543 - 	CGI_10016097	superfamily	245205	197	298	2.08E-51	173.587	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#10543 - 	CGI_10016097	superfamily	245205	326	426	1.43E-39	140.412	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#10543 - 	CGI_10016097	superfamily	245205	13	87	1.15E-22	93.416	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#10544 - 	CGI_10016098	superfamily	247725	210	306	6.21E-62	200.936	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10544 - 	CGI_10016098	superfamily	215882	103	216	8.66E-28	107.752	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#10544 - 	CGI_10016098	superfamily	220215	18	96	5.72E-19	81.8878	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#10547 - 	CGI_10016101	superfamily	245201	219	490	4.35E-56	191.194	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10548 - 	CGI_10011881	superfamily	246902	115	247	0.00224838	36.3847	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10549 - 	CGI_10011882	superfamily	243092	18	216	7.50E-26	102.413	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10550 - 	CGI_10011883	superfamily	241599	131	190	3.32E-12	61.4904	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#10552 - 	CGI_10011885	superfamily	245864	31	235	4.93E-62	204.049	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#10553 - 	CGI_10011886	superfamily	245864	125	229	8.33E-05	41.8802	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#10554 - 	CGI_10011887	superfamily	241611	94	237	1.10E-06	46.6128	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#10554 - 	CGI_10011887	superfamily	241619	306	367	0.00092955	37.1732	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#10555 - 	CGI_10011888	superfamily	220097	25	129	0.00143326	35.0721	cl08518	Phospholip_A2_3 superfamily	 - 	 - 	"Prokaryotic phospholipase A2; The prokaryotic phospholipase A2 domain is predominantly found in bacterial and fungal phospholipases, as well as various hypothetical and putative proteins. It enables the liberation of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments."
Q#10557 - 	CGI_10011891	superfamily	241568	885	940	0.00389603	36.672	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#10557 - 	CGI_10011891	superfamily	243124	95	251	4.01E-40	146.803	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#10557 - 	CGI_10011891	superfamily	155088	434	562	1.09E-23	99.5926	cl02758	AMOP superfamily	 - 	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#10557 - 	CGI_10011891	superfamily	243065	605	776	0.00143117	39.3473	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#10560 - 	CGI_10011894	superfamily	247058	3	160	9.51E-38	130.758	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#10561 - 	CGI_10011895	superfamily	247058	3	179	3.32E-44	148.478	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#10565 - 	CGI_10012957	superfamily	217062	122	331	6.04E-43	152.038	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#10568 - 	CGI_10012960	superfamily	216363	40	121	1.34E-13	62.873	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#10570 - 	CGI_10012962	superfamily	243083	87	142	1.41E-14	70.1078	cl02554	PWWP superfamily	C	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#10570 - 	CGI_10012962	superfamily	219431	19	67	6.05E-13	63.9892	cl06504	zf-CW superfamily	 - 	 - 	"CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found."
Q#10570 - 	CGI_10012962	superfamily	243120	362	423	6.06E-08	50.3072	cl02633	ARID superfamily	C	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#10573 - 	CGI_10012965	superfamily	246925	549	795	1.97E-15	77.0105	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#10573 - 	CGI_10012965	superfamily	246925	682	911	4.09E-05	45.4242	cl15309	LRR_RI superfamily	C	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#10575 - 	CGI_10012967	superfamily	247044	371	456	1.79E-20	86.1492	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#10575 - 	CGI_10012967	superfamily	247044	198	247	5.55E-18	79.5744	cl15697	ADF_gelsolin superfamily	N	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#10575 - 	CGI_10012967	superfamily	247044	261	335	1.81E-14	69.1884	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#10576 - 	CGI_10012968	superfamily	241563	68	109	1.71E-06	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10576 - 	CGI_10012968	superfamily	241563	28	59	0.000904387	37.4588	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10579 - 	CGI_10010711	superfamily	247725	1	89	1.34E-33	123.84	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10579 - 	CGI_10010711	superfamily	246675	259	333	8.62E-52	178.685	cl14615	PI-PLCc_GDPD_SF superfamily	C	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#10579 - 	CGI_10010711	superfamily	150071	168	258	2.40E-22	91.481	cl08538	efhand_like superfamily	 - 	 - 	"Phosphoinositide-specific phospholipase C, efhand-like; Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme."
Q#10579 - 	CGI_10010711	superfamily	246675	475	524	1.48E-19	87.7782	cl14615	PI-PLCc_GDPD_SF superfamily	NC	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#10580 - 	CGI_10010712	superfamily	247805	1	131	1.11E-10	60.814	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10580 - 	CGI_10010712	superfamily	247905	291	397	2.98E-09	56.4773	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#10580 - 	CGI_10010712	superfamily	241598	1144	1182	1.30E-05	44.3848	cl00083	HNHc superfamily	N	 - 	"HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins."
Q#10580 - 	CGI_10010712	superfamily	207690	599	623	0.000446118	39.6085	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#10581 - 	CGI_10010713	superfamily	243106	3	175	1.39E-88	277.35	cl02608	BAH superfamily	 - 	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#10581 - 	CGI_10010713	superfamily	212559	275	320	9.84E-25	98.0702	cl18297	SANT_MTA3_like superfamily	 - 	 - 	"Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle.  MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis."
Q#10581 - 	CGI_10010713	superfamily	241648	370	422	2.81E-08	51.2194	cl00158	ZnF_GATA superfamily	 - 	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#10581 - 	CGI_10010713	superfamily	216509	154	209	2.46E-12	63.0266	cl03218	ELM2 superfamily	 - 	 - 	"ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a member from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain."
Q#10582 - 	CGI_10010714	superfamily	247805	27	227	2.98E-94	301.326	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10582 - 	CGI_10010714	superfamily	247905	238	367	2.22E-42	152.777	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#10583 - 	CGI_10010715	superfamily	244363	8	181	1.41E-50	163.066	cl06336	Commd superfamily	 - 	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#10584 - 	CGI_10010716	superfamily	234278	249	445	2.46E-17	83.8121	cl15938	non_repeat_PQQ superfamily	C	 - 	"dehydrogenase, PQQ-dependent, s-GDH family; PQQ, or pyrroloquinoline-quinone, serves as a cofactor for a number of sugar and alcohol dehydrogenases in a limited number of bacterial species. Most characterized PQQ-dependent enzymes have multiple repeats of a sequence region described by pfam01011 (PQQ enzyme repeat), but this protein family in unusual in lacking that repeat. Below the noise cutoff are related proteins mostly from species that lack PQQ biosynthesis."
Q#10584 - 	CGI_10010716	superfamily	217324	26	126	1.89E-09	56.303	cl03844	Folate_rec superfamily	C	 - 	Folate receptor family; This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anchor. The proteins contain 16 conserved cysteines that form eight disulphide bridges.
Q#10585 - 	CGI_10010717	superfamily	241749	20	164	9.14E-25	94.7601	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#10586 - 	CGI_10010718	superfamily	243077	33	79	2.55E-11	56.0145	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#10589 - 	CGI_10010721	superfamily	245323	2954	3243	1.02E-99	325.737	cl10511	Beach superfamily	 - 	 - 	"BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins."
Q#10589 - 	CGI_10010721	superfamily	247725	2833	2943	5.73E-27	109.692	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10589 - 	CGI_10010721	superfamily	243092	3349	3590	2.72E-22	100.487	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10590 - 	CGI_10010722	superfamily	241563	1	22	0.00873532	34.2351	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10592 - 	CGI_10010724	superfamily	217078	52	226	4.70E-58	188.909	cl15643	CoA_transf_3 superfamily	 - 	 - 	"CoA-transferase family III; CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases."
Q#10593 - 	CGI_10010725	superfamily	221831	195	263	8.16E-12	59.0617	cl15144	TORC_C superfamily	 - 	 - 	"Transducer of regulated CREB activity, C terminus; This family includes the C terminal region of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding). The C terminus region is negatively charged, resembling the transcription activation domains. When this domain, from all three human TORC proteins, was expressed as fusion proteins with the DNA-binding domain of GAL4 (GAL4-BD), and tested for induction of a minimal promoter linked to GAL4-binding sites (UAS-GAL4), UAS-GAL4 was potently induced by GAL4-BD fusions containing the C-terminal portion of all three human TORCs."
Q#10596 - 	CGI_10006020	superfamily	245835	18	225	4.56E-62	196.82	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#10597 - 	CGI_10006021	superfamily	241559	27	111	1.62E-14	64.6395	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#10598 - 	CGI_10006022	superfamily	150420	22	176	1.80E-60	206.125	cl18042	Jnk-SapK_ap_N superfamily	 - 	 - 	JNK_SAPK-associated protein-1; This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end.
Q#10600 - 	CGI_10006024	superfamily	245819	142	303	2.89E-51	178.927	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#10600 - 	CGI_10006024	superfamily	245819	820	1005	9.74E-40	146.185	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#10601 - 	CGI_10006025	superfamily	111102	319	398	1.56E-30	112.54	cl03478	KIX superfamily	 - 	 - 	KIX domain; CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.
Q#10601 - 	CGI_10006025	superfamily	243131	245	298	5.38E-15	69.6919	cl02660	zf-TAZ superfamily	C	 - 	"TAZ zinc finger; The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC."
Q#10602 - 	CGI_10006026	superfamily	243131	108	186	4.12E-27	102.049	cl02660	zf-TAZ superfamily	 - 	 - 	"TAZ zinc finger; The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC."
Q#10602 - 	CGI_10006026	superfamily	111102	223	285	2.43E-21	85.9612	cl03478	KIX superfamily	 - 	 - 	KIX domain; CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.
Q#10603 - 	CGI_10006027	superfamily	243131	105	183	7.75E-27	99.3522	cl02660	zf-TAZ superfamily	 - 	 - 	"TAZ zinc finger; The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC."
Q#10604 - 	CGI_10006028	superfamily	245205	59	113	0.000678235	36.4469	cl09930	RPA_2b-aaRSs_OBF_like superfamily	C	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#10604 - 	CGI_10006028	superfamily	245205	156	208	0.00135703	35.2913	cl09930	RPA_2b-aaRSs_OBF_like superfamily	C	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#10605 - 	CGI_10006029	superfamily	111102	17	75	1.68E-24	89.428	cl03478	KIX superfamily	N	 - 	KIX domain; CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.
Q#10606 - 	CGI_10003614	superfamily	241583	27	202	1.44E-18	84.5975	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#10606 - 	CGI_10003614	superfamily	246918	285	339	1.69E-11	60.2931	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10607 - 	CGI_10003615	superfamily	246918	522	576	3.59E-12	62.9895	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10607 - 	CGI_10003615	superfamily	241583	334	427	1.91E-08	54.1439	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#10607 - 	CGI_10003615	superfamily	216572	125	234	4.47E-08	52.2771	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#10608 - 	CGI_10003616	superfamily	241637	584	819	1.85E-26	111.715	cl00146	TFIIS_I superfamily	N	 - 	N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Q#10609 - 	CGI_10003617	superfamily	241734	17	104	9.32E-34	118.84	cl00261	PLPDE_III superfamily	C	 - 	"Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity."
Q#10611 - 	CGI_10004830	superfamily	222150	369	396	0.00111071	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10611 - 	CGI_10004830	superfamily	222150	805	828	0.00324397	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10611 - 	CGI_10004830	superfamily	222150	775	802	0.00347616	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10612 - 	CGI_10004831	superfamily	243074	4	49	1.57E-13	64.0649	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#10613 - 	CGI_10004832	superfamily	247858	187	402	4.65E-26	102.851	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#10614 - 	CGI_10004833	superfamily	220830	283	416	2.63E-21	93.9296	cl11246	Ofd1_CTDD superfamily	N	 - 	"Oxoglutarate and iron-dependent oxygenase degradation C-term; Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen. The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts."
Q#10614 - 	CGI_10004833	superfamily	247858	149	247	7.46E-17	77.0557	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#10614 - 	CGI_10004833	superfamily	243169	549	600	0.00127552	37.8408	cl02766	NGN superfamily	C	 - 	"N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization Substance G (NusG) and its eukaryotic homolog Spt5 are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms a Spt4-Spt5 complex that is an essential RNA Polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria."
Q#10615 - 	CGI_10004834	superfamily	245213	420	454	1.39E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10615 - 	CGI_10004834	superfamily	222669	86	152	1.82E-09	55.8628	cl17048	Fn3-like superfamily	 - 	 - 	Fibronectin type III-like domain; This domain has a fibronectin type III-like structure. It is often found in association with pfam00933 and pfam01915. Its function is unknown.
Q#10615 - 	CGI_10004834	superfamily	243028	465	498	3.51E-07	48.4442	cl02419	Notch superfamily	 - 	 - 	LNR domain; The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
Q#10616 - 	CGI_10004835	superfamily	247803	210	366	8.73E-119	355.068	cl17249	YlqF_related_GTPase superfamily	 - 	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#10616 - 	CGI_10004835	superfamily	149291	45	175	3.85E-58	194.015	cl06961	NGP1NT superfamily	 - 	 - 	NGP1NT (NUC091) domain; This N terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1.
Q#10617 - 	CGI_10004836	superfamily	247856	24	80	2.09E-05	37.9125	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10622 - 	CGI_10018870	superfamily	241574	968	1196	3.85E-90	293.338	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#10622 - 	CGI_10018870	superfamily	241574	1260	1491	8.51E-64	218.609	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#10622 - 	CGI_10018870	superfamily	241584	595	683	4.25E-10	58.6619	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10622 - 	CGI_10018870	superfamily	241584	500	590	8.64E-08	51.7283	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10622 - 	CGI_10018870	superfamily	241584	409	495	1.05E-07	51.7283	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10622 - 	CGI_10018870	superfamily	241585	44	90	8.10E-07	48.284	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#10622 - 	CGI_10018870	superfamily	241585	11	41	0.000132448	41.7356	cl00066	FU superfamily	C	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#10623 - 	CGI_10018871	superfamily	243061	24	124	3.82E-44	152.881	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10623 - 	CGI_10018871	superfamily	243068	285	531	1.85E-27	110.939	cl02523	Zona_pellucida superfamily	 - 	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#10623 - 	CGI_10018871	superfamily	243061	163	270	3.86E-20	86.2418	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10624 - 	CGI_10018872	superfamily	243061	20	122	9.38E-34	125.147	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10624 - 	CGI_10018872	superfamily	243068	321	528	1.08E-27	112.254	cl02523	Zona_pellucida superfamily	 - 	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#10624 - 	CGI_10018872	superfamily	243061	160	267	5.78E-22	91.6346	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10625 - 	CGI_10018873	superfamily	247856	100	172	1.83E-13	62.1801	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10625 - 	CGI_10018873	superfamily	247856	67	125	2.00E-12	59.0985	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10626 - 	CGI_10018874	superfamily	241762	572	631	2.40E-19	83.2149	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#10626 - 	CGI_10018874	superfamily	241575	279	335	0.003407	36.0963	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#10626 - 	CGI_10018874	superfamily	152387	39	100	2.74E-13	66.6081	cl13399	DUF3469 superfamily	C	 - 	Protein of unknown function (DUF3469); This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 108 to 439 amino acids in length.
Q#10628 - 	CGI_10018876	superfamily	247684	9	182	3.48E-20	86.4887	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10630 - 	CGI_10018878	superfamily	246902	212	347	9.20E-58	185.9	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10630 - 	CGI_10018878	superfamily	246902	20	163	1.67E-52	172.479	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10631 - 	CGI_10018879	superfamily	246902	133	207	6.88E-18	76.5036	cl15239	PLDc_SF superfamily	N	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10631 - 	CGI_10018879	superfamily	246902	46	117	2.13E-17	75.0231	cl15239	PLDc_SF superfamily	N	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10632 - 	CGI_10018880	superfamily	246902	156	279	5.90E-49	170.107	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10632 - 	CGI_10018880	superfamily	246902	563	688	3.81E-41	148.151	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10632 - 	CGI_10018880	superfamily	246902	751	845	9.68E-33	124.268	cl15239	PLDc_SF superfamily	C	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10632 - 	CGI_10018880	superfamily	246902	2	113	1.06E-21	92.7423	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10632 - 	CGI_10018880	superfamily	246902	452	526	1.55E-16	77.7195	cl15239	PLDc_SF superfamily	N	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10632 - 	CGI_10018880	superfamily	246902	405	446	2.40E-11	62.2512	cl15239	PLDc_SF superfamily	NC	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#10633 - 	CGI_10018881	superfamily	215821	174	268	1.16E-32	123.505	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#10633 - 	CGI_10018881	superfamily	247725	59	149	4.98E-05	42.8219	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10634 - 	CGI_10018882	superfamily	217925	63	183	8.37E-25	94.4953	cl04417	Ctr superfamily	 - 	 - 	"Ctr copper transporter family; The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport."
Q#10635 - 	CGI_10018883	superfamily	243053	217	487	1.19E-68	225.98	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#10635 - 	CGI_10018883	superfamily	243067	62	184	1.67E-19	85.5419	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#10635 - 	CGI_10018883	superfamily	241645	569	648	2.58E-15	72.4519	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#10636 - 	CGI_10018884	superfamily	217519	5	193	2.37E-56	184.67	cl04030	PRP38 superfamily	 - 	 - 	PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation.
Q#10637 - 	CGI_10018885	superfamily	247912	97	488	1.70E-41	151.885	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#10638 - 	CGI_10018886	superfamily	241622	1085	1168	1.19E-12	65.6658	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10639 - 	CGI_10018887	superfamily	243570	270	619	6.36E-112	343.451	cl03905	EXS superfamily	 - 	 - 	"EXS family; We have named this region the EXS family after (ERD1, XPR1, and SYG1). This family includes C-terminus portions from the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be murine leukaemia virus (MLV) receptors (XPR1). N-terminus portions from these proteins are aligned in the SPX pfam03105 family. The previously noted similarity between SYG1 and MLV receptors over their whole sequences is thus borne out in pfam03105 and this family. While the N-termini aligned in pfam03105 are thought to be involved in signal transduction, the role of the C-terminus sequences aligned in this family is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention defective) yeast proteins. ERD1 proteins are involved in the localisation of endogenous endoplasmic reticulum (ER) proteins. erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localisation label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via `salvage' vesicles."
Q#10639 - 	CGI_10018887	superfamily	217372	1	182	4.33E-42	150.659	cl18405	SPX superfamily	 - 	 - 	"SPX domain; We have named this region the SPX domain after (SYG1, Pho81 and XPR1). This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N-terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal. This finding suggests that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2 NUC-2 contains several ankyrin repeats pfam00023. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine leukaemia viruses (MLV). The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor."
Q#10640 - 	CGI_10018888	superfamily	190601	1	44	7.08E-06	44.3371	cl10605	GerA superfamily	N	 - 	Bacillus/Clostridium GerA spore germination protein; Bacillus/Clostridium GerA spore germination protein.  
Q#10641 - 	CGI_10018889	superfamily	248458	91	262	4.15E-18	84.2877	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#10641 - 	CGI_10018889	superfamily	248458	316	506	5.65E-09	56.5533	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#10643 - 	CGI_10018891	superfamily	241629	1234	1387	2.63E-33	127.636	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#10643 - 	CGI_10018891	superfamily	243034	762	830	4.75E-09	55.464	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10643 - 	CGI_10018891	superfamily	243034	1010	1070	0.000258214	41.2116	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10643 - 	CGI_10018891	superfamily	247743	257	411	5.40E-07	49.8908	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#10643 - 	CGI_10018891	superfamily	205451	13	127	5.63E-06	46.0323	cl16203	DUF4062 superfamily	 - 	 - 	"Domain of unknown function (DUF4062); This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif."
Q#10644 - 	CGI_10018892	superfamily	247775	267	398	1.37E-24	103.434	cl17221	ArsB_NhaD_permease superfamily	N	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#10644 - 	CGI_10018892	superfamily	247775	105	170	1.09E-09	58.8943	cl17221	ArsB_NhaD_permease superfamily	NC	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#10644 - 	CGI_10018892	superfamily	247775	1	31	0.000171625	42.187	cl17221	ArsB_NhaD_permease superfamily	NC	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#10646 - 	CGI_10018894	superfamily	245206	1	143	3.63E-34	123.103	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#10651 - 	CGI_10018899	superfamily	241563	62	103	0.0034338	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10651 - 	CGI_10018899	superfamily	217316	111	168	0.00621647	36.4504	cl03832	DUF234 superfamily	C	 - 	Archaea bacterial proteins of unknown function; Archaea bacterial proteins of unknown function.  
Q#10652 - 	CGI_10018900	superfamily	247046	241	393	3.31E-06	46.2741	cl15705	DUF563 superfamily	C	 - 	Protein of unknown function (DUF563); Family of uncharacterized proteins.
Q#10654 - 	CGI_10018902	superfamily	245599	428	649	1.99E-110	335.842	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#10654 - 	CGI_10018902	superfamily	207662	176	258	6.91E-56	186.122	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#10655 - 	CGI_10018903	superfamily	245230	46	121	2.57E-40	142.045	cl10017	Tubulin_FtsZ superfamily	C	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#10656 - 	CGI_10013953	superfamily	248312	21	205	1.68E-07	48.1185	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#10657 - 	CGI_10013954	superfamily	206609	421	528	2.97E-54	185.676	cl16886	DBC1 superfamily	C	 - 	DBC1; DBC1 and it homologs from diverse eukaryotes are a catalytically inactive version of the Nudix hydrolase (MutT) domain. DBC1 is predicted to bind NAD metabolites and regulate the activity of SIRT1 or related deacetylases by sensing the soluble products or substrates of the NAD-dependent deacetylation reaction.
Q#10657 - 	CGI_10013954	superfamily	206610	128	185	2.64E-32	121.306	cl16887	S1-like superfamily	 - 	 - 	S1-like; S1-like RNA binding domain found in DBC1
Q#10657 - 	CGI_10013954	superfamily	207684	577	605	0.000657444	38.8992	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#10657 - 	CGI_10013954	superfamily	221533	972	1035	0.000826785	38.832	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#10658 - 	CGI_10013955	superfamily	241626	162	277	5.07E-48	158.18	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#10658 - 	CGI_10013955	superfamily	241626	7	137	2.70E-47	156.24	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#10659 - 	CGI_10013956	superfamily	241675	117	331	4.58E-95	296.905	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#10662 - 	CGI_10013959	superfamily	241622	22	69	2.40E-10	58.7322	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10662 - 	CGI_10013959	superfamily	128974	398	423	1.71E-06	46.442	cl00302	ZM superfamily	 - 	 - 	"ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules."
Q#10663 - 	CGI_10013960	superfamily	149077	1398	1510	4.88E-33	125.815	cl06719	TMC superfamily	 - 	 - 	"TMC domain; These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters."
Q#10664 - 	CGI_10013961	superfamily	217293	59	270	2.75E-65	213.263	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10664 - 	CGI_10013961	superfamily	202474	291	387	8.42E-11	60.7453	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10665 - 	CGI_10013962	superfamily	217293	22	124	9.58E-32	120.045	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10665 - 	CGI_10013962	superfamily	202474	132	202	5.97E-10	57.6637	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10666 - 	CGI_10013963	superfamily	241762	132	194	7.13E-15	69.6607	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#10666 - 	CGI_10013963	superfamily	247723	365	394	1.14E-09	55.0829	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10666 - 	CGI_10013963	superfamily	248145	232	316	4.43E-06	46.474	cl17591	CAF1 superfamily	N	 - 	CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Q#10667 - 	CGI_10013964	superfamily	246925	370	605	3.12E-10	60.447	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#10668 - 	CGI_10013965	superfamily	245303	44	263	3.64E-113	332.725	cl10447	GH18_chitinase-like superfamily	C	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#10670 - 	CGI_10021845	superfamily	241574	18	179	1.10E-05	43.3434	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#10673 - 	CGI_10021848	superfamily	147609	12	176	1.24E-17	75.4707	cl05205	p25-alpha superfamily	 - 	 - 	"p25-alpha; This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila."
Q#10674 - 	CGI_10021849	superfamily	151166	1	60	5.26E-17	70.7645	cl11265	MitoNEET_N superfamily	 - 	 - 	"Iron-containing outer mitochondrial membrane protein N-terminus; MitoNEET_N is the N-terminal region of the MitoNEET and Miner-type proteins that carry a zf-CDGSH, pfam09360, redox-active 2Fe-2S cluster. The whole protein regulates oxidative capacity. The domain is an anchor sequence that tethers the protein to the outer membrane."
Q#10674 - 	CGI_10021849	superfamily	243164	78	116	1.29E-15	66.2116	cl02748	zf-CDGSH superfamily	 - 	 - 	"Iron-binding zinc finger CDGSH type; The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, pfam10660. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm."
Q#10675 - 	CGI_10021850	superfamily	241644	4	144	2.31E-56	175.083	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#10676 - 	CGI_10021851	superfamily	247723	225	301	8.87E-51	167.793	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10676 - 	CGI_10021851	superfamily	247723	114	195	8.16E-47	157.317	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10676 - 	CGI_10021851	superfamily	247723	329	416	7.15E-28	105.331	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10677 - 	CGI_10021852	superfamily	241776	18	184	3.50E-64	202.812	cl00315	RPS2 superfamily	 - 	 - 	"Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane and subsequent signalling events, and has been linked to several diseases. Some evidence also suggests that the precursor of 67LR, 37LRP is also present in the nucleus in animals, where it appears associated with histones."
Q#10679 - 	CGI_10021854	superfamily	213458	1	47	1.90E-11	54.2021	cl17044	DD_cGKI superfamily	 - 	 - 	"Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I; Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a  soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing their targeting to different subcellular compartments and intracellular substrates."
Q#10681 - 	CGI_10021856	superfamily	245201	384	644	3.14E-169	488.282	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10681 - 	CGI_10021856	superfamily	241570	242	355	1.91E-28	110.493	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#10681 - 	CGI_10021856	superfamily	241570	123	230	7.13E-25	100.478	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#10681 - 	CGI_10021856	superfamily	213458	10	61	1.82E-05	43.0997	cl17044	DD_cGKI superfamily	 - 	 - 	"Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I; Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a  soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing their targeting to different subcellular compartments and intracellular substrates."
Q#10681 - 	CGI_10021856	superfamily	245597	639	667	3.14E-08	51.2072	cl11395	Pkinase_C superfamily	C	 - 	Protein kinase C terminal domain; Protein kinase C terminal domain.  
Q#10682 - 	CGI_10021857	superfamily	147395	1	42	9.64E-11	53.7424	cl04973	Dpy-30 superfamily	 - 	 - 	Dpy-30 motif; This motif is found in a wide variety of domain contexts. It is found in the Dpy-30 proteins hence the motifs name. It is about 40 residues long and is probably fomed of two alpha-helices. It may be a dimerisation motif analogous to pfam02197 (Bateman A pers obs).
Q#10685 - 	CGI_10021860	superfamily	220695	21	68	0.00461153	36.4027	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#10686 - 	CGI_10021861	superfamily	207654	244	309	5.41E-22	87.113	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10686 - 	CGI_10021861	superfamily	207654	85	150	8.41E-22	86.7278	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10686 - 	CGI_10021861	superfamily	207654	14	77	2.62E-20	82.4906	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10686 - 	CGI_10021861	superfamily	207654	169	234	4.55E-17	73.631	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10688 - 	CGI_10021863	superfamily	207654	97	162	1.67E-26	99.8246	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10688 - 	CGI_10021863	superfamily	207654	256	321	7.11E-24	92.5058	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10688 - 	CGI_10021863	superfamily	207654	26	90	4.96E-23	90.1946	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10688 - 	CGI_10021863	superfamily	207654	180	246	1.50E-20	83.261	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10689 - 	CGI_10021864	superfamily	207654	1	57	6.71E-13	57.4526	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#10691 - 	CGI_10021866	superfamily	245815	10	175	2.87E-97	292.33	cl11961	ALDH-SF superfamily	C	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#10692 - 	CGI_10021867	superfamily	241584	579	673	9.46E-08	52.4987	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10692 - 	CGI_10021867	superfamily	241584	1598	1678	9.28E-05	43.2539	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10692 - 	CGI_10021867	superfamily	241584	256	308	0.00076795	40.5575	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10692 - 	CGI_10021867	superfamily	241584	1527	1596	0.00209673	39.0167	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10692 - 	CGI_10021867	superfamily	241584	1419	1522	0.00352976	38.2463	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10692 - 	CGI_10021867	superfamily	245201	1854	2121	1.50E-144	452.389	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10694 - 	CGI_10021869	superfamily	248097	3	120	1.71E-16	70.3718	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10695 - 	CGI_10021870	superfamily	217414	115	476	3.56E-06	47.7096	cl03927	Otopetrin superfamily	 - 	 - 	"Protein of unknown function, DUF270; Protein of unknown function, DUF270.  "
Q#10696 - 	CGI_10021871	superfamily	241645	8	71	2.50E-12	61.129	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#10696 - 	CGI_10021871	superfamily	245201	137	162	0.00512287	36.5189	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10697 - 	CGI_10021872	superfamily	241926	26	140	3.30E-48	153.944	cl00528	IscU_like superfamily	 - 	 - 	"Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy."
Q#10698 - 	CGI_10021873	superfamily	243099	441	531	0.00707603	34.9275	cl02575	Bcl-2_like superfamily	 - 	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#10699 - 	CGI_10021874	superfamily	241793	119	219	1.19E-37	131.473	cl00333	Ribosomal_L13 superfamily	 - 	 - 	"Ribosomal protein L13.  Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site.  It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer.  L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies."
Q#10700 - 	CGI_10021875	superfamily	202715	150	250	7.29E-29	106.123	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#10701 - 	CGI_10021876	superfamily	248012	334	429	3.99E-19	83.0108	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10702 - 	CGI_10021877	superfamily	243058	86	183	5.84E-08	50.7759	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#10702 - 	CGI_10021877	superfamily	248012	207	302	1.06E-19	84.1664	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10706 - 	CGI_10021881	superfamily	220692	65	246	1.05E-05	45.2729	cl18570	7TM_GPCR_Srw superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#10707 - 	CGI_10021882	superfamily	243066	32	122	5.93E-27	104.557	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#10707 - 	CGI_10021882	superfamily	219619	345	421	6.23E-08	50.284	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#10708 - 	CGI_10021883	superfamily	245814	38	118	9.44E-05	41.3369	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10710 - 	CGI_10001483	superfamily	248097	47	181	6.12E-15	67.7125	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10711 - 	CGI_10013599	superfamily	247723	34	123	6.27E-45	147.02	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10712 - 	CGI_10013600	superfamily	243034	69	150	3.76E-09	51.612	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10712 - 	CGI_10013600	superfamily	215821	1	39	0.00161352	35.2939	cl18346	FKBP_C superfamily	N	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#10713 - 	CGI_10013601	superfamily	243082	121	463	1.16E-63	211.462	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#10713 - 	CGI_10013601	superfamily	245220	4	63	3.40E-17	75.9042	cl09957	zf-UBP superfamily	 - 	 - 	Zn-finger in ubiquitin-hydrolases and other protein; Zn-finger in ubiquitin-hydrolases and other protein.  
Q#10716 - 	CGI_10013604	superfamily	241584	308	410	3.06E-08	52.4987	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10718 - 	CGI_10013606	superfamily	241599	8	51	1.21E-08	46.0825	cl00084	homeodomain superfamily	C	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#10719 - 	CGI_10013607	superfamily	247856	224	290	2.70E-16	71.4249	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10719 - 	CGI_10013607	superfamily	247856	158	213	3.33E-10	54.8613	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10724 - 	CGI_10008493	superfamily	241645	1	76	2.05E-51	159.65	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#10724 - 	CGI_10008493	superfamily	242019	77	128	9.90E-24	87.7376	cl00671	Ribosomal_L40e superfamily	 - 	 - 	Ribosomal L40e family; Bovine L40 has been identified as a secondary RNA binding protein. L40 is fused to a ubiquitin protein.
Q#10725 - 	CGI_10008494	superfamily	242080	234	426	2.88E-43	151.506	cl00771	zpr1_rel superfamily	 - 	 - 	"ZPR1-related zinc finger protein; This model describes a strictly archaeal family homologous to the domain duplicated in the eukaryotic zinc-binding protein ZPR1. ZPR1 was shown experimentally to bind approximately two moles of zinc; each copy of the domain contains a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor, but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by This model by analogy may be suggested to play a role in signal transduction. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1 [Unknown function, General]."
Q#10725 - 	CGI_10008494	superfamily	242080	32	188	1.05E-21	91.4144	cl00771	zpr1_rel superfamily	 - 	 - 	"ZPR1-related zinc finger protein; This model describes a strictly archaeal family homologous to the domain duplicated in the eukaryotic zinc-binding protein ZPR1. ZPR1 was shown experimentally to bind approximately two moles of zinc; each copy of the domain contains a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor, but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by This model by analogy may be suggested to play a role in signal transduction. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1 [Unknown function, General]."
Q#10726 - 	CGI_10008495	superfamily	245814	51	135	7.56E-08	46.208	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10727 - 	CGI_10008496	superfamily	241584	403	495	2.91E-13	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10727 - 	CGI_10008496	superfamily	245814	328	394	5.75E-10	57.8843	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10727 - 	CGI_10008496	superfamily	241584	527	617	1.39E-06	47.8763	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#10727 - 	CGI_10008496	superfamily	245814	43	106	1.23E-13	68.2023	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10727 - 	CGI_10008496	superfamily	245814	126	210	1.13E-08	54.0485	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10727 - 	CGI_10008496	superfamily	245814	244	299	1.40E-07	50.5206	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#10728 - 	CGI_10008497	superfamily	245936	228	434	8.63E-39	139.607	cl12283	IPK superfamily	 - 	 - 	Inositol polyphosphate kinase; ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
Q#10729 - 	CGI_10008498	superfamily	242415	25	220	5.93E-90	275.261	cl01287	AE_Prim_S_like superfamily	 - 	 - 	"AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro."
Q#10729 - 	CGI_10008498	superfamily	242415	303	343	4.80E-20	87.6691	cl01287	AE_Prim_S_like superfamily	N	 - 	"AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro."
Q#10730 - 	CGI_10008499	superfamily	245201	61	323	9.73E-154	435.006	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10731 - 	CGI_10002721	superfamily	248097	1	118	2.73E-20	80.387	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10732 - 	CGI_10002722	superfamily	242232	116	173	3.14E-12	59.2126	cl00984	TM2 superfamily	C	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#10733 - 	CGI_10001621	superfamily	241563	60	102	6.44E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10733 - 	CGI_10001621	superfamily	241563	8	53	0.00383141	35.7759	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10736 - 	CGI_10002173	superfamily	248012	170	282	4.42E-17	78.0032	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10736 - 	CGI_10002173	superfamily	248012	376	469	1.74E-08	52.9653	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10737 - 	CGI_10025516	superfamily	177822	1	189	1.82E-16	75.3417	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#10738 - 	CGI_10025517	superfamily	247725	123	247	1.12E-65	209.064	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10745 - 	CGI_10025524	superfamily	247999	1160	1204	1.58E-15	74.4491	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#10745 - 	CGI_10025524	superfamily	219408	402	484	0.00482452	39.7182	cl06454	DUF1510 superfamily	C	 - 	Protein of unknown function (DUF1510); This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Q#10747 - 	CGI_10025526	superfamily	190706	73	278	1.19E-20	90.9232	cl04201	Glyco_hydro_79n superfamily	N	 - 	"Glycosyl hydrolase family 79, N-terminal domain; Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment. Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesised as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form. Experimental evidence suggests that heparanase may facilitate both tumour cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity."
Q#10748 - 	CGI_10025527	superfamily	241628	48	239	3.33E-61	200.147	cl00130	PseudoU_synth superfamily	 - 	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#10749 - 	CGI_10025528	superfamily	241622	825	862	0.000319112	40.2427	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#10749 - 	CGI_10025528	superfamily	247725	7	78	0.000266361	40.6097	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10753 - 	CGI_10025532	superfamily	246597	2	265	2.68E-77	242.977	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#10755 - 	CGI_10025534	superfamily	241608	21	91	1.27E-45	148.91	cl00098	KH-II superfamily	 - 	 - 	"KH-II  (K homology RNA-binding domain, type II).  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins  (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension."
Q#10755 - 	CGI_10025534	superfamily	215779	102	186	9.70E-24	91.8035	cl02819	Ribosomal_S3_C superfamily	 - 	 - 	"Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer."
Q#10756 - 	CGI_10025535	superfamily	241763	28	170	1.43E-25	98.465	cl00298	Peptidase_C1 superfamily	C	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#10757 - 	CGI_10025536	superfamily	247068	2198	2294	3.11E-31	121.652	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1156	1255	1.49E-27	110.866	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	5	102	3.89E-27	109.71	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1996	2085	3.29E-26	107.014	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	2093	2190	1.93E-24	102.007	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	423	517	2.24E-24	101.621	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247907	2718	2868	2.50E-24	103.267	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#10757 - 	CGI_10025536	superfamily	247068	315	413	5.28E-23	97.7693	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	217	307	3.35E-22	95.4581	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1787	1878	2.45E-21	92.7617	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	625	730	9.85E-21	91.2209	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1891	1983	1.22E-19	88.1393	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1044	1146	9.38E-19	85.4429	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	527	616	1.12E-18	85.0577	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1365	1442	9.82E-18	82.3613	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	940	1032	3.11E-17	80.8205	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1468	1565	1.00E-16	79.6649	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	2303	2395	5.52E-16	77.3537	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	752	829	1.51E-13	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	126	202	2.01E-13	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	839	932	5.83E-13	68.4941	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	247068	1263	1356	1.85E-10	61.1753	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	245213	2990	3022	6.05E-10	58.417	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10757 - 	CGI_10025536	superfamily	247068	1679	1754	5.90E-08	53.4714	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	245213	2946	2984	2.27E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10757 - 	CGI_10025536	superfamily	247068	2419	2491	0.000486948	41.5302	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10757 - 	CGI_10025536	superfamily	245213	2912	2944	0.00321012	38.3866	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#10757 - 	CGI_10025536	superfamily	247068	1576	1667	0.00569888	38.0634	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#10760 - 	CGI_10025539	superfamily	241734	1	136	7.55E-66	204.355	cl00261	PLPDE_III superfamily	N	 - 	"Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity."
Q#10761 - 	CGI_10025540	superfamily	241547	71	199	9.63E-33	120.851	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#10762 - 	CGI_10025541	superfamily	245202	116	217	1.14E-28	113.081	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	243034	1387	1481	3.74E-05	43.908	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10762 - 	CGI_10025541	superfamily	245202	588	657	2.89E-19	84.9699	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	245202	500	566	2.92E-17	79.2045	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	245202	731	800	1.96E-11	62.6053	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	245202	412	480	6.20E-11	60.7391	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	245202	1011	1083	1.33E-09	56.9765	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	245202	228	311	5.07E-09	55.3337	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	245202	329	389	2.09E-08	53.0497	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10762 - 	CGI_10025541	superfamily	245202	678	730	4.46E-07	49.3933	cl09927	S1_like superfamily	C	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#10763 - 	CGI_10025542	superfamily	247792	901	942	5.44E-10	57.4556	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10763 - 	CGI_10025542	superfamily	247684	1071	1319	2.50E-93	310.011	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#10763 - 	CGI_10025542	superfamily	241554	491	660	2.02E-31	123.149	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#10763 - 	CGI_10025542	superfamily	193607	975	1085	1.18E-22	96.4869	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#10763 - 	CGI_10025542	superfamily	247723	3	72	4.67E-05	43.0597	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10764 - 	CGI_10025543	superfamily	248012	63	149	3.31E-17	77.2328	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10765 - 	CGI_10025544	superfamily	216686	70	255	5.24E-52	171.352	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#10767 - 	CGI_10025546	superfamily	217062	142	400	1.22E-42	152.809	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#10768 - 	CGI_10025547	superfamily	241749	33	167	2.62E-22	88.2117	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#10770 - 	CGI_10025549	superfamily	241983	17	323	3.36E-45	157.905	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#10776 - 	CGI_10025555	superfamily	247792	315	357	1.06E-05	42.4328	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10776 - 	CGI_10025555	superfamily	221597	97	242	9.61E-14	67.3805	cl13864	GIDE superfamily	 - 	 - 	"E3 Ubiquitin ligase; This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis."
Q#10777 - 	CGI_10025556	superfamily	247741	13	343	0	636.214	cl17187	Aldolase_Class_I superfamily	 - 	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#10778 - 	CGI_10025557	superfamily	247805	596	744	6.58E-19	86.2372	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10778 - 	CGI_10025557	superfamily	247905	942	1066	1.49E-18	84.982	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#10779 - 	CGI_10025558	superfamily	241832	4	75	2.97E-31	108.099	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#10779 - 	CGI_10025558	superfamily	243175	89	114	3.15E-08	47.5931	cl02776	GST_C_family superfamily	C	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#10782 - 	CGI_10025561	superfamily	241852	845	1100	6.22E-86	278.297	cl00416	CS_ACL-C_CCL superfamily	 - 	 - 	"Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. Some CS proteins function as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs catalyze an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA; they do this in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate CiCoA, and c) the hydrolysis of CiCoA to produce citrate and CoA. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. There are two types of CSs: type I CS and type II CSs.  Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site.  Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism.  In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL."
Q#10782 - 	CGI_10025561	superfamily	215988	649	773	8.98E-23	96.1716	cl18355	Ligase_CoA superfamily	 - 	 - 	"CoA-ligase; This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP."
Q#10782 - 	CGI_10025561	superfamily	247910	483	589	4.34E-07	49.0938	cl17356	CoA_binding superfamily	 - 	 - 	"CoA binding domain; This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases."
Q#10782 - 	CGI_10025561	superfamily	219843	6	203	2.45E-05	45.3077	cl18528	ATP-grasp_2 superfamily	 - 	 - 	ATP-grasp domain; ATP-grasp domain.  
Q#10784 - 	CGI_10025563	superfamily	220097	46	120	2.26E-05	39.6945	cl08518	Phospholip_A2_3 superfamily	N	 - 	"Prokaryotic phospholipase A2; The prokaryotic phospholipase A2 domain is predominantly found in bacterial and fungal phospholipases, as well as various hypothetical and putative proteins. It enables the liberation of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments."
Q#10789 - 	CGI_10025569	superfamily	241578	199	364	2.05E-21	92.278	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10789 - 	CGI_10025569	superfamily	217211	413	479	2.72E-07	48.8198	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#10790 - 	CGI_10025570	superfamily	241578	181	286	3.90E-15	74.3529	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10790 - 	CGI_10025570	superfamily	217211	364	430	1.93E-06	46.5086	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#10791 - 	CGI_10025571	superfamily	241578	164	320	1.99E-19	85.5237	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#10791 - 	CGI_10025571	superfamily	217211	368	434	1.38E-07	48.8198	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#10793 - 	CGI_10025574	superfamily	217293	9	47	0.00113666	34.9159	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10794 - 	CGI_10025575	superfamily	217293	26	224	1.45E-45	152.787	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10796 - 	CGI_10025577	superfamily	241563	18	50	0.00638228	33.2216	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10797 - 	CGI_10025578	superfamily	246680	12	83	3.13E-12	58.6478	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#10799 - 	CGI_10025580	superfamily	216339	779	853	2.39E-23	100.152	cl08308	Tub superfamily	N	 - 	Tub family; Tub family.  
Q#10799 - 	CGI_10025580	superfamily	243073	167	198	0.00725627	35.5284	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#10800 - 	CGI_10002322	superfamily	245847	130	251	0.000103633	40.1784	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#10802 - 	CGI_10003360	superfamily	245596	99	320	1.26E-32	123.36	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#10803 - 	CGI_10003361	superfamily	243072	361	479	3.08E-37	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10803 - 	CGI_10003361	superfamily	243072	288	413	1.80E-35	128.655	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10803 - 	CGI_10003361	superfamily	243072	187	314	1.87E-31	117.485	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10804 - 	CGI_10003362	superfamily	241607	289	327	9.45E-06	43.4126	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#10805 - 	CGI_10003363	superfamily	241649	113	194	5.72E-25	94.7864	cl00159	fer2 superfamily	C	 - 	"2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin."
Q#10805 - 	CGI_10003363	superfamily	241649	57	91	7.54E-08	47.4069	cl00159	fer2 superfamily	C	 - 	"2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin."
Q#10806 - 	CGI_10000576	superfamily	241696	41	141	8.83E-56	179.363	cl00218	Glyco_hydrolase_16 superfamily	C	 - 	"glycosyl hydrolase family 16; The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues."
Q#10807 - 	CGI_10001476	superfamily	246723	1	44	0.000650571	34.8487	cl14813	GluZincin superfamily	C	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#10808 - 	CGI_10019283	superfamily	247723	30	121	7.02E-52	165.562	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10811 - 	CGI_10019286	superfamily	207684	8	42	0.000367264	36.588	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#10813 - 	CGI_10019288	superfamily	241618	48	81	2.26E-05	39.9451	cl00111	PAH superfamily	 - 	 - 	"Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers"
Q#10814 - 	CGI_10019289	superfamily	145281	334	449	0.00508723	37.1877	cl03405	Glyco_hydro_45 superfamily	C	 - 	Glycosyl hydrolase family 45; Glycosyl hydrolase family 45.  
Q#10816 - 	CGI_10019291	superfamily	247099	56	437	0	544.703	cl15845	MntH superfamily	 - 	 - 	Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]
Q#10817 - 	CGI_10019292	superfamily	245201	22	255	1.68E-69	224.723	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#10817 - 	CGI_10019292	superfamily	247057	333	391	3.90E-15	70.6124	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#10820 - 	CGI_10019295	superfamily	216276	18	93	0.00045377	37.1423	cl15639	Activin_recp superfamily	 - 	 - 	"Activin types I and II receptor domain; This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box."
Q#10821 - 	CGI_10019296	superfamily	241563	76	114	0.00042625	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10823 - 	CGI_10019298	superfamily	243061	546	637	4.89E-20	86.627	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10823 - 	CGI_10019298	superfamily	243061	655	747	1.05E-19	85.5962	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10825 - 	CGI_10019300	superfamily	243035	112	199	3.02E-06	44.1478	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10827 - 	CGI_10019302	superfamily	248061	216	301	3.98E-07	47.0082	cl17507	LbR-like superfamily	N	 - 	"Left-handed beta-roll, including virulence factors and various other proteins; This family contains a variety of protein domains with a left-handed beta-roll structure including cell surface adhesion proteins, bacterial virulence factors, and ice-binding proteins, and other activities. UspA1 Head And Neck Domain and YadA of Yersinia are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric beta-rolls of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region. The collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix. These domains form a left handed beta roll made up of a series of short repeated elements."
Q#10828 - 	CGI_10019303	superfamily	243134	205	313	4.22E-22	89.2456	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#10828 - 	CGI_10019303	superfamily	243134	56	177	2.98E-21	86.9344	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#10829 - 	CGI_10019304	superfamily	241600	1	68	2.32E-28	101.933	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10832 - 	CGI_10019307	superfamily	243092	216	436	1.29E-07	51.5668	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10834 - 	CGI_10019309	superfamily	243078	16	145	3.07E-71	229.56	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#10834 - 	CGI_10019309	superfamily	243521	567	682	1.32E-23	97.0378	cl03759	Alpha_adaptinC2 superfamily	 - 	 - 	"Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins."
Q#10834 - 	CGI_10019309	superfamily	190532	206	296	2.44E-19	84.2275	cl03906	GAT superfamily	 - 	 - 	"GAT domain; The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins."
Q#10835 - 	CGI_10019310	superfamily	199156	60	74	0.00563552	33.9669	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#10836 - 	CGI_10019311	superfamily	247856	73	132	8.32E-07	47.9277	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#10836 - 	CGI_10019311	superfamily	243092	349	692	8.71E-25	106.265	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10836 - 	CGI_10019311	superfamily	243092	976	1011	7.04E-05	41.9142	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10838 - 	CGI_10019313	superfamily	202712	587	628	1.50E-21	89.2418	cl04191	CXC superfamily	 - 	 - 	Tesmin/TSO1-like CXC domain; This family includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin and TSO1. This family is called a CXC domain in.
Q#10839 - 	CGI_10019314	superfamily	242889	268	363	2.64E-19	82.2657	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#10840 - 	CGI_10019315	superfamily	221442	44	118	1.38E-07	47.929	cl18607	Hydrolase_4 superfamily	 - 	 - 	"Putative lysophospholipase; This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins."
Q#10840 - 	CGI_10019315	superfamily	247857	126	161	0.000244831	40.69	cl17303	Esterase_713_like superfamily	NC	 - 	Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; This family contains proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible sequence homology to other esterase and lipase enzymes. It is active as a dimer and cleaves esters on halogenated cyclic compounds though its natural substrate is unknown. This enzyme is possibly exported from the cytosol to the periplasmic space. A large majority of sequences in this family have yet to be characterized.
Q#10842 - 	CGI_10008536	superfamily	247692	198	556	5.59E-61	206.988	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#10842 - 	CGI_10008536	superfamily	247692	50	138	8.60E-10	59.4662	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#10843 - 	CGI_10008537	superfamily	217293	340	532	9.80E-34	131.216	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10843 - 	CGI_10008537	superfamily	217293	1042	1209	1.90E-28	115.808	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10843 - 	CGI_10008537	superfamily	217293	707	860	1.57E-24	104.252	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10843 - 	CGI_10008537	superfamily	217293	6	168	2.44E-24	103.481	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#10843 - 	CGI_10008537	superfamily	202474	1241	1346	2.20E-08	54.9673	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10843 - 	CGI_10008537	superfamily	202474	867	1042	1.82E-06	49.1893	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10843 - 	CGI_10008537	superfamily	202474	175	248	0.000943717	41.1001	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#10844 - 	CGI_10008538	superfamily	248458	50	226	6.80E-28	114.333	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#10844 - 	CGI_10008538	superfamily	248458	291	382	4.91E-05	44.6121	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#10847 - 	CGI_10008541	superfamily	247755	397	602	1.88E-83	262.475	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#10847 - 	CGI_10008541	superfamily	241940	45	284	4.07E-92	289.515	cl00549	ABC_membrane_2 superfamily	 - 	 - 	ABC transporter transmembrane region 2; This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with pfam00664. Mutations in this domain in human ABCD3 (PMP70) are believed responsible for Zellweger Syndrome-2; mutations in human ABCD1 (ALD) are responsible for recessive X-linked adrenoleukodystrophy. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids.
Q#10848 - 	CGI_10008542	superfamily	243072	598	715	6.58E-21	90.9058	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10848 - 	CGI_10008542	superfamily	243072	861	1005	1.85E-10	60.0898	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10849 - 	CGI_10008543	superfamily	241600	55	182	2.52E-39	134.712	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10850 - 	CGI_10008544	superfamily	243098	63	111	1.03E-05	44.5111	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#10851 - 	CGI_10008545	superfamily	247725	127	202	2.49E-08	49.4989	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#10852 - 	CGI_10008546	superfamily	241958	27	469	2.39E-80	257.444	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#10854 - 	CGI_10008548	superfamily	241958	25	346	1.30E-33	128.787	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#10857 - 	CGI_10028824	superfamily	241900	3	365	4.85E-158	463.864	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#10858 - 	CGI_10028825	superfamily	241599	165	223	4.81E-19	78.4392	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#10860 - 	CGI_10028827	superfamily	243152	27	154	4.43E-35	121.242	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#10861 - 	CGI_10028828	superfamily	243065	491	668	3.28E-05	43.9697	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#10861 - 	CGI_10028828	superfamily	247724	700	811	0.000205825	42.69	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10861 - 	CGI_10028828	superfamily	247724	58	260	0.00614592	37.436	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#10863 - 	CGI_10028830	superfamily	212639	42	1261	0	985.653	cl17018	FANC superfamily	 - 	 - 	"Fanconi anemia ID complex proteins FANCI and FANCD2; The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA at the ICL site, recognizing branched DNA structures. Defects in the complex cause Fanconi anemia, a cancer predisposition syndrome."
Q#10864 - 	CGI_10028831	superfamily	191698	1630	1808	2.63E-92	298.271	cl06299	Tcp10_C superfamily	 - 	 - 	T-complex protein 10 C-terminus; This family represents the C-terminus (approximately 180 residues) of eukaryotic T-complex protein 10. The T-complex is involved in spermatogenesis in mice.
Q#10864 - 	CGI_10028831	superfamily	247739	78	189	5.28E-15	75.7204	cl17185	LPLAT superfamily	N	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#10864 - 	CGI_10028831	superfamily	243130	232	271	0.000635406	39.7559	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#10866 - 	CGI_10028833	superfamily	243061	54	98	6.01E-19	75.4562	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10866 - 	CGI_10028833	superfamily	243061	1	46	6.14E-14	62.3594	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#10867 - 	CGI_10028834	superfamily	243034	7	106	1.49E-18	77.8055	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#10868 - 	CGI_10028835	superfamily	203324	33	151	4.19E-55	180.91	cl18240	UEV superfamily	 - 	 - 	"UEV domain; This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic transformation and tumorigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but that this gene is not a tumour suppressor for sporadic forms of breast cancer. This family is related to the ubiquitin conjugating enzymes."
Q#10868 - 	CGI_10028835	superfamily	117992	369	415	1.58E-14	68.4264	cl09692	Vps23_core superfamily	C	 - 	Vps23 core domain; ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. The core domain of the Vps23 subunit of the heterotrimeric ESCRT-I complex is a helical hairpin sandwiched in a fan-like formation between two other helical hairpins from Vps28 (pfam03997) and Vps37. Vps23 gives ESCRT-I complex its stability.
Q#10869 - 	CGI_10028836	superfamily	243035	106	218	3.43E-18	77.2749	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10869 - 	CGI_10028836	superfamily	111223	1	48	0.00704446	34.2349	cl15893	MgtC superfamily	C	 - 	MgtC family; The MgtC protein is found in an operon with the Mg2+ transporter protein MgtB. The function of MgtC and its homologues is not known.
Q#10872 - 	CGI_10028839	superfamily	241936	29	121	1.04E-05	43.2107	cl00542	RBFA superfamily	 - 	 - 	Ribosome-binding factor A; Ribosome-binding factor A.  
Q#10875 - 	CGI_10028842	superfamily	247676	67	176	5.36E-41	136.627	cl17012	GINS_A superfamily	 - 	 - 	"Alpha-helical domain of GINS complex proteins; Sld5, Psf1, Psf2 and Psf3; The GINS complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In eukaryotes, GINS is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has been found in eukaryotes and archaea, but not in bacteria. The four subunits of the complex are homologous and consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3."
Q#10876 - 	CGI_10028843	superfamily	247912	85	356	5.69E-27	111.824	cl17358	Beta-lactamase superfamily	C	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#10877 - 	CGI_10028844	superfamily	247639	99	353	1.57E-51	174.187	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#10879 - 	CGI_10028846	superfamily	247792	55	103	0.00740053	33.9584	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10882 - 	CGI_10028849	superfamily	221450	1193	1599	8.07E-86	288.859	cl13584	DUF3595 superfamily	 - 	 - 	Protein of unknown function (DUF3595); This family of proteins is functionally uncharacterized.This family of proteins is found in eukaryotes. Proteins in this family are typically between 578 and 2525 amino acids in length.
Q#10884 - 	CGI_10028851	superfamily	221450	7	92	7.89E-23	90.0961	cl13584	DUF3595 superfamily	N	 - 	Protein of unknown function (DUF3595); This family of proteins is functionally uncharacterized.This family of proteins is found in eukaryotes. Proteins in this family are typically between 578 and 2525 amino acids in length.
Q#10888 - 	CGI_10028856	superfamily	241739	8	254	7.39E-126	383.249	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#10888 - 	CGI_10028856	superfamily	244970	691	749	3.66E-11	60.0886	cl08469	tRNA_SAD superfamily	 - 	 - 	"Threonyl and Alanyl tRNA synthetase second additional domain; The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain."
Q#10888 - 	CGI_10028856	superfamily	243185	503	530	0.000113947	41.3173	cl02787	Translation_Factor_II_like superfamily	N	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#10888 - 	CGI_10028856	superfamily	216955	885	952	0.00495954	36.4343	cl03510	DHHA1 superfamily	 - 	 - 	"DHHA1 domain; This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members. This domains is also found in alanyl tRNA synthetase , suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif."
Q#10889 - 	CGI_10028857	superfamily	245819	128	286	2.01E-50	175.075	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#10889 - 	CGI_10028857	superfamily	245819	650	839	9.93E-43	153.889	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#10889 - 	CGI_10028857	superfamily	218992	334	416	6.50E-07	48.1797	cl05691	DUF1053 superfamily	 - 	 - 	Domain of Unknown Function (DUF1053); This domain is found in Adenylate cyclases.
Q#10890 - 	CGI_10028858	superfamily	220615	1	100	5.68E-11	55.6155	cl10869	MPP6 superfamily	 - 	 - 	M-phase phosphoprotein 6; This is a family of M-phase phosphoprotein 6s which is necessary for generation of the 3' end of the 5.8S rRNA precursor. It preferentially binds to poly(C) and poly(U).
Q#10891 - 	CGI_10028859	superfamily	243098	1304	1351	7.24E-11	60.3043	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#10891 - 	CGI_10028859	superfamily	247905	817	903	4.43E-06	47.2325	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#10891 - 	CGI_10028859	superfamily	243098	1064	1116	0.00605706	36.8072	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#10891 - 	CGI_10028859	superfamily	241659	1812	1911	6.90E-20	88.0352	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#10891 - 	CGI_10028859	superfamily	247805	580	738	6.33E-19	87.9253	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#10894 - 	CGI_10028862	superfamily	243065	208	362	5.67E-06	45.5105	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#10895 - 	CGI_10028863	superfamily	243074	13	58	5.79E-11	57.5165	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#10897 - 	CGI_10028865	superfamily	241900	25	64	7.36E-05	42.3307	cl00490	EEP superfamily	C	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#10899 - 	CGI_10028867	superfamily	219525	103	159	2.00E-07	47.0285	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10899 - 	CGI_10028867	superfamily	219525	166	221	0.000869164	36.6282	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10900 - 	CGI_10028868	superfamily	219525	294	332	8.94E-06	43.5618	cl06646	GCC2_GCC3 superfamily	N	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10900 - 	CGI_10028868	superfamily	219525	339	395	9.58E-06	43.1766	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10900 - 	CGI_10028868	superfamily	219525	402	458	7.98E-05	40.4802	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#10902 - 	CGI_10028870	superfamily	248012	79	188	4.88E-08	50.6541	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10903 - 	CGI_10028871	superfamily	218258	168	268	5.55E-14	67.4372	cl04741	HABP4_PAI-RBP1 superfamily	 - 	 - 	"Hyaluronan / mRNA binding family; This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function."
Q#10904 - 	CGI_10028872	superfamily	197676	56	77	0.000992172	36.6749	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#10904 - 	CGI_10028872	superfamily	222150	100	126	0.00125208	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10904 - 	CGI_10028872	superfamily	222150	69	94	0.00162867	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#10905 - 	CGI_10028873	superfamily	241804	127	348	2.27E-22	94.0188	cl00348	COG0182 superfamily	N	 - 	"Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]"
Q#10907 - 	CGI_10028875	superfamily	238191	634	1123	3.12E-122	387.458	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#10907 - 	CGI_10028875	superfamily	238191	34	537	2.47E-107	347.397	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#10909 - 	CGI_10028877	superfamily	238191	1	419	5.99E-96	299.633	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#10910 - 	CGI_10028878	superfamily	238191	27	522	5.58E-113	348.168	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#10912 - 	CGI_10028880	superfamily	243072	159	285	4.92E-32	122.492	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#10913 - 	CGI_10028881	superfamily	245836	240	458	1.69E-101	317.983	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#10913 - 	CGI_10028881	superfamily	244947	462	602	1.60E-60	202.405	cl08424	OBF_DNA_ligase_family superfamily	 - 	 - 	"The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain."
Q#10913 - 	CGI_10028881	superfamily	241565	818	902	1.22E-05	44.2347	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10913 - 	CGI_10028881	superfamily	241565	666	736	0.000234908	40.3827	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10913 - 	CGI_10028881	superfamily	151850	761	789	0.000186683	40.119	cl12940	DNA_ligase_IV superfamily	 - 	 - 	"DNA ligase IV; DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface."
Q#10914 - 	CGI_10028882	superfamily	245838	276	420	1.03E-22	95.9747	cl12018	Peptidase_M48 superfamily	N	 - 	Peptidase family M48; Peptidase family M48.  
Q#10915 - 	CGI_10028883	superfamily	244947	214	304	3.01E-40	143.469	cl08424	OBF_DNA_ligase_family superfamily	N	 - 	"The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain."
Q#10915 - 	CGI_10028883	superfamily	241565	522	606	3.88E-06	45.0051	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10915 - 	CGI_10028883	superfamily	241565	368	438	0.00012995	40.3827	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10915 - 	CGI_10028883	superfamily	241565	59	117	3.98E-05	41.8116	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10915 - 	CGI_10028883	superfamily	151850	463	493	0.00827217	34.7262	cl12940	DNA_ligase_IV superfamily	 - 	 - 	"DNA ligase IV; DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface."
Q#10916 - 	CGI_10028884	superfamily	204929	19	69	9.62E-12	61.0657	cl13846	MMS19_N superfamily	N	 - 	"NER and RNAPII transcription protein n terminal; This domain family is found in eukaryotes, and is approximately 60 amino acids in length. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription."
Q#10916 - 	CGI_10028884	superfamily	245838	467	559	1.43E-09	57.0696	cl12018	Peptidase_M48 superfamily	N	 - 	Peptidase family M48; Peptidase family M48.  
Q#10917 - 	CGI_10028885	superfamily	241645	150	219	1.16E-23	91.0668	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#10919 - 	CGI_10028887	superfamily	220692	93	368	5.01E-11	62.2217	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#10921 - 	CGI_10028889	superfamily	241583	252	414	3.91E-43	152.358	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#10921 - 	CGI_10028889	superfamily	243048	439	630	9.76E-17	78.8924	cl02471	HX superfamily	 - 	 - 	Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat.
Q#10921 - 	CGI_10028889	superfamily	216518	105	129	0.00251889	36.7393	cl18368	PG_binding_1 superfamily	N	 - 	Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.
Q#10924 - 	CGI_10028892	superfamily	243485	62	96	0.000261951	36.9488	cl03649	HemD superfamily	N	 - 	"Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease."
Q#10925 - 	CGI_10028893	superfamily	243485	18	182	3.01E-30	112.015	cl03649	HemD superfamily	C	 - 	"Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease."
Q#10927 - 	CGI_10028895	superfamily	243035	31	140	9.63E-10	51.8518	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#10928 - 	CGI_10028896	superfamily	243100	187	236	9.80E-10	53.3367	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#10929 - 	CGI_10028897	superfamily	216347	342	760	1.49E-121	374.95	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#10929 - 	CGI_10028897	superfamily	145726	93	177	0.00111511	38.0954	cl08353	Cu_amine_oxidN2 superfamily	 - 	 - 	"Copper amine oxidase, N2 domain; This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ)."
Q#10930 - 	CGI_10028898	superfamily	241607	737	770	0.0065922	35.7086	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#10930 - 	CGI_10028898	superfamily	241607	617	637	0.000203939	40.3451	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#10931 - 	CGI_10028900	superfamily	247792	799	844	0.00144988	37.4252	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10931 - 	CGI_10028900	superfamily	243092	52	157	2.30E-05	45.7888	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10931 - 	CGI_10028900	superfamily	150957	721	825	0.00245145	37.2105	cl11034	Vps39_2 superfamily	 - 	 - 	"Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11."
Q#10932 - 	CGI_10028901	superfamily	241599	414	471	1.82E-16	73.8168	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#10932 - 	CGI_10028901	superfamily	198730	318	392	7.78E-35	125.11	cl02582	Pou superfamily	 - 	 - 	Pou domain - N-terminal to homeobox domain; Pou domain - N-terminal to homeobox domain.  
Q#10934 - 	CGI_10028903	superfamily	238191	15	505	2.33E-108	334.301	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#10935 - 	CGI_10028904	superfamily	248054	22	220	1.44E-09	56.5419	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#10936 - 	CGI_10028905	superfamily	248012	289	383	3.95E-10	57.2833	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10937 - 	CGI_10028906	superfamily	241600	84	214	6.10E-62	208.634	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10938 - 	CGI_10028907	superfamily	241600	309	516	4.20E-96	292.992	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10938 - 	CGI_10028907	superfamily	241600	84	256	1.22E-82	258.324	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10941 - 	CGI_10028910	superfamily	241600	84	234	1.64E-81	245.613	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#10942 - 	CGI_10028911	superfamily	248318	286	352	2.44E-18	80.5577	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#10942 - 	CGI_10028911	superfamily	243092	23	279	1.46E-26	110.502	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10942 - 	CGI_10028911	superfamily	216421	521	844	5.43E-23	100.19	cl03153	Lamp superfamily	 - 	 - 	Lysosome-associated membrane glycoprotein (Lamp); Lysosome-associated membrane glycoprotein (Lamp).  
Q#10944 - 	CGI_10028913	superfamily	247723	541	619	1.75E-23	96.5472	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#10944 - 	CGI_10028913	superfamily	245716	511	534	1.38E-05	43.3159	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#10945 - 	CGI_10028914	superfamily	201362	63	148	4.04E-13	63.1531	cl08277	Motile_Sperm superfamily	C	 - 	MSP (Major sperm protein) domain; Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
Q#10946 - 	CGI_10028915	superfamily	152807	1369	1411	6.79E-09	54.7557	cl13765	DUF3652 superfamily	 - 	 - 	"Huntingtin protein region; This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam02985. This family is in the middle region of the Huntingtin protein associated with Huntington's disease. The protein is of unknown function, however it is known that a polyglutamine (CAG) repeat in the gene coding for it results in the development of Huntington's disease."
Q#10948 - 	CGI_10028917	superfamily	245670	149	332	1.62E-58	196.239	cl11519	DENN superfamily	 - 	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#10948 - 	CGI_10028917	superfamily	243635	15	85	1.91E-18	81.2268	cl04085	uDENN superfamily	N	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#10951 - 	CGI_10028920	superfamily	245599	159	364	8.63E-102	302.677	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#10951 - 	CGI_10028920	superfamily	207662	8	100	1.35E-66	208.119	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#10952 - 	CGI_10028921	superfamily	245599	165	371	1.41E-79	245.667	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#10952 - 	CGI_10028921	superfamily	207662	9	100	5.71E-60	191.17	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#10953 - 	CGI_10028922	superfamily	248012	2	51	0.000121818	36.4825	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10954 - 	CGI_10028923	superfamily	248012	2	94	5.23E-11	55.7425	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#10958 - 	CGI_10028927	superfamily	246748	14	375	1.89E-155	445.765	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#10959 - 	CGI_10028928	superfamily	246748	14	361	5.42E-147	426.505	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#10961 - 	CGI_10028930	superfamily	247792	17	60	4.21E-08	50.522	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#10961 - 	CGI_10028930	superfamily	241563	154	189	7.92E-06	43.8151	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#10961 - 	CGI_10028930	superfamily	128778	200	325	0.000686807	38.7851	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#10962 - 	CGI_10028931	superfamily	243092	797	1083	2.57E-44	163.275	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#10962 - 	CGI_10028931	superfamily	222477	120	746	0	544.678	cl16505	SID-1_RNA_chan superfamily	 - 	 - 	dsRNA-gated channel SID-1; This is a family of proteins that are transmembrane dsRNA-gated channels. They passively transport dsRNA into cells and do not act as ATP-dependent pumps. They are required for systemic RNA interference.
Q#10964 - 	CGI_10028933	superfamily	205570	66	105	7.40E-06	41.6498	cl16264	HNH_3 superfamily	 - 	 - 	HNH endonuclease; HNH endonuclease.  
Q#10965 - 	CGI_10028934	superfamily	241583	162	361	5.32E-60	202.854	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#10965 - 	CGI_10028934	superfamily	216572	31	136	3.51E-19	85.019	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#10965 - 	CGI_10028934	superfamily	246918	749	799	0.000254422	39.8775	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10965 - 	CGI_10028934	superfamily	246918	483	513	0.000280568	39.8775	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#10968 - 	CGI_10028938	superfamily	217410	11	108	0.00148501	35.7928	cl18409	DDE_1 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere."
Q#10971 - 	CGI_10013357	superfamily	241750	9	348	6.27E-101	303.741	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#10972 - 	CGI_10013358	superfamily	216423	208	330	9.07E-38	141.99	cl18367	Glyco_hydro_35 superfamily	N	 - 	Glycosyl hydrolases family 35; Glycosyl hydrolases family 35.  
Q#10972 - 	CGI_10013358	superfamily	216423	65	118	7.44E-08	53.0091	cl18367	Glyco_hydro_35 superfamily	NC	 - 	Glycosyl hydrolases family 35; Glycosyl hydrolases family 35.  
Q#10973 - 	CGI_10013359	superfamily	243029	23	88	2.16E-12	61.5977	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#10975 - 	CGI_10013361	superfamily	248097	142	262	3.85E-27	102.729	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10976 - 	CGI_10013362	superfamily	248097	11	132	2.93E-27	99.2618	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#10978 - 	CGI_10013364	superfamily	241565	155	254	0.000832484	37.3558	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10979 - 	CGI_10013365	superfamily	241565	110	179	1.16E-10	59.6426	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10979 - 	CGI_10013365	superfamily	241565	203	273	2.38E-10	58.487	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10979 - 	CGI_10013365	superfamily	241565	366	437	2.87E-07	49.6275	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10979 - 	CGI_10013365	superfamily	241565	643	717	5.88E-07	48.4719	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#10980 - 	CGI_10013366	superfamily	152088	123	203	4.77E-20	81.0951	cl13155	DUF3259 superfamily	 - 	 - 	Protein of unknown function (DUF3259); This eukaryotic family of proteins has no known function.
Q#10982 - 	CGI_10013368	superfamily	214806	200	293	8.42E-18	76.5653	cl15966	CRA superfamily	 - 	 - 	"CT11-RanBPM; protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)"
Q#10982 - 	CGI_10013368	superfamily	199226	108	141	7.81E-07	45.118	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#10982 - 	CGI_10013368	superfamily	128914	148	186	0.000249311	38.321	cl15352	CTLH superfamily	C	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#10984 - 	CGI_10013370	superfamily	241647	132	157	0.00110689	37.9332	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#10985 - 	CGI_10013371	superfamily	243095	137	322	1.56E-103	304.314	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#10985 - 	CGI_10013371	superfamily	243052	1	126	1.71E-20	85.8751	cl02480	MyTH4 superfamily	N	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#10986 - 	CGI_10013372	superfamily	247999	68	111	6.85E-05	37.0848	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#10987 - 	CGI_10013373	superfamily	222055	312	431	1.57E-24	99.3244	cl16245	AATF-Che1 superfamily	 - 	 - 	Apoptosis antagonizing transcription factor; The N-terminal and leucine-zipper region of the apoptosis antagonizing transcription factor-Che1.
Q#10987 - 	CGI_10013373	superfamily	219734	480	596	4.50E-17	76.8788	cl06972	TRAUB superfamily	 - 	 - 	"Apoptosis-antagonizing transcription factor, C-terminal; This C terminal domain is found in traube proteins. This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcription."
Q#10988 - 	CGI_10013374	superfamily	243028	432	468	6.63E-12	62.3114	cl02419	Notch superfamily	 - 	 - 	LNR domain; The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
Q#10988 - 	CGI_10013374	superfamily	221100	318	428	1.51E-08	57.2193	cl15596	DUF3184 superfamily	C	 - 	Protein of unknown function (DUF3184); This eukaryotic family of proteins has no known function.
Q#10988 - 	CGI_10013374	superfamily	243028	490	525	7.26E-07	47.6738	cl02419	Notch superfamily	 - 	 - 	LNR domain; The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
Q#10996 - 	CGI_10013382	superfamily	243066	23	124	9.99E-12	62.2497	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#10997 - 	CGI_10013383	superfamily	242685	83	115	3.55E-17	74.5359	cl01749	UPF0160 superfamily	C	 - 	Uncharacterized protein family (UPF0160); This family of proteins contains a large number of metal binding residues. The patterns are suggestive of a phosphoesterase function. The conserved DHH motif may mean this family is related to pfam01368.
Q#10998 - 	CGI_10013384	superfamily	242685	19	340	1.13E-177	498.641	cl01749	UPF0160 superfamily	 - 	 - 	Uncharacterized protein family (UPF0160); This family of proteins contains a large number of metal binding residues. The patterns are suggestive of a phosphoesterase function. The conserved DHH motif may mean this family is related to pfam01368.
Q#11006 - 	CGI_10003404	superfamily	242877	20	81	3.30E-26	96.9141	cl02093	Coq4 superfamily	C	 - 	"Coenzyme Q (ubiquinone) biosynthesis protein Coq4; Coq4p was shown to peripherally associate with the matrix face of the mitochondrial inner membrane. The putative mitochondrial- targeting sequence present at the amino-terminus of the polypeptide efficiently imported it to mitochondria. The function of Coq4p is unknown, although its presence is required to maintain a steady-state level of Coq7p, another component of the Q biosynthetic pathway. The overall structure of Coq4 is alpha helical and shows resemblance to haemoglobin/myoglobin (information from TOPSAN)."
Q#11007 - 	CGI_10022762	superfamily	245201	7	157	5.22E-110	322.689	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11008 - 	CGI_10022763	superfamily	245201	17	58	6.51E-24	91.2184	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11010 - 	CGI_10022765	superfamily	247744	47	166	5.87E-08	48.804	cl17190	NK superfamily	N	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#11011 - 	CGI_10022766	superfamily	247805	351	580	7.14E-83	264.732	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#11011 - 	CGI_10022766	superfamily	247905	597	723	2.23E-36	133.902	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#11013 - 	CGI_10022768	superfamily	243127	6	38	4.56E-11	54.2346	cl02651	FYRC superfamily	N	 - 	F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.
Q#11015 - 	CGI_10022771	superfamily	247057	663	731	1.20E-26	104.273	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#11015 - 	CGI_10022771	superfamily	241622	3	89	1.75E-14	69.903	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11017 - 	CGI_10022773	superfamily	247805	318	425	8.31E-13	67.7476	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#11017 - 	CGI_10022773	superfamily	247905	592	685	2.04E-11	63.0256	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#11017 - 	CGI_10022773	superfamily	219729	1190	1366	1.21E-72	240.966	cl06956	DSHCT superfamily	 - 	 - 	DSHCT (NUC185) domain; This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases.
Q#11017 - 	CGI_10022773	superfamily	219729	1034	1144	5.54E-35	133.495	cl06956	DSHCT superfamily	C	 - 	DSHCT (NUC185) domain; This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases.
Q#11018 - 	CGI_10022774	superfamily	207662	65	152	3.75E-64	206.152	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#11018 - 	CGI_10022774	superfamily	245599	316	538	9.27E-95	291.107	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#11019 - 	CGI_10022775	superfamily	246918	568	621	2.60E-12	63.7599	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11019 - 	CGI_10022775	superfamily	246918	338	390	9.90E-12	62.2191	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11019 - 	CGI_10022775	superfamily	246918	626	678	1.32E-11	61.8339	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11019 - 	CGI_10022775	superfamily	246918	453	505	2.91E-11	60.6783	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11019 - 	CGI_10022775	superfamily	246918	395	445	4.81E-09	54.1299	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11019 - 	CGI_10022775	superfamily	243060	763	830	6.15E-06	45.8328	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#11019 - 	CGI_10022775	superfamily	246918	508	563	0.000212422	40.6479	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11019 - 	CGI_10022775	superfamily	241672	830	881	0.00153836	40.3579	cl00192	ribokinase_pfkB_like superfamily	NC	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#11020 - 	CGI_10022776	superfamily	242730	162	217	0.00100415	38.3963	cl01825	Phage_Mu_Gam superfamily	C	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#11021 - 	CGI_10022777	superfamily	242730	162	203	0.00594752	36.0851	cl01825	Phage_Mu_Gam superfamily	C	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#11021 - 	CGI_10022777	superfamily	241563	64	101	0.00709639	34.9556	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11022 - 	CGI_10022778	superfamily	246908	109	152	0.00649459	35.0194	cl15255	SH2 superfamily	N	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#11023 - 	CGI_10022779	superfamily	217293	1	159	3.27E-35	128.905	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11023 - 	CGI_10022779	superfamily	202474	167	338	8.87E-25	100.036	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11024 - 	CGI_10022780	superfamily	177822	32	180	6.59E-16	73.8009	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#11025 - 	CGI_10022781	superfamily	245008	211	275	2.80E-12	60.2796	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#11025 - 	CGI_10022781	superfamily	207794	1	193	2.43E-59	196.744	cl02948	GH20_hexosaminidase superfamily	N	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#11026 - 	CGI_10022783	superfamily	245213	69	107	4.19E-08	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11026 - 	CGI_10022783	superfamily	245213	31	66	3.95E-07	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11026 - 	CGI_10022783	superfamily	216897	123	202	4.05E-25	94.6704	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#11027 - 	CGI_10022784	superfamily	241832	7	79	3.07E-16	70.6556	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#11027 - 	CGI_10022784	superfamily	243175	90	205	1.65E-14	66.4922	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#11028 - 	CGI_10022785	superfamily	245201	386	469	6.72E-13	67.1597	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11028 - 	CGI_10022785	superfamily	247724	172	283	3.60E-05	42.919	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11030 - 	CGI_10022787	superfamily	245226	180	353	9.52E-101	299.532	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#11030 - 	CGI_10022787	superfamily	243082	2	109	3.61E-07	49.8184	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#11032 - 	CGI_10022789	superfamily	245201	18	246	6.32E-63	200.802	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11033 - 	CGI_10022790	superfamily	245201	15	260	2.78E-106	325.222	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11034 - 	CGI_10001202	superfamily	247692	1	68	2.94E-14	65.3382	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#11038 - 	CGI_10005349	superfamily	222429	19	98	4.07E-08	46.85	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#11041 - 	CGI_10016318	superfamily	248097	51	177	1.75E-18	77.3054	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11045 - 	CGI_10016322	superfamily	242274	29	94	1.32E-06	42.993	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#11046 - 	CGI_10016323	superfamily	221602	506	741	4.15E-25	105.571	cl13871	BCAS3 superfamily	 - 	 - 	"Breast carcinoma amplified sequence 3; This domain family is found in eukaryotes, and is typically between 229 and 245 amino acids in length. The proteins in this family have been shown to be proto-oncogenes implicated in the development of breast cancer."
Q#11047 - 	CGI_10016324	superfamily	241636	85	270	2.36E-121	361.135	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#11048 - 	CGI_10016325	superfamily	241636	10	195	1.63E-124	354.972	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#11050 - 	CGI_10016327	superfamily	219153	196	360	3.63E-52	182.555	cl15854	DEAD_2 superfamily	 - 	 - 	"DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast."
Q#11050 - 	CGI_10016327	superfamily	248014	622	811	2.08E-47	168.899	cl17460	Csf4_U superfamily	 - 	 - 	CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Q#11052 - 	CGI_10016329	superfamily	245208	662	1052	0	662.163	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#11052 - 	CGI_10016329	superfamily	247824	258	506	1.48E-98	312.984	cl17270	APH_ChoK_like superfamily	 - 	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#11052 - 	CGI_10016329	superfamily	248469	100	195	8.18E-05	42.3571	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#11053 - 	CGI_10016330	superfamily	247941	134	264	6.95E-05	40.7821	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#11054 - 	CGI_10016331	superfamily	247723	115	188	6.57E-49	158.752	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#11054 - 	CGI_10016331	superfamily	247723	27	101	1.27E-44	147.578	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#11057 - 	CGI_10016334	superfamily	245206	6	351	6.78E-64	208.9	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#11059 - 	CGI_10015011	superfamily	243035	107	234	6.57E-27	101.157	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11059 - 	CGI_10015011	superfamily	243051	12	87	0.00104654	37.3574	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11060 - 	CGI_10015012	superfamily	241610	521	574	5.56E-22	90.0018	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#11061 - 	CGI_10015013	superfamily	241645	48	110	3.88E-37	122.823	cl00155	UBQ superfamily	N	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#11062 - 	CGI_10015014	superfamily	194922	1	174	7.50E-90	263.033	cl04601	SPC22 superfamily	 - 	 - 	"Signal peptidase subunit; Translocation of polypeptide chains across the endoplasmic reticulum membrane is triggered by signal sequences. During translocation of the nascent chain through the membrane, the signal sequence of most secretory and membrane proteins is cleaved off. Cleavage occurs by the signal peptidase complex (SPC) which consists of four subunits in yeast and five in mammals. This family is common to yeast and mammals."
Q#11064 - 	CGI_10015016	superfamily	192535	49	151	0.000353982	40.2718	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#11066 - 	CGI_10015018	superfamily	216188	236	497	5.34E-67	221.708	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#11066 - 	CGI_10015018	superfamily	205965	75	158	4.27E-35	127.529	cl18285	Sulfate_tra_GLY superfamily	 - 	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#11067 - 	CGI_10015019	superfamily	217293	22	227	1.54E-44	155.869	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11067 - 	CGI_10015019	superfamily	202474	234	420	7.90E-32	120.836	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11068 - 	CGI_10015020	superfamily	245596	390	597	7.92E-22	93.9229	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#11069 - 	CGI_10015021	superfamily	241995	27	327	1.23E-129	374.246	cl00635	Ntn_Asparaginase_2_like superfamily	 - 	 - 	"Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and  L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue."
Q#11070 - 	CGI_10015022	superfamily	243056	479	679	1.23E-48	171.773	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#11070 - 	CGI_10015022	superfamily	245201	45	276	6.84E-27	111.11	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11070 - 	CGI_10015022	superfamily	241626	801	889	1.25E-23	97.5249	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#11071 - 	CGI_10015023	superfamily	222150	139	164	0.00403941	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11071 - 	CGI_10015023	superfamily	222150	167	190	0.00464249	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11073 - 	CGI_10015025	superfamily	247919	368	577	0.00704434	38.8106	cl17365	TrkH superfamily	NC	 - 	Cation transport protein; This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilising ATP in the process. TrkH a member of the family from E. coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in E. coli.
Q#11074 - 	CGI_10015026	superfamily	219000	432	582	3.46E-19	87.7019	cl05717	Drf_FH3 superfamily	C	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#11074 - 	CGI_10015026	superfamily	219001	376	428	6.81E-05	43.8367	cl05720	Drf_GBD superfamily	N	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#11075 - 	CGI_10015027	superfamily	216686	119	307	8.48E-37	133.217	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#11077 - 	CGI_10015029	superfamily	243670	7	366	4.50E-88	273.15	cl04217	UPF0075 superfamily	 - 	 - 	Uncharacterized protein family (UPF0075); The proteins is this family are about 370 amino acids long and have no known function.
Q#11078 - 	CGI_10015030	superfamily	241554	482	569	2.13E-13	69.4857	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#11078 - 	CGI_10015030	superfamily	241752	873	1002	2.67E-12	65.0333	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#11079 - 	CGI_10015031	superfamily	241554	149	279	2.69E-30	116.976	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#11079 - 	CGI_10015031	superfamily	241752	596	728	4.03E-17	78.5153	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#11080 - 	CGI_10015032	superfamily	247769	1379	1555	1.09E-13	70.8313	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#11080 - 	CGI_10015032	superfamily	248010	1103	1255	2.98E-27	110.549	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#11080 - 	CGI_10015032	superfamily	248010	229	376	2.13E-08	54.3096	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#11081 - 	CGI_10015033	superfamily	247986	276	369	8.80E-15	73.5614	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#11081 - 	CGI_10015033	superfamily	247986	489	624	4.46E-05	43.901	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#11081 - 	CGI_10015033	superfamily	245225	16	232	5.21E-38	145.146	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#11082 - 	CGI_10015034	superfamily	247986	4	87	8.32E-14	69.3242	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#11082 - 	CGI_10015034	superfamily	247986	207	342	1.26E-05	45.0566	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#11083 - 	CGI_10015035	superfamily	247684	8	176	1.35E-48	164.373	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11085 - 	CGI_10015037	superfamily	247684	1	189	2.25E-50	169.765	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11090 - 	CGI_10013910	superfamily	241867	21	96	3.01E-06	42.1554	cl00446	Lactamase_B superfamily	N	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#11091 - 	CGI_10013911	superfamily	245847	142	262	4.70E-20	83.7601	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#11091 - 	CGI_10013911	superfamily	241619	27	71	0.00760107	33.7097	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#11095 - 	CGI_10013915	superfamily	245040	26	100	1.25E-05	39.2071	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#11096 - 	CGI_10013916	superfamily	245040	25	83	0.000439274	34.5847	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#11097 - 	CGI_10013917	superfamily	245040	19	80	0.000186569	38.224	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#11097 - 	CGI_10013917	superfamily	245040	139	174	0.00107976	35.7403	cl09238	CY superfamily	NC	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#11098 - 	CGI_10013918	superfamily	248325	80	413	3.54E-88	272.639	cl17771	Methyltransf_5 superfamily	 - 	 - 	MraW methylase family; Members of this family are probably SAM dependent methyltransferases based on Escherichia coli rsmH. This family appears to be related to pfam01596.
Q#11100 - 	CGI_10013920	superfamily	246679	6	128	3.93E-67	201.265	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#11101 - 	CGI_10013921	superfamily	241768	179	351	4.30E-42	146.87	cl00305	Sua5_yciO_yrdC superfamily	 - 	 - 	Telomere recombination; This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.
Q#11103 - 	CGI_10013923	superfamily	241768	43	229	6.15E-29	109.121	cl00305	Sua5_yciO_yrdC superfamily	 - 	 - 	Telomere recombination; This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.
Q#11104 - 	CGI_10013924	superfamily	247866	8	203	1.22E-28	109.079	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#11105 - 	CGI_10013925	superfamily	242187	57	499	1.29E-36	140.15	cl00912	MmgE_PrpD superfamily	 - 	 - 	MmgE/PrpD family; This family includes 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyzes the third step of the 2-methylcitric acid cycle.
Q#11108 - 	CGI_10013928	superfamily	241737	58	333	9.76E-137	394.3	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#11110 - 	CGI_10013930	superfamily	204056	354	406	2.43E-10	56.3373	cl07395	DEK_C superfamily	 - 	 - 	DEK C terminal domain; DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family. This domain is also found in chitin synthase proteins and in protein phosphatases.
Q#11114 - 	CGI_10016255	superfamily	248312	13	164	2.21E-07	46.9629	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#11115 - 	CGI_10016256	superfamily	241563	68	109	7.45E-06	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11116 - 	CGI_10016257	superfamily	245084	29	349	0	661.472	cl09506	catalase_like superfamily	 - 	 - 	"Catalase-like heme-binding proteins and protein domains; Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity."
Q#11116 - 	CGI_10016257	superfamily	245084	351	397	1.29E-12	67.557	cl09506	catalase_like superfamily	N	 - 	"Catalase-like heme-binding proteins and protein domains; Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity."
Q#11117 - 	CGI_10016258	superfamily	242385	163	449	0	580.608	cl01244	arom_aa_hydroxylase superfamily	 - 	 - 	"Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers."
Q#11117 - 	CGI_10016258	superfamily	245020	66	138	1.55E-29	110.921	cl09141	ACT superfamily	 - 	 - 	"ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but  the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times."
Q#11118 - 	CGI_10016259	superfamily	241787	1	49	3.89E-07	43.7374	cl00326	Ribosomal_L23 superfamily	C	 - 	Ribosomal protein L23; Ribosomal protein L23.  
Q#11119 - 	CGI_10016260	superfamily	241567	178	308	6.84E-25	100.367	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#11119 - 	CGI_10016260	superfamily	241567	42	155	8.13E-07	47.9803	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#11120 - 	CGI_10016261	superfamily	245605	22	90	1.60E-36	130.43	cl11409	RNAP_RPB11_RPB3 superfamily	 - 	 - 	"RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts."
Q#11120 - 	CGI_10016261	superfamily	241567	101	239	1.03E-29	116.546	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#11120 - 	CGI_10016261	superfamily	241567	440	530	0.000290325	41.432	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#11121 - 	CGI_10016262	superfamily	245213	72	112	3.26E-11	54.565	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11121 - 	CGI_10016262	superfamily	241571	14	68	6.10E-05	38.9327	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#11122 - 	CGI_10016263	superfamily	243831	17	178	1.84E-50	177.846	cl04653	TAF7 superfamily	 - 	 - 	"TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and is not universally involved for transcription as are GTFs. TAF7 is involved in the regulation of the transition from PIC assembly to initiation and elongation. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers."
Q#11122 - 	CGI_10016263	superfamily	247684	360	788	3.59E-72	249.117	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11123 - 	CGI_10016264	superfamily	247684	11	428	2.03E-107	330.779	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11129 - 	CGI_10016270	superfamily	220695	112	240	2.04E-06	47.9587	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#11130 - 	CGI_10016271	superfamily	246751	54	348	1.25E-109	328.819	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#11131 - 	CGI_10016272	superfamily	246751	1	275	1.82E-115	336.138	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#11134 - 	CGI_10016275	superfamily	246751	1	178	6.27E-69	213.259	cl14883	Lipase superfamily	N	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#11135 - 	CGI_10016276	superfamily	246751	59	352	1.20E-107	319.189	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#11136 - 	CGI_10016277	superfamily	241563	98	138	2.31E-07	48.2444	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11137 - 	CGI_10016011	superfamily	245531	9	87	2.93E-10	52.3935	cl11158	BEN superfamily	 - 	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#11141 - 	CGI_10016015	superfamily	241583	395	567	6.52E-25	103.857	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#11142 - 	CGI_10016016	superfamily	241578	1	152	8.77E-29	116.237	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11142 - 	CGI_10016016	superfamily	241568	2089	2145	3.60E-07	50.154	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1684	1738	2.16E-06	47.8428	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1971	2026	5.91E-06	46.6872	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1283	1337	1.17E-05	45.9168	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1455	1509	1.28E-05	45.5316	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	939	993	1.55E-05	45.5316	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	235	289	3.55E-05	44.376	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	2262	2316	0.00012806	42.8352	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	178	231	0.000206618	42.0648	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	2148	2202	0.000344014	41.2944	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1569	1624	0.00069444	40.524	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	768	822	0.000706774	40.524	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	349	403	0.000825637	40.1388	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	996	1050	0.00140676	39.3684	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1167	1217	0.00150021	39.3684	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	566	620	0.00315669	38.598	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	825	879	0.00508527	37.8276	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1340	1395	0.00558025	37.8276	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1798	1853	0.00652644	37.4424	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1627	1681	0.00750045	37.4424	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1398	1452	0.00792475	37.0572	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	292	346	0.00945493	37.0572	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	243119	2344	2386	0.00266198	38.579	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11142 - 	CGI_10016016	superfamily	241568	1110	1163	0.00759221	37.1696	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	882	935	0.00859975	37.1696	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11142 - 	CGI_10016016	superfamily	241568	1914	1967	0.00892065	37.1209	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11143 - 	CGI_10016017	superfamily	218263	532	664	2.51E-39	141.487	cl04748	DUF547 superfamily	 - 	 - 	"Protein of unknown function, DUF547; Family of uncharacterized proteins from C. elegans and A. thaliana."
Q#11143 - 	CGI_10016017	superfamily	243119	48	98	0.000197544	40.1097	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11143 - 	CGI_10016017	superfamily	247824	416	480	0.00606666	36.6137	cl17270	APH_ChoK_like superfamily	N	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#11144 - 	CGI_10016018	superfamily	245606	56	210	9.29E-60	198.525	cl11410	TPP_enzyme_PYR superfamily	 - 	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#11144 - 	CGI_10016018	superfamily	242611	453	626	1.95E-51	176.184	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#11144 - 	CGI_10016018	superfamily	215786	274	411	1.04E-14	71.8133	cl18345	TPP_enzyme_M superfamily	 - 	 - 	"Thiamine pyrophosphate enzyme, central domain; The central domain of TPP enzymes contains a 2-fold Rossman fold."
Q#11145 - 	CGI_10016019	superfamily	248458	463	623	4.91E-10	60.4053	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11145 - 	CGI_10016019	superfamily	248458	36	182	5.18E-07	50.7753	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11146 - 	CGI_10016020	superfamily	241659	134	210	2.84E-25	97.5906	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#11146 - 	CGI_10016020	superfamily	241659	270	348	1.52E-21	87.5754	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#11147 - 	CGI_10016021	superfamily	248097	131	241	1.64E-24	95.0246	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11147 - 	CGI_10016021	superfamily	247746	16	90	0.00297245	35.3118	cl17192	ATP-synt_B superfamily	N	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#11148 - 	CGI_10016022	superfamily	248097	271	381	4.80E-22	90.017	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11148 - 	CGI_10016022	superfamily	147120	71	174	0.00245117	36.5828	cl04763	Cor1 superfamily	 - 	 - 	"Cor1/Xlr/Xmr conserved region; Cor1 is a component of the chromosome core in the meiotic prophase chromosomes. Xlr is a lymphoid cell specific protein. Xlm is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner. The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes."
Q#11149 - 	CGI_10016023	superfamily	248097	310	417	2.98E-23	93.869	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11151 - 	CGI_10016025	superfamily	243029	16	41	0.00173982	32.7078	cl02422	HRM superfamily	C	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#11154 - 	CGI_10016028	superfamily	247743	295	434	3.05E-23	99.1427	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#11154 - 	CGI_10016028	superfamily	144608	243	262	0.000255461	42.8873	cl18013	Mg_chelatase superfamily	C	 - 	"Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa."
Q#11154 - 	CGI_10016028	superfamily	204202	501	533	0.00750814	36.4645	cl07827	Vps4_C superfamily	N	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#11163 - 	CGI_10000733	superfamily	242685	1	93	1.60E-38	133.086	cl01749	UPF0160 superfamily	N	 - 	Uncharacterized protein family (UPF0160); This family of proteins contains a large number of metal binding residues. The patterns are suggestive of a phosphoesterase function. The conserved DHH motif may mean this family is related to pfam01368.
Q#11164 - 	CGI_10016812	superfamily	247724	24	171	7.45E-87	256.339	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11165 - 	CGI_10016813	superfamily	241900	42	320	2.78E-112	329.769	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#11167 - 	CGI_10016815	superfamily	241672	67	294	2.17E-71	224.029	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#11169 - 	CGI_10016817	superfamily	247068	455	551	1.33E-25	103.547	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11169 - 	CGI_10016817	superfamily	247068	242	341	1.43E-25	103.162	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11169 - 	CGI_10016817	superfamily	247068	559	654	7.42E-21	89.6801	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11169 - 	CGI_10016817	superfamily	247068	356	447	4.06E-17	78.8945	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11169 - 	CGI_10016817	superfamily	247068	135	233	1.31E-16	77.3537	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11169 - 	CGI_10016817	superfamily	247068	674	757	1.13E-07	51.1602	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11169 - 	CGI_10016817	superfamily	247068	9	94	2.10E-10	59.0435	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11170 - 	CGI_10016818	superfamily	247068	220	320	3.16E-27	108.17	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11170 - 	CGI_10016818	superfamily	247068	434	530	5.37E-23	95.8433	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11170 - 	CGI_10016818	superfamily	247068	540	634	1.19E-20	89.2949	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11170 - 	CGI_10016818	superfamily	247068	109	212	2.17E-20	88.5245	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11170 - 	CGI_10016818	superfamily	247068	335	426	9.77E-16	75.0425	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11170 - 	CGI_10016818	superfamily	247068	654	736	1.15E-15	74.6573	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11170 - 	CGI_10016818	superfamily	247068	2	78	8.48E-08	51.3395	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11172 - 	CGI_10016820	superfamily	248458	487	737	1.96E-14	74.2725	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11172 - 	CGI_10016820	superfamily	248458	194	299	1.31E-07	53.0865	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11173 - 	CGI_10016821	superfamily	220238	51	151	2.43E-26	99.2888	cl18552	DUF2012 superfamily	 - 	 - 	Protein of unknown function (DUF2012); This is a eukaryotic family of uncharacterized proteins.
Q#11174 - 	CGI_10016822	superfamily	248345	551	674	5.23E-38	138.926	cl17791	SAC3_GANP superfamily	 - 	 - 	"SAC3/GANP/Nin1/mts3/eIF-3 p25 family; This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits."
Q#11177 - 	CGI_10016825	superfamily	218721	14	366	1.60E-64	215.058	cl05344	TROVE superfamily	 - 	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#11178 - 	CGI_10016826	superfamily	243072	116	183	1.58E-13	67.7938	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11179 - 	CGI_10016827	superfamily	248264	46	214	2.81E-18	79.9737	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#11180 - 	CGI_10016828	superfamily	110440	97	123	0.000208047	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11182 - 	CGI_10016830	superfamily	243092	11	32	0.00250558	31.1684	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11183 - 	CGI_10016831	superfamily	243092	11	90	4.73E-09	50.7964	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11185 - 	CGI_10016833	superfamily	222150	136	154	0.00196285	33.9045	cl16282	zf-H2C2_2 superfamily	C	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11185 - 	CGI_10016833	superfamily	222150	107	132	0.00239574	33.5193	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11186 - 	CGI_10016834	superfamily	243092	15	255	2.63E-44	153.645	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11187 - 	CGI_10016835	superfamily	241563	69	109	3.37E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11187 - 	CGI_10016835	superfamily	241563	15	60	0.00669859	34.7624	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11188 - 	CGI_10016836	superfamily	117343	17	71	1.08E-14	66.3185	cl07399	CathepsinC_exc superfamily	C	 - 	"Cathepsin C exclusion domain; Cathepsin C (dipeptidyl peptidase I) is the physiological activator of a group of serine proteases. This domain corresponds to the exclusion domain whose structure excludes the approach of a polypeptide apart from its termini. It forms an enclosed beta barrel structure composed from 8 anti-parallel beta strands. Based on a structural comparison and interaction data, it is suggested that the exclusion domain originates from a metallo-protease inhibitor."
Q#11189 - 	CGI_10016837	superfamily	247724	22	180	1.58E-111	317.723	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11190 - 	CGI_10016838	superfamily	247724	106	308	1.70E-87	269.79	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11190 - 	CGI_10016838	superfamily	207690	55	77	0.00642841	34.6329	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#11197 - 	CGI_10000848	superfamily	245814	17	97	0.000994005	34.7885	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11198 - 	CGI_10001011	superfamily	238012	229	287	1.18E-05	42.3414	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#11198 - 	CGI_10001011	superfamily	243198	2	227	2.21E-86	264.222	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#11198 - 	CGI_10001011	superfamily	238012	288	333	0.000728128	37.3338	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#11200 - 	CGI_10014349	superfamily	150784	106	485	6.01E-103	319.559	cl10848	DUF2359 superfamily	 - 	 - 	"Uncharacterized conserved protein (DUF2359); This is a 450 amino acid region of a family of proteins conserved from insects to humans. The mouse protein, Q8BM55, is annotated as being a putative Vitamin K-dependent carboxylation gamma-carboxyglutamic (GLA) domain containing protein, but this could not be confirmed. The function is not known."
Q#11201 - 	CGI_10014350	superfamily	222429	9	84	1.40E-05	39.5313	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#11202 - 	CGI_10014351	superfamily	217473	133	324	6.22E-23	98.9765	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#11206 - 	CGI_10014355	superfamily	241600	91	290	4.98E-80	244.072	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11207 - 	CGI_10014356	superfamily	241600	131	328	4.43E-82	252.161	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11208 - 	CGI_10014357	superfamily	241600	32	207	2.79E-73	223.271	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11209 - 	CGI_10014358	superfamily	245213	166	206	6.33E-11	55.7206	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11209 - 	CGI_10014358	superfamily	241571	71	162	1.09E-07	48.1775	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#11210 - 	CGI_10014359	superfamily	241600	137	353	1.59E-94	283.362	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11210 - 	CGI_10014359	superfamily	241619	37	81	0.00028797	38.3321	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#11211 - 	CGI_10014360	superfamily	241600	125	345	1.86E-93	280.281	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11211 - 	CGI_10014360	superfamily	241619	37	81	0.000221476	38.7173	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#11212 - 	CGI_10014361	superfamily	248458	286	471	3.22E-10	60.4053	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11212 - 	CGI_10014361	superfamily	248458	73	224	0.00749326	37.2933	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11220 - 	CGI_10014369	superfamily	241546	564	683	8.29E-41	149.348	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#11220 - 	CGI_10014369	superfamily	248011	1496	1566	0.000166302	42.0142	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#11220 - 	CGI_10014369	superfamily	243086	454	505	0.00125704	39.293	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#11220 - 	CGI_10014369	superfamily	248011	1603	1677	0.00234116	38.5862	cl17457	PKD superfamily	N	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#11220 - 	CGI_10014369	superfamily	248011	1706	1753	0.00879091	37.0066	cl17457	PKD superfamily	C	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#11223 - 	CGI_10001097	superfamily	245213	28	61	4.46E-06	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11223 - 	CGI_10001097	superfamily	246918	75	126	4.80E-14	65.6859	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11223 - 	CGI_10001097	superfamily	221695	10	31	3.27E-06	43.2126	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#11224 - 	CGI_10001167	superfamily	241563	72	109	4.39E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11224 - 	CGI_10001167	superfamily	241563	21	58	0.00700125	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11225 - 	CGI_10022791	superfamily	193256	241	451	2.08E-65	216.352	cl18189	AAA_8 superfamily	C	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#11225 - 	CGI_10022791	superfamily	193251	6	204	1.11E-40	148.546	cl18188	AAA_7 superfamily	N	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#11225 - 	CGI_10022791	superfamily	193253	491	540	5.50E-07	50.4205	cl15084	MT superfamily	NC	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#11226 - 	CGI_10022792	superfamily	193251	1466	1581	1.02E-16	81.5208	cl18188	AAA_7 superfamily	C	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#11226 - 	CGI_10022792	superfamily	193256	240	292	5.80E-09	57.65	cl18189	AAA_8 superfamily	NC	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#11226 - 	CGI_10022792	superfamily	241619	39	102	0.00022386	41.4137	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#11226 - 	CGI_10022792	superfamily	247743	894	1015	0.00281984	38.4304	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#11227 - 	CGI_10022793	superfamily	245206	5	139	4.46E-42	141.284	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#11228 - 	CGI_10022794	superfamily	245206	5	233	4.58E-62	197.138	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#11229 - 	CGI_10022795	superfamily	245206	5	233	1.01E-62	199.064	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#11230 - 	CGI_10022796	superfamily	245847	41	156	0.00137951	37.8672	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#11231 - 	CGI_10022797	superfamily	241563	61	96	0.00223025	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11235 - 	CGI_10022802	superfamily	245226	38	152	2.44E-14	66.5552	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#11237 - 	CGI_10022804	superfamily	246925	122	309	7.87E-09	57.3654	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#11237 - 	CGI_10022804	superfamily	246925	2	207	1.20E-05	47.3502	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#11239 - 	CGI_10022806	superfamily	242087	462	589	5.42E-27	107.943	cl00781	DUF389 superfamily	 - 	 - 	Domain of unknown function (DUF389); Family of hypothetical bacterial proteins with an undetermined function.
Q#11240 - 	CGI_10022807	superfamily	220653	104	156	4.24E-12	58.5371	cl10936	PP28 superfamily	C	 - 	"Casein kinase substrate phosphoprotein PP28; This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II."
Q#11241 - 	CGI_10022808	superfamily	243100	278	339	1.58E-10	56.4183	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#11243 - 	CGI_10022810	superfamily	222005	55	136	3.75E-08	51.9692	cl18632	AAA_19 superfamily	 - 	 - 	Part of AAA domain; Part of AAA domain.  
Q#11244 - 	CGI_10022811	superfamily	247637	9	371	0	710.537	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#11246 - 	CGI_10022813	superfamily	247916	318	369	0.000316691	39.2883	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#11251 - 	CGI_10022818	superfamily	243088	544	660	2.90E-51	174.073	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#11251 - 	CGI_10022818	superfamily	243142	13	106	1.01E-21	91.9191	cl02689	RUN superfamily	N	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#11251 - 	CGI_10022818	superfamily	191369	338	516	0.00989919	36.3162	cl05372	DUF837 superfamily	 - 	 - 	Protein of unknown function (DUF837); This family consists of several eukaryotic proteins of unknown function. One of the family members is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke).
Q#11252 - 	CGI_10022819	superfamily	243142	54	197	9.73E-27	104.245	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#11253 - 	CGI_10022820	superfamily	241809	41	165	2.63E-40	135.312	cl00353	Ribosomal_L16_L10e superfamily	 - 	 - 	"Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus."
Q#11257 - 	CGI_10022824	superfamily	241550	241	604	3.32E-169	488.681	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#11257 - 	CGI_10022824	superfamily	247744	41	190	1.31E-91	281.674	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#11258 - 	CGI_10022825	superfamily	245601	235	396	7.52E-23	95.9039	cl11399	HP superfamily	N	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#11260 - 	CGI_10022827	superfamily	243061	1	99	6.18E-29	101.65	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11261 - 	CGI_10022828	superfamily	243061	14	96	8.35E-11	56.9666	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11262 - 	CGI_10001181	superfamily	243092	42	158	2.00E-10	56.1892	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11263 - 	CGI_10001182	superfamily	241563	62	102	6.77E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11264 - 	CGI_10001199	superfamily	246684	30	125	2.22E-42	138.078	cl14651	RNA_pol_Rpb6 superfamily	N	 - 	"RNA polymerase Rpb6; Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly."
Q#11265 - 	CGI_10001200	superfamily	214545	425	565	2.51E-54	184.06	cl10551	CULLIN superfamily	 - 	 - 	Cullin; Cullin.  
Q#11265 - 	CGI_10001200	superfamily	245539	688	755	5.21E-22	91.0761	cl11186	Cullin_Nedd8 superfamily	 - 	 - 	"Cullin protein neddylation domain; This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue."
Q#11267 - 	CGI_10022543	superfamily	221312	415	577	5.50E-78	247.873	cl13369	Vac14_Fig4_bd superfamily	 - 	 - 	"Vacuolar protein 14 C-terminal Fig4p binding; Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. The C-terminal region of Vac14 binds to Fig4p. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system."
Q#11267 - 	CGI_10022543	superfamily	193231	66	162	1.97E-38	136.915	cl15071	Vac14_Fab1_bd superfamily	 - 	 - 	"Vacuolar 14 Fab1-binding region; Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. This domain appears to be the one responsible for binding to Fab1. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system."
Q#11268 - 	CGI_10022544	superfamily	216411	110	170	0.000300087	38.4119	cl15974	MARVEL superfamily	NC	 - 	"Membrane-associating domain; MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis."
Q#11269 - 	CGI_10022545	superfamily	241680	39	206	2.08E-44	152.022	cl00200	MIP superfamily	C	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#11271 - 	CGI_10022547	superfamily	241680	15	222	2.35E-53	175.134	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#11273 - 	CGI_10022549	superfamily	247856	21	81	2.45E-11	55.2465	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11273 - 	CGI_10022549	superfamily	247856	56	130	2.31E-09	49.8537	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11274 - 	CGI_10022550	superfamily	243061	769	869	6.91E-38	138.244	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11274 - 	CGI_10022550	superfamily	243061	443	544	1.00E-34	129.384	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11274 - 	CGI_10022550	superfamily	243061	662	763	1.36E-34	128.999	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11274 - 	CGI_10022550	superfamily	243061	117	218	7.01E-34	126.688	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11274 - 	CGI_10022550	superfamily	243061	225	326	8.62E-33	123.606	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11274 - 	CGI_10022550	superfamily	243061	553	653	1.42E-29	114.361	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11274 - 	CGI_10022550	superfamily	243061	335	435	6.15E-29	112.821	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11274 - 	CGI_10022550	superfamily	243061	9	109	1.55E-28	111.665	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11275 - 	CGI_10022551	superfamily	242281	41	267	6.77E-45	155.225	cl01067	Dyp_perox superfamily	N	 - 	Dyp-type peroxidase family; This family of dye-decolourising peroxidases lack a typical heme-binding region.
Q#11276 - 	CGI_10022552	superfamily	207654	221	286	1.27E-22	88.6538	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#11276 - 	CGI_10022552	superfamily	207654	145	211	4.15E-17	73.2458	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#11276 - 	CGI_10022552	superfamily	207654	28	99	6.75E-16	70.1642	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#11276 - 	CGI_10022552	superfamily	207654	1	21	0.00910864	33.5702	cl02574	Annexin superfamily	N	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#11277 - 	CGI_10022553	superfamily	201431	615	727	2.32E-41	147.269	cl08290	THF_DHG_CYH superfamily	 - 	 - 	"Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain.  "
Q#11278 - 	CGI_10022554	superfamily	245323	165	442	2.28E-163	478.276	cl10511	Beach superfamily	 - 	 - 	"BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins."
Q#11278 - 	CGI_10022554	superfamily	247725	75	136	9.19E-16	74.6391	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11278 - 	CGI_10022554	superfamily	243092	557	811	1.73E-17	82.768	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11279 - 	CGI_10022555	superfamily	217473	61	347	1.59E-100	301.591	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#11281 - 	CGI_10022557	superfamily	219043	1886	2062	5.06E-83	272.094	cl05796	DUF1088 superfamily	 - 	 - 	Domain of Unknown Function (DUF1088); This family is found in the neurobeachins. The function of this region is not known.
Q#11281 - 	CGI_10022557	superfamily	241611	216	386	1.11E-12	68.184	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#11281 - 	CGI_10022557	superfamily	247725	2069	2102	4.96E-05	43.8232	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11282 - 	CGI_10022558	superfamily	247724	102	370	1.39E-147	425.421	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11285 - 	CGI_10022561	superfamily	243091	1788	1909	3.24E-37	138.621	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#11285 - 	CGI_10022561	superfamily	248279	1443	1521	8.05E-26	104.756	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#11285 - 	CGI_10022561	superfamily	243126	1565	1621	1.17E-21	91.4983	cl02650	FYRN superfamily	 - 	 - 	F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.
Q#11285 - 	CGI_10022561	superfamily	243127	1623	1708	7.12E-20	87.3618	cl02651	FYRC superfamily	 - 	 - 	F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.
Q#11285 - 	CGI_10022561	superfamily	214703	1911	1927	0.00219995	38.1552	cl02636	PostSET superfamily	 - 	 - 	Cysteine-rich motif following a subset of SET domains; Cysteine-rich motif following a subset of SET domains.  
Q#11286 - 	CGI_10022562	superfamily	148739	138	239	3.47E-18	80.7582	cl06366	SRA1 superfamily	N	 - 	Steroid receptor RNA activator (SRA1); This family consists of several hypothetical mammalian steroid receptor RNA activator proteins. SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs.
Q#11286 - 	CGI_10022562	superfamily	148739	247	356	6.44E-16	74.2098	cl06366	SRA1 superfamily	N	 - 	Steroid receptor RNA activator (SRA1); This family consists of several hypothetical mammalian steroid receptor RNA activator proteins. SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs.
Q#11287 - 	CGI_10022563	superfamily	212596	390	481	1.22E-29	113.494	cl17033	SOAR superfamily	 - 	 - 	"STIM1 Orai1-activating region; STIM1 (stromal interaction module 1) is a metazoan transmembrane protein located in the endoplasmic reticulum (ER) membrane, which functions as a sensor for ER calcium ion levels and activates store-operated Ca2+ influx channels (SOCs), such as the Orai1 Ca2+ channel located in the plasma membrane. STIM1 has an N-terminal Ca-binding EF-hand domain, which is located in the ER lumen. Responding to the release of Ca2+ from the ER, STIM1 was found to aggregate near the plasma membrane and contact Orai1. This model describes a region near the C-terminus of STIM1, which has been shown to mediate the interaction with Orai1 and has been labeled SOAR (STIM1 Orai1-activating region). STIM1 has also been linked to sensing oxidative and temperature-variation stress and may play a rather general role in mediating calcium signaling in response to stress. Dimerization of STIM1 via the SOAR domain appears required for the activation of the Orai1 calcium channel. A model for STIM1 activation has been proposed, in which an inhibitory helix N-terminal to the SOAR domain prevents STIM1 clustering or aggregation, and in which conformational changes triggered by depletion of the calcium stores allow the clustering and activation of Orai1."
Q#11287 - 	CGI_10022563	superfamily	247057	182	255	4.16E-29	111.271	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#11288 - 	CGI_10022564	superfamily	243095	515	716	3.30E-81	263.532	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#11291 - 	CGI_10022567	superfamily	241900	411	583	1.45E-09	57.7956	cl00490	EEP superfamily	C	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#11292 - 	CGI_10022568	superfamily	245596	52	272	1.98E-108	316.817	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#11299 - 	CGI_10022575	superfamily	248458	9	166	2.63E-11	63.4869	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11299 - 	CGI_10022575	superfamily	248458	234	382	0.000146902	42.3009	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11301 - 	CGI_10022577	superfamily	247727	55	181	1.20E-06	44.7283	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#11302 - 	CGI_10022578	superfamily	245864	34	102	1.34E-13	68.0738	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#11303 - 	CGI_10022579	superfamily	246723	223	466	1.68E-98	311.16	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#11303 - 	CGI_10022579	superfamily	248136	102	208	4.27E-51	171.732	cl17582	Sybindin superfamily	 - 	 - 	"Sybindin-like family; Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses."
Q#11304 - 	CGI_10022580	superfamily	243072	38	161	1.13E-34	125.959	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11304 - 	CGI_10022580	superfamily	243072	169	290	7.67E-33	120.566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11304 - 	CGI_10022580	superfamily	243072	268	331	4.80E-07	47.7634	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11305 - 	CGI_10022581	superfamily	245614	1	57	0.000106412	38.7856	cl11433	FtsL superfamily	C	 - 	"Cell division protein FtsL; In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein pfam04977, however this interaction may be indirect."
Q#11307 - 	CGI_10022583	superfamily	245814	50	110	0.000290203	39.344	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11308 - 	CGI_10022584	superfamily	245304	1	92	3.25E-42	152.329	cl10459	Peptidases_S8_S53 superfamily	C	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#11308 - 	CGI_10022584	superfamily	201820	220	300	1.31E-25	99.6222	cl08326	P_proprotein superfamily	 - 	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#11308 - 	CGI_10022584	superfamily	245304	92	179	2.01E-25	104.179	cl10459	Peptidases_S8_S53 superfamily	N	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#11309 - 	CGI_10001342	superfamily	215647	585	774	1.36E-33	130.036	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#11315 - 	CGI_10001479	superfamily	243161	4	86	3.97E-13	61.2561	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#11316 - 	CGI_10001480	superfamily	206130	178	269	0.000477244	39.1091	cl16501	DUF4218 superfamily	C	 - 	Domain of unknown function (DUF4218); Domain of unknown function (DUF4218).  
Q#11317 - 	CGI_10001636	superfamily	245864	1	415	3.65E-62	209.442	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#11319 - 	CGI_10001056	superfamily	222150	29	54	2.28E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11319 - 	CGI_10001056	superfamily	222150	57	80	0.000393989	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11319 - 	CGI_10001056	superfamily	246975	16	37	0.00869124	34.6301	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#11320 - 	CGI_10002345	superfamily	248458	87	219	3.01E-06	46.5381	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11321 - 	CGI_10002346	superfamily	247743	8	148	3.45E-16	73.3793	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#11321 - 	CGI_10002346	superfamily	209247	156	243	4.41E-10	54.7571	cl11083	ClpB_D2-small superfamily	 - 	 - 	"C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighboring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724."
Q#11322 - 	CGI_10002347	superfamily	219667	73	156	1.97E-33	121.176	cl06829	Swi3 superfamily	 - 	 - 	"Replication Fork Protection Component Swi3; Replication fork pausing is required to initiate a recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1 Swi3, together with Swi1, define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks. The Swi1-Swi3 complex is required for accurate replication, fork protection and replication checkpoint signalling"
Q#11325 - 	CGI_10002419	superfamily	114049	71	187	5.27E-44	150.681	cl05052	Mec-17 superfamily	 - 	 - 	Touch receptor neuron protein Mec-17; Mec-17 is the protein product of one of the 18 genes required for the development and function of the touch receptor neuron for gentle touch. Mec-17 is specifically required for maintaining the differentiation of the touch receptor. This family is conserved to higher eukaryotes.
Q#11326 - 	CGI_10002420	superfamily	247803	159	243	4.17E-25	101.155	cl17249	YlqF_related_GTPase superfamily	C	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#11326 - 	CGI_10002420	superfamily	247803	328	384	1.01E-24	99.9991	cl17249	YlqF_related_GTPase superfamily	N	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#11327 - 	CGI_10002421	superfamily	245303	32	363	6.33E-143	422.738	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#11331 - 	CGI_10002937	superfamily	241868	52	159	1.15E-29	106.805	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#11332 - 	CGI_10002938	superfamily	177822	36	247	1.74E-13	69.1785	cl18088	PLN02164 superfamily	 - 	 - 	sulfotransferase
Q#11332 - 	CGI_10002938	superfamily	238012	298	319	0.00671188	33.867	cl11390	EGF_Lam superfamily	NC	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#11335 - 	CGI_10003954	superfamily	245205	150	231	6.20E-09	54.9365	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#11335 - 	CGI_10003954	superfamily	245205	33	100	0.000291174	40.6841	cl09930	RPA_2b-aaRSs_OBF_like superfamily	C	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#11335 - 	CGI_10003954	superfamily	241578	505	679	8.75E-22	95.5389	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11335 - 	CGI_10003954	superfamily	241578	1264	1360	2.98E-11	63.5673	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11335 - 	CGI_10003954	superfamily	217211	727	793	1.95E-08	53.4422	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#11338 - 	CGI_10001075	superfamily	247905	161	300	9.20E-20	84.2116	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#11338 - 	CGI_10001075	superfamily	247805	23	131	6.67E-07	47.332	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#11340 - 	CGI_10001077	superfamily	110440	213	239	0.00320276	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11341 - 	CGI_10003999	superfamily	241550	39	325	2.34E-88	269.861	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#11342 - 	CGI_10004000	superfamily	247739	63	232	8.67E-54	177.816	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#11344 - 	CGI_10004002	superfamily	241568	74	133	1.38E-07	49.7688	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11344 - 	CGI_10004002	superfamily	245213	453	487	1.77E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11344 - 	CGI_10004002	superfamily	241568	148	195	0.000299548	39.7536	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#11344 - 	CGI_10004002	superfamily	245213	490	526	0.000640925	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11344 - 	CGI_10004002	superfamily	246918	534	585	1.00E-16	76.0863	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#11344 - 	CGI_10004002	superfamily	219525	710	755	2.27E-07	48.9545	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#11344 - 	CGI_10004002	superfamily	111397	195	277	7.67E-07	47.7211	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#11346 - 	CGI_10014927	superfamily	246664	335	710	2.96E-155	458.963	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#11347 - 	CGI_10014928	superfamily	246664	191	318	1.34E-26	109.707	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#11348 - 	CGI_10014929	superfamily	241802	59	359	1.69E-136	403.818	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#11348 - 	CGI_10014929	superfamily	246936	513	637	2.47E-47	162.88	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#11348 - 	CGI_10014929	superfamily	246936	402	500	3.81E-37	134.76	cl15354	CBS_pair superfamily	C	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#11349 - 	CGI_10014930	superfamily	245201	417	688	5.42E-77	250.146	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11349 - 	CGI_10014930	superfamily	245814	246	302	0.000250671	39.7799	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11349 - 	CGI_10014930	superfamily	245814	146	208	0.00109279	37.8539	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11349 - 	CGI_10014930	superfamily	245814	73	127	0.00380164	36.3131	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11350 - 	CGI_10014931	superfamily	247684	106	352	2.91E-51	180.936	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11350 - 	CGI_10014931	superfamily	247684	21	113	3.69E-15	76.1619	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11351 - 	CGI_10014932	superfamily	247684	95	327	1.90E-31	123.927	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11351 - 	CGI_10014932	superfamily	247684	18	109	1.81E-09	58.0575	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11352 - 	CGI_10014933	superfamily	247684	85	269	1.97E-30	120.075	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11352 - 	CGI_10014933	superfamily	247684	1	81	7.85E-17	80.3991	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11353 - 	CGI_10014934	superfamily	247684	22	114	6.89E-14	70.3839	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11353 - 	CGI_10014934	superfamily	247684	136	161	0.00545843	36.886	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11354 - 	CGI_10014935	superfamily	247684	28	317	2.98E-58	199.041	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11356 - 	CGI_10014937	superfamily	245201	400	497	4.78E-18	83.4401	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11356 - 	CGI_10014937	superfamily	245201	621	768	8.37E-21	92.9933	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11357 - 	CGI_10014938	superfamily	243072	594	691	2.06E-30	117.099	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11357 - 	CGI_10014938	superfamily	246675	306	549	6.80E-82	266.082	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#11357 - 	CGI_10014938	superfamily	246935	28	147	7.85E-19	83.9116	cl15347	CBM20 superfamily	 - 	 - 	"The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch."
Q#11357 - 	CGI_10014938	superfamily	243073	757	803	0.000168634	40.5453	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#11360 - 	CGI_10014941	superfamily	241886	81	226	2.08E-09	55.7242	cl00470	Aldo_ket_red superfamily	NC	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#11362 - 	CGI_10014943	superfamily	243026	34	242	4.79E-05	42.4431	cl02417	Myelin_PLP superfamily	 - 	 - 	Myelin proteolipid protein (PLP or lipophilin); Myelin proteolipid protein (PLP or lipophilin).  
Q#11363 - 	CGI_10014944	superfamily	248097	15	137	2.98E-22	86.165	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11364 - 	CGI_10014945	superfamily	248097	151	250	2.89E-18	78.0758	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11364 - 	CGI_10014945	superfamily	248097	1	96	2.49E-15	69.6014	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11365 - 	CGI_10003530	superfamily	243092	12	253	6.10E-38	136.311	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11366 - 	CGI_10003531	superfamily	241596	125	183	2.82E-17	73.0171	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#11367 - 	CGI_10003532	superfamily	243092	212	529	6.15E-30	119.747	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11368 - 	CGI_10003533	superfamily	245227	2	388	0	628.075	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#11370 - 	CGI_10003535	superfamily	245201	42	334	0	554.078	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11374 - 	CGI_10015431	superfamily	241587	8	65	1.18E-14	62.3066	cl00069	GGL superfamily	 - 	 - 	"G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors"
Q#11375 - 	CGI_10015432	superfamily	241587	139	193	1.29E-09	51.1358	cl00069	GGL superfamily	 - 	 - 	"G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors"
Q#11376 - 	CGI_10015433	superfamily	243092	40	331	7.09E-27	107.421	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11381 - 	CGI_10015438	superfamily	190277	30	95	2.51E-12	57.3104	cl03535	UCR_hinge superfamily	 - 	 - 	Ubiquinol-cytochrome C reductase hinge protein; The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c complex.
Q#11382 - 	CGI_10015439	superfamily	241567	13	96	3.00E-13	67.2403	cl00042	CASc superfamily	NC	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#11382 - 	CGI_10015439	superfamily	241567	253	356	4.92E-05	42.9728	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#11383 - 	CGI_10015440	superfamily	114645	45	365	1.66E-23	104.455	cl05479	MCLC superfamily	N	 - 	Mid-1-related chloride channel (MCLC); This family consists of several mid-1-related chloride channels. mid-1-related chloride channel (MCLC) proteins function as a chloride channel when incorporated in the planar lipid bilayer.
Q#11383 - 	CGI_10015440	superfamily	248097	402	522	8.87E-18	81.1574	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11386 - 	CGI_10015444	superfamily	245596	1	99	3.41E-35	129.735	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#11388 - 	CGI_10015446	superfamily	242274	10	161	4.88E-07	47.8913	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#11391 - 	CGI_10015449	superfamily	241589	48	169	6.74E-33	120.817	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#11391 - 	CGI_10015449	superfamily	241589	187	315	3.66E-32	118.891	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#11391 - 	CGI_10015449	superfamily	241589	324	394	1.96E-16	74.9779	cl00071	GLECT superfamily	C	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#11392 - 	CGI_10015450	superfamily	241609	1	73	1.30E-22	90.1299	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#11392 - 	CGI_10015450	superfamily	241609	251	327	4.86E-22	88.2039	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#11392 - 	CGI_10015450	superfamily	241609	157	240	1.86E-20	83.9667	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#11392 - 	CGI_10015450	superfamily	241609	81	156	6.02E-20	82.8111	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#11393 - 	CGI_10015451	superfamily	241589	375	492	6.77E-34	124.669	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#11393 - 	CGI_10015451	superfamily	241589	41	149	1.72E-29	112.728	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#11393 - 	CGI_10015451	superfamily	241589	280	359	1.54E-16	76.0903	cl00071	GLECT superfamily	C	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#11393 - 	CGI_10015451	superfamily	241589	173	264	1.20E-13	68.0444	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#11395 - 	CGI_10002561	superfamily	241580	211	286	1.51E-35	126.515	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#11397 - 	CGI_10002563	superfamily	247684	170	275	0.000621351	39.8796	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11397 - 	CGI_10002563	superfamily	247684	480	581	0.000378555	41.6786	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11397 - 	CGI_10002563	superfamily	247684	224	374	0.00240582	38.9822	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11398 - 	CGI_10002564	superfamily	241628	87	186	0.00269006	36.6313	cl00130	PseudoU_synth superfamily	C	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#11399 - 	CGI_10002565	superfamily	220611	3	106	4.95E-09	49.4655	cl10864	Laps superfamily	 - 	 - 	Learning-associated protein; This is a family of 121-amino acid secretory proteins. Laps functions in the regulation of neuronal cell adhesion and/or movement and synapse attachment. Laps binds to the ApC/EBP (Aplysia CCAAT/enhancer binding protein) promoter and activates the transcription of ApC/EBP mRNA.
Q#11400 - 	CGI_10004248	superfamily	245847	1	142	1.01E-16	72.2041	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#11401 - 	CGI_10004249	superfamily	245847	18	150	8.75E-15	69.1225	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#11401 - 	CGI_10004249	superfamily	242406	159	259	4.43E-14	66.8461	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#11402 - 	CGI_10004536	superfamily	148810	518	598	1.86E-16	77.9897	cl06447	Geminin superfamily	N	 - 	"Geminin; This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle."
Q#11404 - 	CGI_10004538	superfamily	245840	59	191	3.42E-10	56.5619	cl12022	Ribosomal_L18e superfamily	 - 	 - 	Ribosomal protein L18e/L15; This family includes eukaryotic L18 as well as prokaryotic L15.
Q#11405 - 	CGI_10004539	superfamily	217545	258	553	2.62E-113	355.089	cl04056	Peptidase_C54 superfamily	 - 	 - 	Peptidase family C54; Peptidase family C54.  
Q#11406 - 	CGI_10004540	superfamily	242564	42	114	3.73E-07	45.3285	cl01534	NDUFA12 superfamily	C	 - 	"NADH ubiquinone oxidoreductase subunit NDUFA12; This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologues. The family also contains a second related eukaryotic protein of unknown function, ."
Q#11407 - 	CGI_10004541	superfamily	241565	737	801	4.23E-07	48.4719	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#11407 - 	CGI_10004541	superfamily	241565	66	127	0.000658047	38.8419	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#11407 - 	CGI_10004541	superfamily	241565	844	900	0.00212005	37.3011	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#11408 - 	CGI_10005881	superfamily	246669	131	185	6.12E-13	65.4662	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#11410 - 	CGI_10005883	superfamily	248012	4	89	2.00E-07	44.6216	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11414 - 	CGI_10005887	superfamily	246680	445	533	0.00526861	35.4436	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#11415 - 	CGI_10005888	superfamily	241550	450	717	2.24E-98	317.651	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#11415 - 	CGI_10005888	superfamily	245839	719	853	1.66E-42	152.711	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#11415 - 	CGI_10005888	superfamily	241550	120	274	1.07E-81	271.813	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#11415 - 	CGI_10005888	superfamily	222257	302	392	5.86E-10	58.6415	cl16317	tRNA-synt_1_2 superfamily	C	 - 	"Leucyl-tRNA synthetase, Domain 2; This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4."
Q#11415 - 	CGI_10005888	superfamily	241634	970	1037	0.00107211	38.4899	cl00143	SynN superfamily	C	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#11416 - 	CGI_10005889	superfamily	243694	16	376	1.64E-127	377.325	cl04289	Tfb2 superfamily	 - 	 - 	Transcription factor Tfb2; Transcription factor Tfb2.  
Q#11417 - 	CGI_10005890	superfamily	246721	140	500	6.45E-116	366.968	cl14807	ACE1-Sec16-like superfamily	 - 	 - 	"Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16; COPII coat complex plays an important role in vesicular traffic of newly synthezised proteins from the endoplasmatic reticulum (ER) to the Golgi apparatus by mediating the formation of transport vesicles. COPII consists of an outer coat, made up of the scaffold proteins Sec31 and Sec13, and the cargo adaptor complex, Sec23 and Sec24, which are recruited by the small GTPase Sar1. Sec16 is involved in the early steps of the assembly process. Sec16 forms elongated heterotetramers with Sec13, Sec13-(Sec16)2-Sec13. It interacts with Sec13 by insertion of a single beta-blade to close the six-bladded beta propeller of Sec13. In the same way Sec13 interacts with Sec31 and Nup145C, a nuclear pore protein, all of these contain a structurally related ancestral coatomer element 1 (ACE1). Sec16 is believed to be a key component in maintaining the integrity of the ER exit site."
Q#11418 - 	CGI_10005891	superfamily	241900	1	103	0.00229577	34.3609	cl00490	EEP superfamily	N	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#11421 - 	CGI_10020153	superfamily	241972	2	188	3.84E-55	177.733	cl00600	Ribosomal_L7Ae superfamily	N	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#11422 - 	CGI_10020154	superfamily	247792	29	71	1.83E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11422 - 	CGI_10020154	superfamily	207713	97	147	1.30E-13	65.0537	cl02729	WWE superfamily	C	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#11425 - 	CGI_10020157	superfamily	217293	64	278	8.02E-82	256.791	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11425 - 	CGI_10020157	superfamily	202474	285	535	8.12E-40	144.719	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11427 - 	CGI_10020159	superfamily	217473	557	629	5.58E-05	43.893	cl03978	Mab-21 superfamily	NC	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#11429 - 	CGI_10020161	superfamily	241644	10	169	1.25E-57	193.573	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#11429 - 	CGI_10020161	superfamily	246722	192	364	1.14E-05	45.9501	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#11430 - 	CGI_10020162	superfamily	241574	487	721	3.72E-102	315.679	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#11430 - 	CGI_10020162	superfamily	247069	126	280	1.87E-31	120.953	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#11433 - 	CGI_10020165	superfamily	243072	110	202	2.62E-30	109.781	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11435 - 	CGI_10020167	superfamily	245213	407	435	0.00345938	35.6902	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11435 - 	CGI_10020167	superfamily	214531	201	235	4.43E-07	47.2113	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11437 - 	CGI_10020169	superfamily	248012	13	105	1.69E-12	60.3649	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11438 - 	CGI_10020170	superfamily	241563	63	100	0.00176002	35.726	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11440 - 	CGI_10020172	superfamily	110440	768	794	0.000102963	40.8541	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11442 - 	CGI_10020174	superfamily	247724	18	152	9.76E-95	300.093	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11442 - 	CGI_10020174	superfamily	247792	186	226	6.41E-12	62.4632	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11442 - 	CGI_10020174	superfamily	207684	416	450	0.00116114	38.1288	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#11442 - 	CGI_10020174	superfamily	128973	369	392	0.00137158	37.9722	cl02765	ZnF_Rad18 superfamily	 - 	 - 	Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Q#11447 - 	CGI_10020179	superfamily	243066	42	131	7.66E-36	126.899	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11447 - 	CGI_10020179	superfamily	152037	2	27	6.40E-11	56.9092	cl13109	Shal-type superfamily	 - 	 - 	Shal-type voltage-gated potassium channels; This family of proteins represents Shal-type voltage-gated potassium channels which interact with Kv channel-interacting proteins to modulate cell surface expression and function of Kv4 channels. The interaction of the Shal-type protein Kv4.2 and the Kv interacting protein KChiP1 forms a structure which is like the structure between calmodulin and its target peptides when they interact. Interactions of an N terminal alpha helix in Kv4.2 and a C terminal alpha helix in KChIP1 are essential for the modulation of Kv4.2 by KChIPs.
Q#11447 - 	CGI_10020179	superfamily	219619	328	369	0.00918597	34.1056	cl18518	Ion_trans_2 superfamily	C	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#11449 - 	CGI_10020181	superfamily	221286	75	164	3.28E-15	69.2048	cl13340	DUF3399 superfamily	 - 	 - 	"Domain of unknown function (DUF3399); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 100 amino acids in length. This domain is found associated with pfam02214, pfam00520."
Q#11450 - 	CGI_10020182	superfamily	241578	19	196	1.69E-44	156.606	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11450 - 	CGI_10020182	superfamily	148333	431	558	1.12E-08	54.2094	cl05947	ITI_HC_C superfamily	C	 - 	"Inter-alpha-trypsin inhibitor heavy chain C-terminus; This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix. All family members contain the pfam00092 domain."
Q#11451 - 	CGI_10020183	superfamily	110440	89	110	0.00377798	32.7649	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11454 - 	CGI_10020186	superfamily	248264	54	139	1.35E-05	41.4538	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#11459 - 	CGI_10020191	superfamily	241610	131	181	1.50E-12	59.571	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#11459 - 	CGI_10020191	superfamily	241610	12	62	8.63E-10	52.2522	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#11460 - 	CGI_10005131	superfamily	247792	57	99	6.11E-09	48.53	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11462 - 	CGI_10005133	superfamily	241606	215	319	8.24E-29	113.54	cl00096	IRF superfamily	 - 	 - 	Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
Q#11463 - 	CGI_10005134	superfamily	217293	26	226	2.08E-33	125.053	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11463 - 	CGI_10005134	superfamily	202474	234	372	3.87E-09	55.3525	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11464 - 	CGI_10005135	superfamily	248097	89	201	1.10E-11	58.8158	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11465 - 	CGI_10005136	superfamily	241584	446	538	1.08E-13	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#11465 - 	CGI_10005136	superfamily	241584	357	441	9.83E-11	59.0471	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#11465 - 	CGI_10005136	superfamily	241584	64	154	1.60E-09	55.5803	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#11465 - 	CGI_10005136	superfamily	241584	146	227	9.43E-09	53.2691	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#11465 - 	CGI_10005136	superfamily	245814	12	56	7.15E-06	44.8414	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11468 - 	CGI_10016126	superfamily	246680	478	560	0.00184464	36.9298	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#11470 - 	CGI_10016128	superfamily	218570	144	166	0.00595769	33.5301	cl05109	Pacifastin_I superfamily	NC	 - 	"Pacifastin inhibitor (LCMII); Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors."
Q#11470 - 	CGI_10016128	superfamily	218570	229	256	0.00645024	33.5301	cl05109	Pacifastin_I superfamily	N	 - 	"Pacifastin inhibitor (LCMII); Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors."
Q#11471 - 	CGI_10016129	superfamily	216212	466	990	0	682.095	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#11472 - 	CGI_10016130	superfamily	241596	107	165	7.04E-18	76.8691	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#11472 - 	CGI_10016130	superfamily	221625	167	231	1.02E-17	78.1703	cl13910	Neuro_bHLH superfamily	C	 - 	"Neuronal helix-loop-helix transcription factor; This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found C-terminal to pfam00010. There is a single completely conserved residue W that may be functionally important. Neuronal basic helix-loop-helix (bHLH) transcription factors such as neuroD and neurogenin have been shown to play important roles in neuronal development."
Q#11473 - 	CGI_10016131	superfamily	241669	11	113	6.04E-16	74.2336	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11473 - 	CGI_10016131	superfamily	241669	382	499	1.60E-14	69.9964	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11473 - 	CGI_10016131	superfamily	241669	259	364	1.06E-11	61.9072	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11473 - 	CGI_10016131	superfamily	241669	136	253	3.46E-11	60.3664	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11474 - 	CGI_10016132	superfamily	241669	9	112	3.77E-16	74.6188	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11474 - 	CGI_10016132	superfamily	241669	259	368	1.75E-09	55.3589	cl00187	Fascin superfamily	 - 	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11474 - 	CGI_10016132	superfamily	241669	385	480	2.99E-06	45.3437	cl00187	Fascin superfamily	C	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11474 - 	CGI_10016132	superfamily	241669	148	230	0.000835185	38.0371	cl00187	Fascin superfamily	C	 - 	"Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)"
Q#11477 - 	CGI_10016135	superfamily	246683	20	276	5.69E-91	273.331	cl14648	Aldose_epim superfamily	 - 	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#11478 - 	CGI_10016136	superfamily	242465	115	251	6.03E-16	73.63	cl01378	LicD superfamily	 - 	 - 	"LicD family; The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent. These proteins are part of the nucleotidyltransferase superfamily."
Q#11480 - 	CGI_10016138	superfamily	217293	2	157	2.21E-26	108.874	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11480 - 	CGI_10016138	superfamily	202474	190	240	2.85E-11	63.4417	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11480 - 	CGI_10016138	superfamily	204434	935	958	2.20E-08	51.8117	cl10963	zf-CCHH superfamily	 - 	 - 	"Zinc-finger (CX5CX6HX5H) motif; This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism."
Q#11480 - 	CGI_10016138	superfamily	241592	365	381	0.00827556	35.8702	cl00074	H2A superfamily	NC	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#11480 - 	CGI_10016138	superfamily	241581	457	522	0.00829773	35.6499	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#11481 - 	CGI_10016139	superfamily	202837	71	120	0.000615189	36.4569	cl04354	Nnf1 superfamily	N	 - 	Nnf1; NNF1 is an essential yeast gene that is necessary for chromosome segregation. It is associated with the spindle poles and forms part of a kinetochore subcomplex called MIND.
Q#11482 - 	CGI_10016140	superfamily	245815	31	507	0	903.425	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#11483 - 	CGI_10016141	superfamily	241659	289	356	0.00414332	36.7983	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#11485 - 	CGI_10016143	superfamily	241982	20	215	2.29E-56	181.226	cl00613	ATP-synt_D superfamily	 - 	 - 	ATP synthase subunit D; This is a family of subunit D form various ATP synthases including V-type H+ transporting and Na+ dependent. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase.
Q#11486 - 	CGI_10016144	superfamily	151110	15	188	1.36E-49	162.367	cl11201	UPF0552 superfamily	N	 - 	Uncharacterized protein family UPF0552; This family of proteins has no known function.
Q#11487 - 	CGI_10016145	superfamily	247683	39	109	2.59E-16	76.7504	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#11488 - 	CGI_10016146	superfamily	247692	34	680	0	831.263	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#11489 - 	CGI_10016147	superfamily	243072	241	366	3.71E-35	127.5	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11489 - 	CGI_10016147	superfamily	243072	307	432	2.37E-29	111.707	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11489 - 	CGI_10016147	superfamily	243072	75	199	7.07E-17	77.0386	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11490 - 	CGI_10016148	superfamily	245814	148	197	3.03E-06	43.6852	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11490 - 	CGI_10016148	superfamily	245814	42	110	0.00528069	34.0482	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11491 - 	CGI_10016149	superfamily	241622	228	308	1.95E-18	83.7702	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11491 - 	CGI_10016149	superfamily	241622	675	761	3.67E-13	68.3622	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11491 - 	CGI_10016149	superfamily	241622	2704	2789	4.21E-12	65.2806	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11491 - 	CGI_10016149	superfamily	241622	816	892	9.07E-10	58.347	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11491 - 	CGI_10016149	superfamily	241622	2428	2497	5.42E-07	49.9965	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11491 - 	CGI_10016149	superfamily	241622	1584	1652	1.25E-06	48.8409	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11491 - 	CGI_10016149	superfamily	241622	391	432	0.00226767	39.0871	cl00117	PDZ superfamily	C	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11491 - 	CGI_10016149	superfamily	218881	1320	1539	0.00295199	41.8148	cl18482	Herpes_UL32 superfamily	N	 - 	Herpesvirus large structural phosphoprotein UL32; The large phosphorylated protein (UL32-like) of herpes viruses is the polypeptide most frequently reactive in immuno-blotting analyses with antisera when compared with other viral proteins.
Q#11493 - 	CGI_10006112	superfamily	216554	27	165	3.06E-23	92.1573	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#11494 - 	CGI_10006113	superfamily	241645	250	317	1.32E-29	109.357	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#11494 - 	CGI_10006113	superfamily	241643	6	39	2.70E-08	49.3799	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#11495 - 	CGI_10006114	superfamily	243176	28	524	1.32E-36	141.211	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#11497 - 	CGI_10006116	superfamily	241563	73	106	1.93E-05	42.2744	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11500 - 	CGI_10006119	superfamily	247856	64	125	3.21E-16	68.3433	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11500 - 	CGI_10006119	superfamily	247856	2	52	4.10E-11	54.4761	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11502 - 	CGI_10006121	superfamily	243034	2	123	0.000131611	38.13	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#11503 - 	CGI_10006122	superfamily	248345	59	189	7.85E-34	119.687	cl17791	SAC3_GANP superfamily	 - 	 - 	"SAC3/GANP/Nin1/mts3/eIF-3 p25 family; This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits."
Q#11506 - 	CGI_10006125	superfamily	241599	77	135	8.88E-23	88.8396	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#11507 - 	CGI_10014791	superfamily	243092	1161	1449	1.73E-92	303.102	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11507 - 	CGI_10014791	superfamily	241578	327	497	1.81E-11	64.1242	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11513 - 	CGI_10014799	superfamily	248264	215	376	1.47E-05	43.765	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#11514 - 	CGI_10014800	superfamily	220672	44	227	1.03E-23	95.7766	cl10957	Frag1 superfamily	 - 	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#11515 - 	CGI_10014801	superfamily	246748	32	425	0	603.117	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#11516 - 	CGI_10014802	superfamily	245814	46	98	7.31E-10	51.4469	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11518 - 	CGI_10015070	superfamily	241629	29	151	1.79E-37	129.948	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#11520 - 	CGI_10015072	superfamily	243066	118	218	3.26E-12	64.1757	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11520 - 	CGI_10015072	superfamily	198867	387	473	6.73E-10	57.3512	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#11520 - 	CGI_10015072	superfamily	243066	220	377	1.13E-06	47.6121	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11521 - 	CGI_10015073	superfamily	246669	610	710	2.87E-23	96.7522	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#11521 - 	CGI_10015073	superfamily	246669	334	419	1.09E-17	80.5739	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#11523 - 	CGI_10015075	superfamily	241829	1	52	0.00225821	33.5761	cl00383	Ribosomal_L33 superfamily	 - 	 - 	Ribosomal protein L33; Ribosomal protein L33.  
Q#11524 - 	CGI_10015076	superfamily	216301	1	179	3.93E-57	179.767	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#11527 - 	CGI_10015079	superfamily	222313	1	40	1.03E-10	56.4314	cl18662	Methyltransf_32 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#11528 - 	CGI_10015080	superfamily	243092	9	305	1.52E-23	97.0204	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11529 - 	CGI_10015081	superfamily	247725	680	775	2.15E-41	148.985	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11529 - 	CGI_10015081	superfamily	247725	790	881	0.000239237	41.1868	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11529 - 	CGI_10015081	superfamily	247725	1322	1424	4.36E-34	128.317	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11529 - 	CGI_10015081	superfamily	243052	925	1120	4.67E-27	109.757	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#11529 - 	CGI_10015081	superfamily	215882	1238	1326	2.48E-05	44.1939	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#11531 - 	CGI_10015083	superfamily	245716	152	178	4.21E-10	54.8719	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#11531 - 	CGI_10015083	superfamily	245716	114	139	8.84E-10	54.1015	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#11534 - 	CGI_10015086	superfamily	204716	42	192	4.97E-05	42.2275	cl18257	Git3 superfamily	C	 - 	"G protein-coupled glucose receptor regulating Gpa2; Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This is the conserved N-terminus of these proteins, and the C-terminal conserved region is now in family Git3_C."
Q#11537 - 	CGI_10015089	superfamily	247743	4	135	1.44E-05	40.9775	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#11540 - 	CGI_10015093	superfamily	241732	1521	1685	4.75E-37	138.515	cl00258	RIBOc superfamily	 - 	 - 	"RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing."
Q#11540 - 	CGI_10015093	superfamily	247905	522	577	1.19E-09	58.4033	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#11540 - 	CGI_10015093	superfamily	241765	911	1033	3.42E-46	164.155	cl00301	PAZ superfamily	 - 	 - 	"PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain."
Q#11540 - 	CGI_10015093	superfamily	190615	648	742	3.60E-28	111.545	cl04028	dsRNA_bind superfamily	 - 	 - 	"Double stranded RNA binding domain; This domain is a divergent double stranded RNA-binding domain. It is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules."
Q#11540 - 	CGI_10015093	superfamily	241732	1426	1467	3.00E-05	44.5259	cl00258	RIBOc superfamily	N	 - 	"RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing."
Q#11540 - 	CGI_10015093	superfamily	247805	45	193	0.00368357	38.4724	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#11541 - 	CGI_10015094	superfamily	241782	10	162	1.14E-58	193.055	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#11542 - 	CGI_10007754	superfamily	217293	240	368	5.81E-20	89.9995	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11542 - 	CGI_10007754	superfamily	215647	721	843	2.48E-16	79.1896	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#11542 - 	CGI_10007754	superfamily	202474	375	425	1.06E-07	52.2709	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11542 - 	CGI_10007754	superfamily	221370	530	694	0.000101157	43.5141	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#11543 - 	CGI_10007755	superfamily	245213	227	263	1.10E-09	56.1058	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	949	984	4.02E-08	51.4834	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	986	1022	4.90E-08	51.4834	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	151	187	9.05E-08	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	75	111	1.06E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	37	73	2.39E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	113	149	2.80E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	1	35	3.47E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	189	224	4.49E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	1024	1060	4.95E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	245213	1062	1098	1.20E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11543 - 	CGI_10007755	superfamily	215647	562	660	5.99E-17	81.5008	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#11543 - 	CGI_10007755	superfamily	216897	880	946	1.08E-11	63.0841	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#11543 - 	CGI_10007755	superfamily	221370	1261	1352	3.01E-06	48.5217	cl13441	DUF3497 superfamily	C	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#11543 - 	CGI_10007755	superfamily	243029	1178	1229	4.99E-05	42.7229	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#11543 - 	CGI_10007755	superfamily	221370	472	551	8.32E-05	44.2845	cl13441	DUF3497 superfamily	C	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#11544 - 	CGI_10007756	superfamily	215647	10	105	5.00E-10	53.3813	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#11547 - 	CGI_10007332	superfamily	241571	517	640	8.29E-14	68.9782	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#11547 - 	CGI_10007332	superfamily	241571	140	266	1.55E-11	62.0446	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#11547 - 	CGI_10007332	superfamily	245213	689	720	2.99E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11547 - 	CGI_10007332	superfamily	245213	648	681	1.35E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11547 - 	CGI_10007332	superfamily	245213	315	346	0.000192373	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11547 - 	CGI_10007332	superfamily	241583	410	512	2.71E-28	112.665	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#11547 - 	CGI_10007332	superfamily	241583	1	96	6.78E-23	96.8714	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#11550 - 	CGI_10007335	superfamily	241802	11	125	4.19E-36	134.288	cl00342	Trp-synth-beta_II superfamily	NC	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#11551 - 	CGI_10007336	superfamily	241802	2	462	0	529.118	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#11552 - 	CGI_10007337	superfamily	219732	472	633	6.35E-50	177.022	cl06969	NUC173 superfamily	 - 	 - 	NUC173 domain; This is the central domain of of novel family of hypothetical nucleolar proteins.
Q#11553 - 	CGI_10014061	superfamily	247676	1	93	2.31E-30	108.467	cl17012	GINS_A superfamily	N	 - 	"Alpha-helical domain of GINS complex proteins; Sld5, Psf1, Psf2 and Psf3; The GINS complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In eukaryotes, GINS is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has been found in eukaryotes and archaea, but not in bacteria. The four subunits of the complex are homologous and consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3."
Q#11555 - 	CGI_10014063	superfamily	243267	7	351	7.19E-49	170.872	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#11556 - 	CGI_10014064	superfamily	243267	126	257	6.15E-18	81.8912	cl03000	Innexin superfamily	N	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#11556 - 	CGI_10014064	superfamily	243267	5	111	3.11E-09	56.0828	cl03000	Innexin superfamily	C	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#11562 - 	CGI_10014070	superfamily	247794	1	260	6.62E-129	371.342	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#11563 - 	CGI_10014071	superfamily	241764	25	88	1.36E-05	41.8179	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#11564 - 	CGI_10014072	superfamily	217293	51	240	9.03E-35	128.905	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11565 - 	CGI_10014073	superfamily	247637	5	328	1.45E-151	432.072	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#11568 - 	CGI_10014076	superfamily	110440	408	435	0.00433506	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11571 - 	CGI_10014079	superfamily	245936	207	417	1.35E-54	181.594	cl12283	IPK superfamily	 - 	 - 	Inositol polyphosphate kinase; ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
Q#11572 - 	CGI_10014080	superfamily	217584	37	156	3.21E-27	103.591	cl04100	MOSC_N superfamily	 - 	 - 	"MOSC N-terminal beta barrel domain; This domain is found to the N-terminus of pfam03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold."
Q#11572 - 	CGI_10014080	superfamily	217583	186	320	6.18E-11	58.5283	cl04097	MOSC superfamily	 - 	 - 	"MOSC domain; The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters."
Q#11573 - 	CGI_10014081	superfamily	245201	301	514	9.69E-118	355.658	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11573 - 	CGI_10014081	superfamily	247725	23	130	4.50E-18	80.877	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11573 - 	CGI_10014081	superfamily	245201	266	303	6.86E-14	71.7657	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11573 - 	CGI_10014081	superfamily	245201	521	584	1.73E-08	55.2022	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11573 - 	CGI_10014081	superfamily	247736	167	219	0.000227053	40.4585	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#11574 - 	CGI_10014082	superfamily	241971	106	381	7.61E-110	325.3	cl00599	Extradiol_Dioxygenase_3B_like superfamily	 - 	 - 	"Subunit B of Class III Extradiol ring-cleavage dioxygenases; Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be further divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two-domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B. This model represents the catalytic subunit B of extradiol dioxygenase class III enzymes. Enzymes belonging to this family include Protocatechuate 4,5-dioxygenase (LigAB), 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB), 4,5-DOPA Dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase, and 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD). There are also some family members that do not show the typical dioxygenase activity."
Q#11574 - 	CGI_10014082	superfamily	241971	6	109	9.45E-43	151.575	cl00599	Extradiol_Dioxygenase_3B_like superfamily	C	 - 	"Subunit B of Class III Extradiol ring-cleavage dioxygenases; Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be further divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two-domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B. This model represents the catalytic subunit B of extradiol dioxygenase class III enzymes. Enzymes belonging to this family include Protocatechuate 4,5-dioxygenase (LigAB), 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB), 4,5-DOPA Dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase, and 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD). There are also some family members that do not show the typical dioxygenase activity."
Q#11576 - 	CGI_10014084	superfamily	243072	326	450	1.92E-28	110.166	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11576 - 	CGI_10014084	superfamily	243072	256	384	4.14E-26	103.617	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11576 - 	CGI_10014084	superfamily	243072	191	318	1.61E-22	93.6022	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11576 - 	CGI_10014084	superfamily	243072	123	241	1.29E-20	88.2094	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11577 - 	CGI_10014085	superfamily	241872	30	172	1.37E-20	86.4366	cl00453	CDP-OH_P_transf superfamily	N	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#11580 - 	CGI_10007098	superfamily	218493	466	613	1.43E-45	159.445	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#11580 - 	CGI_10007098	superfamily	248097	628	750	1.49E-14	71.1422	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11580 - 	CGI_10007098	superfamily	180442	263	323	0.00249391	39.6677	cl18106	PRK06175 superfamily	NC	 - 	L-aspartate oxidase; Provisional
Q#11581 - 	CGI_10007099	superfamily	150464	26	134	7.86E-21	82.297	cl10773	Transmemb_17 superfamily	 - 	 - 	Predicted membrane protein; This is a 100 amino acid region of a family of proteins conserved from nematodes to humans. It is predicted to be a transmembrane region but its function is not known.
Q#11583 - 	CGI_10008805	superfamily	202367	4	183	1.37E-51	170.028	cl18226	3HCDH_N superfamily	 - 	 - 	"3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda crystallin."
Q#11583 - 	CGI_10008805	superfamily	216084	188	256	1.10E-13	65.3057	cl08285	3HCDH superfamily	C	 - 	"3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; This family also includes lambda crystallin. Some proteins include two copies of this domain."
Q#11584 - 	CGI_10008806	superfamily	243099	578	683	1.47E-06	47.3276	cl02575	Bcl-2_like superfamily	N	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#11586 - 	CGI_10008808	superfamily	243099	466	593	1.29E-33	125.523	cl02575	Bcl-2_like superfamily	 - 	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#11586 - 	CGI_10008808	superfamily	243099	288	389	2.76E-08	52.3352	cl02575	Bcl-2_like superfamily	N	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#11587 - 	CGI_10008809	superfamily	246671	61	154	4.09E-10	57.4328	cl14606	Reeler_cohesin_like superfamily	N	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#11588 - 	CGI_10008810	superfamily	241884	7	206	5.31E-134	379.712	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#11589 - 	CGI_10008811	superfamily	221323	323	501	1.29E-86	266.821	cl13383	DUF3449 superfamily	 - 	 - 	Domain of unknown function (DUF3449); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 181 to 207 amino acids in length. This domain has two conserved sequence motifs: PIP and CEICG. The domain carries a zinc-finger domain of the C2H2-type.
Q#11589 - 	CGI_10008811	superfamily	205477	244	303	3.51E-29	109.155	cl16217	Telomere_Sde2_2 superfamily	 - 	 - 	"Telomere stability C-terminal; This short C-terminal domain is found in higher eukaryotes further downstream from the Sde2 family, pfam13019. It is found in all Sde2-related proteins except those from fission yeast, fly, and mosquito. Its exact function in telomere formation and maintenance has not yet been established."
Q#11589 - 	CGI_10008811	superfamily	192937	74	100	4.45E-07	46.7375	cl13534	SF3a60_bindingd superfamily	 - 	 - 	"Splicing factor SF3a60 binding domain; This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription."
Q#11590 - 	CGI_10008812	superfamily	243072	492	603	1.30E-32	123.263	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11591 - 	CGI_10008813	superfamily	243066	268	359	2.57E-21	86.8381	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11592 - 	CGI_10008814	superfamily	242898	40	135	4.43E-22	85.6409	cl02130	Got1 superfamily	 - 	 - 	"Got1/Sft2-like family; Traffic through the yeast Golgi complex depends on a member of the syntaxin family of SNARE proteins, Sed5, present in early Golgi cisternae. Got1 is thought to facilitate Sed5-dependent fusion events. This is a family of sequences derived from eukaryotic proteins. They are similar to a region of a SNARE-like protein required for traffic through the Golgi complex, SFT2 protein. This is a conserved protein with four putative transmembrane helices, thought to be involved in vesicular transport in later Golgi compartments."
Q#11593 - 	CGI_10008815	superfamily	247724	43	249	1.79E-135	391.631	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11593 - 	CGI_10008815	superfamily	243185	250	362	1.12E-63	203.902	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#11593 - 	CGI_10008815	superfamily	150009	369	460	3.74E-45	153.888	cl08529	eIF2_C superfamily	 - 	 - 	"Initiation factor eIF2 gamma, C terminal; Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA."
Q#11594 - 	CGI_10008816	superfamily	245232	7	197	4.25E-64	211.116	cl10020	S2P-M50 superfamily	C	 - 	"Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-binding proteins (SREBPs) from membranes of the ER. These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD superfamily. Prokaryotic S2P/M50 homologs have been shown to regulate stress responses, sporulation, cell division, and cell differentiation. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses, and in Bacillus subtilis, the S2P homolog SpoIVFB is involved in the pro-sigmaK pathway of spore formation. Some of the subfamilies within this hierarchy contain one or two PDZ domain insertions, with putative regulatory roles, such as the inhibition of substrate cleavage as seen by the RseP PDZ domain."
Q#11594 - 	CGI_10008816	superfamily	245232	409	477	2.25E-19	87.0818	cl10020	S2P-M50 superfamily	N	 - 	"Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-binding proteins (SREBPs) from membranes of the ER. These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD superfamily. Prokaryotic S2P/M50 homologs have been shown to regulate stress responses, sporulation, cell division, and cell differentiation. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses, and in Bacillus subtilis, the S2P homolog SpoIVFB is involved in the pro-sigmaK pathway of spore formation. Some of the subfamilies within this hierarchy contain one or two PDZ domain insertions, with putative regulatory roles, such as the inhibition of substrate cleavage as seen by the RseP PDZ domain."
Q#11597 - 	CGI_10008819	superfamily	241609	26	108	2.30E-18	73.9515	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#11597 - 	CGI_10008819	superfamily	241609	4	24	1.26E-07	44.6763	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#11599 - 	CGI_10011322	superfamily	245201	690	884	4.37E-26	109.569	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11600 - 	CGI_10011323	superfamily	177822	62	173	0.000443865	38.7477	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#11601 - 	CGI_10011324	superfamily	241547	46	244	2.01E-48	161.297	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#11602 - 	CGI_10011325	superfamily	243109	9	65	0.00176935	36.4106	cl02614	SPRY superfamily	C	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#11603 - 	CGI_10011326	superfamily	247792	26	70	1.91E-05	42.818	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11603 - 	CGI_10011326	superfamily	128778	213	339	3.86E-06	45.7187	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#11604 - 	CGI_10011327	superfamily	247792	61	104	3.44E-06	45.1292	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11604 - 	CGI_10011327	superfamily	128778	251	373	1.79E-05	43.7927	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#11604 - 	CGI_10011327	superfamily	241563	195	239	0.000227382	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11604 - 	CGI_10011327	superfamily	243109	557	648	0.000432866	40.3653	cl02614	SPRY superfamily	C	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#11604 - 	CGI_10011327	superfamily	216033	410	501	0.000960857	38.0836	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#11605 - 	CGI_10011328	superfamily	219502	363	581	3.14E-79	251.98	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#11605 - 	CGI_10011328	superfamily	201962	181	252	4.01E-21	88.2016	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#11605 - 	CGI_10011328	superfamily	219507	260	358	2.80E-12	63.7975	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#11606 - 	CGI_10011329	superfamily	245226	296	465	4.90E-23	95.8304	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#11608 - 	CGI_10011331	superfamily	216686	278	454	3.88E-49	169.041	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#11609 - 	CGI_10005366	superfamily	109891	28	160	1.64E-72	229.685	cl02989	Runt superfamily	 - 	 - 	Runt domain; Runt domain.  
Q#11611 - 	CGI_10005368	superfamily	241571	177	293	3.01E-08	50.1035	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#11611 - 	CGI_10005368	superfamily	241583	15	172	4.43E-31	115.746	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#11612 - 	CGI_10013251	superfamily	243072	98	224	8.06E-20	83.2018	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11612 - 	CGI_10013251	superfamily	243072	30	154	6.90E-18	77.809	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11612 - 	CGI_10013251	superfamily	243072	165	300	1.12E-06	45.8374	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11615 - 	CGI_10013254	superfamily	220003	608	873	1.41E-106	331.923	cl07388	Gamma-COP superfamily	 - 	 - 	"Coatomer gamma subunit appendage domain; COPI-coated vesicles function in retrograde transport from the Golgi to the ER, and in intra-Golgi transport. This domain corresponds to the coatomer gamma subunit appendage domain. It contains a protein-protein interaction site and a second proposed binding site that interacts with the alpha, beta,epsilon COPI subcomplex."
Q#11616 - 	CGI_10013255	superfamily	243119	75	116	0.000652323	36.6429	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11617 - 	CGI_10013256	superfamily	243119	35	74	1.72E-06	45.1273	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11617 - 	CGI_10013256	superfamily	243119	270	318	0.000437874	38.1837	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11617 - 	CGI_10013256	superfamily	243119	331	380	0.00388348	35.4974	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11617 - 	CGI_10013256	superfamily	243119	91	140	0.00651294	34.727	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11619 - 	CGI_10013258	superfamily	243119	5	54	0.000131731	38.1837	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11620 - 	CGI_10013259	superfamily	243119	32	73	6.32E-06	42.0357	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#11621 - 	CGI_10013260	superfamily	245847	31	112	6.01E-08	47.1662	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#11622 - 	CGI_10013261	superfamily	245040	42	99	2.70E-06	41.5183	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#11623 - 	CGI_10013262	superfamily	241574	388	613	1.70E-92	288.33	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#11624 - 	CGI_10013263	superfamily	241752	112	231	2.77E-35	123.198	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#11625 - 	CGI_10013264	superfamily	241563	62	100	2.21E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11628 - 	CGI_10013269	superfamily	241563	60	96	4.90E-05	41.1188	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11628 - 	CGI_10013269	superfamily	110440	521	548	0.00885849	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11629 - 	CGI_10013270	superfamily	207662	104	177	1.38E-30	113.811	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#11629 - 	CGI_10013270	superfamily	245599	333	506	1.08E-22	94.9822	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#11630 - 	CGI_10013271	superfamily	241659	20	86	3.42E-23	89.576	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#11631 - 	CGI_10013272	superfamily	190308	140	287	1.96E-09	56.5583	cl18163	Fringe superfamily	C	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#11632 - 	CGI_10001796	superfamily	247057	304	365	1.30E-07	48.3012	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#11633 - 	CGI_10001797	superfamily	247725	25	113	4.46E-33	125.445	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11634 - 	CGI_10001798	superfamily	215825	5	106	6.80E-33	120.485	cl02828	Calreticulin superfamily	N	 - 	Calreticulin family; Calreticulin family.  
Q#11636 - 	CGI_10026148	superfamily	242173	47	186	9.63E-15	67.2771	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#11640 - 	CGI_10026152	superfamily	241564	95	163	4.41E-21	82.6987	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#11641 - 	CGI_10026153	superfamily	245847	346	491	1.39E-11	62.1889	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#11641 - 	CGI_10026153	superfamily	216939	9	66	5.39E-11	58.8285	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#11641 - 	CGI_10026153	superfamily	241619	117	163	0.00518663	35.2505	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#11642 - 	CGI_10026155	superfamily	241613	234	268	1.63E-11	62.2241	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	274	308	1.63E-11	62.2241	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	152	186	4.99E-10	57.987	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	313	347	8.64E-10	57.2166	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	694	728	1.35E-09	56.4462	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	652	686	1.58E-09	56.4462	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	32	66	2.46E-09	55.6758	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	193	228	1.25E-07	50.6682	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	241613	360	389	2.40E-07	49.8978	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11642 - 	CGI_10026155	superfamily	245213	773	806	2.07E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11642 - 	CGI_10026155	superfamily	214531	1191	1233	7.79E-13	66.086	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1804	1846	2.07E-12	64.9304	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	970	1011	6.15E-11	60.6932	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1278	1320	1.12E-10	59.9228	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	543	585	7.90E-10	57.2264	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	215683	1254	1295	1.89E-09	56.4095	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#11642 - 	CGI_10026155	superfamily	214531	499	542	6.46E-09	54.5301	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1500	1540	1.13E-08	54.1449	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1891	1933	1.73E-08	53.3745	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	215683	1561	1601	2.17E-08	53.3279	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#11642 - 	CGI_10026155	superfamily	214531	1585	1627	4.37E-08	52.2189	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	883	922	4.41E-08	52.2189	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	462	498	7.36E-08	51.4485	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1847	1890	2.15E-07	50.2929	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	925	968	1.24E-06	47.9817	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1459	1497	1.27E-06	47.9817	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	221695	753	776	1.09E-05	45.1386	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#11642 - 	CGI_10026155	superfamily	214531	1149	1190	1.10E-05	45.2853	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1012	1053	5.07E-05	43.3593	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1767	1802	7.55E-05	42.5889	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	841	878	0.000109729	42.2037	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	414	455	0.000180809	41.8185	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11642 - 	CGI_10026155	superfamily	214531	1933	1974	0.000336455	40.6629	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#11646 - 	CGI_10026159	superfamily	241571	357	468	1.25E-08	53.185	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#11646 - 	CGI_10026159	superfamily	241583	130	314	8.15E-48	166.284	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#11646 - 	CGI_10026159	superfamily	243051	484	637	6.43E-09	54.6913	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11647 - 	CGI_10026160	superfamily	247044	11	146	5.49E-48	153.481	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#11648 - 	CGI_10026162	superfamily	248458	60	227	4.38E-16	78.5097	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11648 - 	CGI_10026162	superfamily	243161	495	556	1.56E-08	52.3966	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#11649 - 	CGI_10026163	superfamily	243072	123	272	2.20E-14	67.4086	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11649 - 	CGI_10026163	superfamily	243072	20	173	3.28E-09	52.771	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11654 - 	CGI_10026168	superfamily	248281	79	146	7.37E-09	52.6579	cl17727	GT1 superfamily	N	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#11655 - 	CGI_10026169	superfamily	248458	43	151	2.08E-09	57.3237	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11655 - 	CGI_10026169	superfamily	248458	215	378	0.000298131	41.1453	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11656 - 	CGI_10026170	superfamily	247805	15	78	4.97E-09	49.9503	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#11658 - 	CGI_10026172	superfamily	248458	1	169	7.00E-08	50.3901	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11659 - 	CGI_10026173	superfamily	243303	5	73	1.80E-38	124.654	cl03104	CKS superfamily	 - 	 - 	Cyclin-dependent kinase regulatory subunit; Cyclin-dependent kinase regulatory subunit.  
Q#11660 - 	CGI_10026174	superfamily	248012	955	1048	6.07E-24	99.1892	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11660 - 	CGI_10026174	superfamily	248012	1148	1256	7.02E-23	96.1076	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11660 - 	CGI_10026174	superfamily	246680	859	935	2.01E-08	53.548	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#11661 - 	CGI_10026175	superfamily	243035	2	92	5.50E-09	48.7702	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11662 - 	CGI_10026176	superfamily	248012	690	783	5.31E-24	98.804	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11662 - 	CGI_10026176	superfamily	248012	885	993	6.09E-23	95.7224	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11662 - 	CGI_10026176	superfamily	246680	594	670	1.75E-08	53.1628	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#11663 - 	CGI_10026177	superfamily	241574	12	145	2.99E-52	170.482	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#11664 - 	CGI_10026178	superfamily	247744	353	515	1.29E-47	165.864	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#11664 - 	CGI_10026178	superfamily	201217	218	267	6.22E-15	69.862	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#11664 - 	CGI_10026178	superfamily	201217	165	215	2.19E-12	62.5432	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#11664 - 	CGI_10026178	superfamily	201217	112	162	5.90E-09	52.9132	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#11664 - 	CGI_10026178	superfamily	201217	270	333	0.000673108	37.8904	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#11665 - 	CGI_10026179	superfamily	245206	7	259	8.15E-116	335.28	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#11666 - 	CGI_10026180	superfamily	207637	308	378	5.07E-12	61.3999	cl02541	CIDE_N superfamily	 - 	 - 	"CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein."
Q#11667 - 	CGI_10026181	superfamily	247856	114	176	3.82E-14	63.7209	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11667 - 	CGI_10026181	superfamily	247856	41	103	1.42E-11	56.4021	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11668 - 	CGI_10026182	superfamily	245201	117	413	1.39E-36	140.926	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11669 - 	CGI_10026183	superfamily	243092	57	353	5.91E-36	140.548	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11669 - 	CGI_10026183	superfamily	243092	717	1020	3.14E-32	129.377	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11669 - 	CGI_10026183	superfamily	243092	1594	1912	1.79E-21	97.0204	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11669 - 	CGI_10026183	superfamily	243092	988	1261	5.27E-21	95.4796	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11669 - 	CGI_10026183	superfamily	243092	285	592	1.02E-19	91.6276	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11669 - 	CGI_10026183	superfamily	243092	1411	1718	1.55E-19	90.8572	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11669 - 	CGI_10026183	superfamily	190637	663	710	2.43E-13	68.1962	cl04081	HELP superfamily	N	 - 	"HELP motif; The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family. The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain. In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation. The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons."
Q#11669 - 	CGI_10026183	superfamily	190637	2	48	3.50E-12	64.7294	cl04081	HELP superfamily	N	 - 	"HELP motif; The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family. The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain. In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation. The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons."
Q#11669 - 	CGI_10026183	superfamily	190637	1357	1399	1.22E-05	45.4694	cl04081	HELP superfamily	N	 - 	"HELP motif; The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family. The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain. In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation. The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons."
Q#11669 - 	CGI_10026183	superfamily	243092	1881	1957	0.000347901	43.4776	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11671 - 	CGI_10026185	superfamily	220377	90	153	7.54E-14	65.134	cl10731	DUF2052 superfamily	C	 - 	"Coiled-coil domain containing protein (DUF2052); This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown."
Q#11672 - 	CGI_10026186	superfamily	241573	189	497	1.89E-131	402.48	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#11672 - 	CGI_10026186	superfamily	241653	512	651	1.68E-47	167.475	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#11672 - 	CGI_10026186	superfamily	247856	922	977	0.00014212	40.9941	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11672 - 	CGI_10026186	superfamily	241653	653	720	3.71E-21	91.6132	cl00165	Calpain_III superfamily	N	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#11672 - 	CGI_10026186	superfamily	241573	100	142	1.22E-10	62.729	cl00051	CysPc superfamily	C	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#11672 - 	CGI_10026186	superfamily	247856	891	946	0.00211737	37.5273	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11678 - 	CGI_10026192	superfamily	243100	99	151	0.000128755	37.9288	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#11682 - 	CGI_10026196	superfamily	243062	297	395	2.42E-27	104.28	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#11682 - 	CGI_10026196	superfamily	216062	38	265	5.51E-18	81.3302	cl02928	TGFb_propeptide superfamily	 - 	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#11683 - 	CGI_10026197	superfamily	243062	253	351	7.64E-30	110.828	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#11683 - 	CGI_10026197	superfamily	216062	83	218	2.23E-17	79.019	cl02928	TGFb_propeptide superfamily	N	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#11685 - 	CGI_10026199	superfamily	248097	13	115	2.74E-12	59.201	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#11686 - 	CGI_10026200	superfamily	241600	115	314	3.58E-81	247.924	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11687 - 	CGI_10026201	superfamily	241600	1	172	1.74E-65	202.085	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11688 - 	CGI_10026202	superfamily	241600	109	311	2.01E-79	243.302	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11688 - 	CGI_10026202	superfamily	241619	4	70	0.00950886	33.7097	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#11689 - 	CGI_10026203	superfamily	199168	190	213	0.00802743	34.6348	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#11692 - 	CGI_10026206	superfamily	243035	131	208	1.69E-09	53.5825	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11692 - 	CGI_10026206	superfamily	241619	28	85	0.00573659	34.0916	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#11693 - 	CGI_10026207	superfamily	248264	369	414	3.38E-08	51.469	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#11693 - 	CGI_10026207	superfamily	243035	165	266	1.55E-07	49.1354	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11693 - 	CGI_10026207	superfamily	243035	296	371	9.26E-07	46.6489	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11694 - 	CGI_10026208	superfamily	246925	46	181	0.000407454	41.187	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#11698 - 	CGI_10016368	superfamily	247905	1572	1681	4.86E-13	68.8036	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#11698 - 	CGI_10016368	superfamily	241571	1737	1819	7.03E-10	58.963	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#11698 - 	CGI_10016368	superfamily	241613	1839	1875	7.09E-09	54.135	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11698 - 	CGI_10016368	superfamily	247792	1487	1534	1.54E-06	47.4404	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11698 - 	CGI_10016368	superfamily	247805	780	912	0.00110439	40.0132	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#11699 - 	CGI_10016369	superfamily	241547	15	113	1.80E-18	83.4863	cl00012	alpha_CA superfamily	C	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#11699 - 	CGI_10016369	superfamily	241547	255	300	6.82E-16	75.7823	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#11700 - 	CGI_10016370	superfamily	245304	105	388	7.53E-98	302.171	cl10459	Peptidases_S8_S53 superfamily	 - 	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#11700 - 	CGI_10016370	superfamily	201820	473	545	4.65E-21	88.0662	cl08326	P_proprotein superfamily	C	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#11702 - 	CGI_10016372	superfamily	241578	76	180	2.54E-05	43.8007	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11703 - 	CGI_10016373	superfamily	243092	172	306	0.00413878	37.3144	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11704 - 	CGI_10016374	superfamily	241563	40	80	5.60E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11704 - 	CGI_10016374	superfamily	243092	286	422	0.00373949	38.0848	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11705 - 	CGI_10016375	superfamily	247725	308	419	9.07E-52	176.396	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#11705 - 	CGI_10016375	superfamily	243072	640	793	5.76E-28	110.166	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11705 - 	CGI_10016375	superfamily	245835	37	247	4.51E-78	253.104	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#11705 - 	CGI_10016375	superfamily	243047	438	560	2.47E-37	136.596	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#11706 - 	CGI_10016376	superfamily	243091	25	154	4.99E-29	105.879	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#11708 - 	CGI_10016378	superfamily	248012	19	102	5.25E-13	61.4397	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11710 - 	CGI_10016380	superfamily	221377	208	346	2.35E-06	45.9227	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#11711 - 	CGI_10016381	superfamily	243092	268	566	4.10E-65	216.047	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11717 - 	CGI_10016387	superfamily	247780	277	554	5.32E-125	371.881	cl17226	NAD_bind_amino_acid_DH superfamily	 - 	 - 	"NAD(P) binding domain of amino acid dehydrogenase-like proteins; Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel  domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts."
Q#11717 - 	CGI_10016387	superfamily	215894	86	267	2.85E-104	314.585	cl02855	malic superfamily	 - 	 - 	"Malic enzyme, N-terminal domain; Malic enzyme, N-terminal domain.  "
Q#11718 - 	CGI_10016388	superfamily	247724	8	214	2.49E-109	315.161	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11719 - 	CGI_10016389	superfamily	243072	220	346	3.34E-31	122.107	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#11719 - 	CGI_10016389	superfamily	241622	1519	1569	6.73E-16	76.4514	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#11719 - 	CGI_10016389	superfamily	247683	734	780	5.58E-15	72.7514	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#11719 - 	CGI_10016389	superfamily	247057	2623	2686	1.22E-21	92.3817	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#11722 - 	CGI_10016392	superfamily	217617	4	46	0.00022776	39.7069	cl15988	Sulfotransfer_2 superfamily	NC	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#11723 - 	CGI_10016393	superfamily	217617	98	280	9.58E-23	95.1756	cl15988	Sulfotransfer_2 superfamily	C	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#11725 - 	CGI_10016395	superfamily	245201	189	371	1.69E-31	120.034	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11725 - 	CGI_10016395	superfamily	245201	58	122	1.57E-11	62.901	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11726 - 	CGI_10016396	superfamily	245201	1	157	2.70E-32	118.493	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11727 - 	CGI_10000467	superfamily	243066	119	222	3.22E-17	76.1904	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11728 - 	CGI_10001206	superfamily	180442	76	405	3.86E-20	92.0549	cl18106	PRK06175 superfamily	C	 - 	L-aspartate oxidase; Provisional
Q#11728 - 	CGI_10001206	superfamily	248236	457	587	3.55E-13	68.8652	cl17682	PRK07189 superfamily	C	 - 	malonate decarboxylase subunit beta; Reviewed
Q#11729 - 	CGI_10022510	superfamily	247068	119	205	6.28E-13	61.5605	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11731 - 	CGI_10022512	superfamily	247684	99	369	5.76E-33	128.549	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11731 - 	CGI_10022512	superfamily	247684	11	105	2.29E-18	85.7919	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11732 - 	CGI_10022513	superfamily	247684	2	255	3.14E-42	152.817	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11734 - 	CGI_10022516	superfamily	247684	11	178	9.05E-40	140.875	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#11739 - 	CGI_10022521	superfamily	241818	1	58	7.52E-31	107.649	cl00366	PMSR superfamily	N	 - 	Peptide methionine sulfoxide reductase; This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine.
Q#11740 - 	CGI_10022522	superfamily	180442	214	649	1.78E-72	244.594	cl18106	PRK06175 superfamily	 - 	 - 	L-aspartate oxidase; Provisional
Q#11740 - 	CGI_10022522	superfamily	217281	644	768	3.44E-43	152.753	cl08378	Succ_DH_flav_C superfamily	 - 	 - 	"Fumarate reductase flavoprotein C-term; This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases."
Q#11741 - 	CGI_10022523	superfamily	243051	3090	3246	7.24E-57	199.141	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	3594	3751	1.10E-53	189.896	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	2391	2549	1.34E-52	186.815	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	5246	5402	7.59E-50	179.111	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	7898	8056	1.48E-49	178.34	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	4168	4326	1.62E-49	177.955	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	2036	2193	5.39E-49	176.414	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	4566	4722	1.56E-48	175.259	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	1514	1673	3.36E-48	174.103	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	6888	7048	3.72E-47	171.407	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	2199	2355	4.58E-47	171.022	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	6724	6882	7.44E-47	170.251	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	1349	1506	8.94E-47	170.251	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	1872	2028	1.61E-46	169.481	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	3252	3407	2.09E-46	169.096	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	4728	4887	4.99E-46	167.94	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	1157	1314	1.16E-45	166.784	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	6540	6699	1.61E-45	166.399	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	474	640	1.62E-45	166.399	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	9413	9567	6.79E-45	164.858	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	296	456	2.65E-44	162.932	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	2559	2722	4.32E-44	162.547	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	6374	6534	6.25E-44	161.777	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	831	978	9.58E-44	161.392	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	3757	3916	1.53E-43	160.621	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	2728	2887	2.03E-43	160.236	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	6211	6368	4.93E-43	159.466	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	8322	8473	1.01E-42	158.31	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	2912	3075	1.24E-42	158.31	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	4893	5048	1.72E-42	157.54	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	994	1151	5.37E-42	156.384	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	3432	3586	1.09E-40	152.532	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	7467	7626	4.10E-40	150.991	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	640	797	6.47E-40	150.221	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	7054	7215	9.15E-39	146.754	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	8746	8905	1.01E-38	146.754	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	5820	5977	3.94E-38	145.213	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	5073	5240	1.00E-37	144.058	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	105	257	8.21E-36	138.28	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	9620	9774	1.09E-35	137.894	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	3960	4113	4.00E-35	136.354	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	5610	5765	2.79E-34	134.042	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	4388	4549	5.66E-34	132.887	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	9193	9353	4.60E-33	130.576	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	5408	5562	2.92E-32	128.264	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	1680	1837	5.92E-32	127.109	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	7260	7414	1.01E-31	126.338	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	2	97	1.24E-26	111.701	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	7685	7848	6.39E-24	103.612	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	6039	6176	1.70E-23	102.456	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	8533	8692	1.31E-20	93.9817	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	243051	8979	9138	1.08E-13	73.5661	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	241613	9375	9409	2.35E-10	60.6833	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	8495	8529	2.99E-10	60.2981	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	9863	9899	6.86E-10	59.5278	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	9578	9613	1.00E-09	58.7574	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	7857	7891	1.33E-09	58.7574	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	6001	6036	1.42E-09	58.3722	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	5775	5808	6.23E-09	56.8314	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	4351	4385	1.03E-08	56.061	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	8074	8108	1.18E-08	55.6758	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	8280	8313	2.43E-08	54.9054	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	8704	8734	4.01E-08	54.135	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	9149	9180	1.07E-07	52.9794	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	4123	4157	1.35E-07	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	9788	9822	2.24E-07	52.209	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	8938	8974	3.72E-07	51.4386	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	7430	7458	1.46E-06	49.8978	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	7651	7682	4.26E-05	45.2754	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	7226	7256	0.000375763	42.579	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	241613	5580	5607	0.00694404	38.727	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11741 - 	CGI_10022523	superfamily	243051	8112	8269	1.53E-12	70.0993	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11741 - 	CGI_10022523	superfamily	241613	9902	9938	0.00718309	38.8162	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#11742 - 	CGI_10022524	superfamily	243051	431	593	3.46E-46	163.703	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11742 - 	CGI_10022524	superfamily	243051	599	757	1.23E-43	156.769	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11742 - 	CGI_10022524	superfamily	243051	114	273	1.22E-40	148.295	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11742 - 	CGI_10022524	superfamily	243051	792	927	9.07E-40	145.598	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11742 - 	CGI_10022524	superfamily	243051	304	412	1.92E-33	127.494	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11742 - 	CGI_10022524	superfamily	243051	1	108	8.99E-29	114.012	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11742 - 	CGI_10022524	superfamily	243051	936	982	0.0014754	38.8709	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	540	696	1.23E-54	189.896	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	720	880	6.77E-49	173.333	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	1615	1771	5.57E-48	171.022	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	885	1042	3.14E-47	168.71	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	1073	1226	6.19E-46	164.858	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	1246	1400	1.45E-45	164.088	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	1406	1563	1.63E-39	146.369	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	21	183	1.09E-37	141.361	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	204	360	1.67E-36	137.894	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	366	497	4.44E-32	125.183	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11743 - 	CGI_10022525	superfamily	243051	1793	1837	2.18E-07	51.5825	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#11744 - 	CGI_10022526	superfamily	241647	145	171	0.00730793	36.0072	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#11745 - 	CGI_10022527	superfamily	248458	210	376	1.24E-09	58.0941	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11746 - 	CGI_10022528	superfamily	241555	9	102	4.99E-21	83.8388	cl00020	GAT_1 superfamily	C	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#11747 - 	CGI_10022529	superfamily	201526	15	83	1.44E-24	91.0604	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#11748 - 	CGI_10022530	superfamily	243689	22	102	2.32E-09	55.7125	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#11748 - 	CGI_10022530	superfamily	219817	104	213	6.31E-05	42.9905	cl07129	Xpo1 superfamily	C	 - 	"Exportin 1-like protein; The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus."
Q#11749 - 	CGI_10022531	superfamily	241832	57	169	1.16E-53	169.291	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#11750 - 	CGI_10022532	superfamily	242206	22	122	2.14E-17	77.529	cl00938	Rieske superfamily	 - 	 - 	"Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis."
Q#11750 - 	CGI_10022532	superfamily	241737	235	362	1.36E-07	49.4168	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#11752 - 	CGI_10022534	superfamily	243091	247	302	3.37E-05	41.7088	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#11753 - 	CGI_10022535	superfamily	243540	157	378	7.41E-57	187.455	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#11756 - 	CGI_10022538	superfamily	243186	4	135	1.30E-43	143.774	cl02788	Ser_Recombinase superfamily	 - 	 - 	"Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are proteins with N-terminal DNA binding domains similar to IS607- and IS1535-transposases from Helicobacter and Mycobacterium."
Q#11756 - 	CGI_10022538	superfamily	247947	147	187	6.19E-10	51.6165	cl17393	HTH_Hin_like superfamily	 - 	 - 	"Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a DNA-binding domain (HTH_Hin) and a catalytic domain."
Q#11757 - 	CGI_10022539	superfamily	203644	62	109	8.92E-13	61.4242	cl10081	Collar superfamily	 - 	 - 	"Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance rhiB from Rhizobium leguminosarum may be involved in plant-microbe interactions. A related protein mrpB is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of Bacteriophage T4 short tail fiber protein appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution."
Q#11759 - 	CGI_10022541	superfamily	241563	71	109	2.19E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11760 - 	CGI_10002919	superfamily	242064	46	150	3.01E-64	194.671	cl00748	Ribosomal_L32_L32e superfamily	 - 	 - 	"Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea."
Q#11761 - 	CGI_10000675	superfamily	247999	614	659	3.88E-14	68.0073	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#11762 - 	CGI_10000676	superfamily	248099	3	79	2.09E-25	97.395	cl17545	Bromo_TP superfamily	 - 	 - 	Bromodomain associated; This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold.
Q#11763 - 	CGI_10000319	superfamily	192535	47	172	1.58E-05	44.509	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#11764 - 	CGI_10015471	superfamily	247675	4	103	3.06E-48	162.928	cl17011	Arginase_HDAC superfamily	N	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#11765 - 	CGI_10015472	superfamily	246664	828	1270	0	775.713	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#11765 - 	CGI_10015472	superfamily	245814	407	488	3.19E-18	82.168	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11765 - 	CGI_10015472	superfamily	245814	316	396	9.65E-16	74.8492	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11765 - 	CGI_10015472	superfamily	248289	1380	1435	7.46E-13	65.9083	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#11765 - 	CGI_10015472	superfamily	245814	222	289	7.80E-12	63.5681	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11765 - 	CGI_10015472	superfamily	246664	757	801	1.75E-08	56.935	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#11765 - 	CGI_10015472	superfamily	245814	506	568	1.91E-08	53.1795	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11766 - 	CGI_10015473	superfamily	247907	2	141	2.23E-14	72.4508	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#11766 - 	CGI_10015473	superfamily	247907	649	815	2.45E-07	50.8797	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#11766 - 	CGI_10015473	superfamily	245213	164	200	0.000149443	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11766 - 	CGI_10015473	superfamily	245213	609	642	0.00038779	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11766 - 	CGI_10015473	superfamily	247907	499	585	0.000518457	40.4006	cl17353	LamG superfamily	N	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#11766 - 	CGI_10015473	superfamily	247907	884	962	0.00131615	38.9688	cl17353	LamG superfamily	N	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#11766 - 	CGI_10015473	superfamily	247907	287	337	0.00361296	37.8132	cl17353	LamG superfamily	C	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#11768 - 	CGI_10015475	superfamily	128837	88	117	2.49E-06	43.5584	cl17973	EZ_HEAT superfamily	 - 	 - 	"E-Z type HEAT repeats; Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role."
Q#11768 - 	CGI_10015475	superfamily	128837	241	270	3.22E-05	40.4768	cl17973	EZ_HEAT superfamily	 - 	 - 	"E-Z type HEAT repeats; Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role."
Q#11768 - 	CGI_10015475	superfamily	128837	177	206	0.00115455	35.8544	cl17973	EZ_HEAT superfamily	 - 	 - 	"E-Z type HEAT repeats; Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role."
Q#11768 - 	CGI_10015475	superfamily	128837	208	236	0.00269869	34.6988	cl17973	EZ_HEAT superfamily	 - 	 - 	"E-Z type HEAT repeats; Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role."
Q#11772 - 	CGI_10015479	superfamily	243061	87	173	2.55E-17	73.5302	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11772 - 	CGI_10015479	superfamily	243061	2	71	5.59E-12	58.5074	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11774 - 	CGI_10015482	superfamily	115363	284	343	2.78E-14	68.5525	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#11774 - 	CGI_10015482	superfamily	115363	213	260	2.19E-08	51.6038	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#11774 - 	CGI_10015482	superfamily	241578	43	116	0.00217367	37.9649	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11775 - 	CGI_10015483	superfamily	115363	269	324	7.47E-13	63.5449	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#11775 - 	CGI_10015483	superfamily	115363	198	256	9.79E-07	45.8258	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#11776 - 	CGI_10015485	superfamily	243035	3	117	2.17E-25	93.8385	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11785 - 	CGI_10009729	superfamily	247727	87	200	1.17E-17	76.6998	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#11787 - 	CGI_10009731	superfamily	245539	418	483	4.51E-26	100.706	cl11186	Cullin_Nedd8 superfamily	 - 	 - 	"Cullin protein neddylation domain; This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue."
Q#11788 - 	CGI_10009732	superfamily	246748	1045	1197	1.98E-25	108.449	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#11788 - 	CGI_10009732	superfamily	216290	836	945	1.12E-21	93.5069	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#11788 - 	CGI_10009732	superfamily	202944	1300	1410	0.00396452	37.6353	cl07854	TFR_dimer superfamily	 - 	 - 	Transferrin receptor-like dimerisation domain; This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
Q#11792 - 	CGI_10020816	superfamily	216599	89	496	0	580.001	cl18372	B56 superfamily	 - 	 - 	"Protein phosphatase 2A regulatory B subunit (B56 family); Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also pfam01240), this family is called the B56 family."
Q#11794 - 	CGI_10020818	superfamily	241610	53	107	1.58E-08	46.8594	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#11794 - 	CGI_10020818	superfamily	241610	15	52	0.00977297	30.681	cl00101	KU superfamily	N	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#11797 - 	CGI_10020821	superfamily	241563	64	96	3.68E-05	41.504	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11797 - 	CGI_10020821	superfamily	245010	103	197	0.00930524	34.9011	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#11799 - 	CGI_10020823	superfamily	241563	77	109	5.82E-05	41.1188	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11799 - 	CGI_10020823	superfamily	245010	110	210	0.000337816	39.1383	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#11800 - 	CGI_10020824	superfamily	241563	64	96	5.25E-05	41.1188	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11800 - 	CGI_10020824	superfamily	245010	103	197	0.00478897	35.6715	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#11804 - 	CGI_10020828	superfamily	241610	23	75	6.66E-22	86.9202	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#11804 - 	CGI_10020828	superfamily	241610	1	23	0.000120229	39.2041	cl00101	KU superfamily	N	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#11805 - 	CGI_10020829	superfamily	241563	64	96	4.27E-05	41.504	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11805 - 	CGI_10020829	superfamily	245010	103	197	0.0035251	36.0567	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#11807 - 	CGI_10020831	superfamily	248312	2	105	0.00178108	35.7921	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#11812 - 	CGI_10020836	superfamily	201590	212	286	5.00E-07	49.5186	cl03090	HH_signal superfamily	N	 - 	"Hedgehog amino-terminal signalling domain; For the carboxyl Hint module, see pfam01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation."
Q#11814 - 	CGI_10020838	superfamily	247724	2594	2758	9.66E-91	296.306	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11814 - 	CGI_10020838	superfamily	243185	2770	2857	9.46E-31	120.667	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#11814 - 	CGI_10020838	superfamily	243185	3030	3117	7.51E-26	106.031	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#11814 - 	CGI_10020838	superfamily	247038	273	333	7.70E-05	44.3677	cl15674	IPT superfamily	N	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#11814 - 	CGI_10020838	superfamily	245201	32	272	3.44E-142	448.81	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11814 - 	CGI_10020838	superfamily	220608	340	459	6.23E-35	133.585	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#11814 - 	CGI_10020838	superfamily	221359	2923	3011	4.74E-26	107.532	cl13429	IF-2 superfamily	 - 	 - 	"Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes, Bacteria and Archaea). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyzes the hydrolysis of GTP following initiation-complex formation."
Q#11814 - 	CGI_10020838	superfamily	220608	1162	1287	1.51E-22	97.7618	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#11820 - 	CGI_10024411	superfamily	110440	85	109	0.000317062	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11820 - 	CGI_10024411	superfamily	110440	124	151	0.000332348	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#11821 - 	CGI_10024412	superfamily	245847	49	104	0.000975553	37.8672	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#11822 - 	CGI_10024413	superfamily	243066	4	93	2.92E-24	96.0828	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11822 - 	CGI_10024413	superfamily	219619	315	391	1.12E-11	60.6843	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#11824 - 	CGI_10024415	superfamily	243035	216	283	3.48E-16	72.2673	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11827 - 	CGI_10024419	superfamily	241578	287	454	2.85E-43	153.91	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11827 - 	CGI_10024419	superfamily	207701	34	147	4.39E-15	72.7759	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#11828 - 	CGI_10024420	superfamily	245814	119	179	1.14E-05	43.2629	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11831 - 	CGI_10024423	superfamily	247792	679	724	6.20E-13	64.7744	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11833 - 	CGI_10024425	superfamily	246681	17	135	9.61E-16	70.0762	cl14643	SRPBCC superfamily	C	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#11834 - 	CGI_10024426	superfamily	247856	46	99	0.00187779	33.6753	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#11842 - 	CGI_10024434	superfamily	246664	2	477	0	667.816	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#11843 - 	CGI_10024435	superfamily	149105	606	678	0.00116859	40.4961	cl12353	TMPIT superfamily	C	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#11844 - 	CGI_10024436	superfamily	241600	45	206	3.36E-21	87.681	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#11845 - 	CGI_10024437	superfamily	243074	54	100	8.58E-14	67.1465	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#11845 - 	CGI_10024437	superfamily	243092	674	737	1.57E-07	52.3372	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11845 - 	CGI_10024437	superfamily	243092	135	168	2.42E-07	48.4626	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11846 - 	CGI_10024438	superfamily	243034	40	134	2.68E-08	51.9972	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#11846 - 	CGI_10024438	superfamily	243034	194	287	2.57E-07	48.9156	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#11846 - 	CGI_10024438	superfamily	243034	259	330	0.00022748	39.6708	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#11846 - 	CGI_10024438	superfamily	245875	428	450	1.40E-05	42.6909	cl12112	GoLoco superfamily	 - 	 - 	GoLoco motif; GoLoco motif.  
Q#11846 - 	CGI_10024438	superfamily	245875	519	539	2.34E-05	41.9205	cl12112	GoLoco superfamily	 - 	 - 	GoLoco motif; GoLoco motif.  
Q#11846 - 	CGI_10024438	superfamily	245875	552	574	4.28E-05	41.1501	cl12112	GoLoco superfamily	 - 	 - 	GoLoco motif; GoLoco motif.  
Q#11846 - 	CGI_10024438	superfamily	245875	473	494	0.000421362	38.4537	cl12112	GoLoco superfamily	 - 	 - 	GoLoco motif; GoLoco motif.  
Q#11848 - 	CGI_10024440	superfamily	247727	263	359	5.20E-07	47.4247	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#11849 - 	CGI_10024441	superfamily	241640	470	647	1.24E-41	150.504	cl00149	Tryp_SPc superfamily	N	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#11849 - 	CGI_10024441	superfamily	241640	246	473	4.45E-34	129.704	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#11849 - 	CGI_10024441	superfamily	243066	31	125	4.65E-14	68.7981	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11851 - 	CGI_10024443	superfamily	219619	382	450	6.21E-19	81.8703	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#11851 - 	CGI_10024443	superfamily	219619	163	216	7.39E-08	50.284	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#11854 - 	CGI_10024446	superfamily	241680	37	241	5.92E-41	144.318	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#11855 - 	CGI_10024447	superfamily	241680	37	243	3.44E-42	146.244	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#11856 - 	CGI_10024448	superfamily	241550	217	361	1.22E-63	209.75	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#11856 - 	CGI_10024448	superfamily	241550	32	130	4.53E-51	176.238	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#11857 - 	CGI_10024449	superfamily	219999	2	125	2.21E-15	69.7385	cl18540	Nse4 superfamily	C	 - 	Nse4; Nse4 is a component of the Smc5/6 DNA repair complex. It forms interactions with Smc5 and Nse1.
Q#11858 - 	CGI_10024450	superfamily	219999	35	302	2.96E-52	181.446	cl18540	Nse4 superfamily	 - 	 - 	Nse4; Nse4 is a component of the Smc5/6 DNA repair complex. It forms interactions with Smc5 and Nse1.
Q#11859 - 	CGI_10024451	superfamily	245814	65	144	0.00685489	34.7723	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11859 - 	CGI_10024451	superfamily	245814	165	248	0.000997832	37.0997	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#11860 - 	CGI_10024452	superfamily	243061	2	71	4.57E-15	64.6706	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11863 - 	CGI_10004311	superfamily	217293	28	226	6.02E-30	115.037	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11863 - 	CGI_10004311	superfamily	202474	233	311	1.10E-12	65.7529	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11868 - 	CGI_10001561	superfamily	241578	118	268	4.98E-27	105.066	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11868 - 	CGI_10001561	superfamily	245213	37	72	4.96E-10	54.565	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11868 - 	CGI_10001561	superfamily	245213	1	34	4.90E-09	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11868 - 	CGI_10001561	superfamily	245213	74	110	3.98E-08	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11868 - 	CGI_10001561	superfamily	241578	304	387	5.13E-07	47.6714	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#11869 - 	CGI_10023652	superfamily	246723	22	591	0	812.952	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#11870 - 	CGI_10023653	superfamily	247775	56	496	2.64E-64	216.297	cl17221	ArsB_NhaD_permease superfamily	 - 	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#11872 - 	CGI_10023655	superfamily	247775	39	565	9.39E-48	174.066	cl17221	ArsB_NhaD_permease superfamily	 - 	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#11874 - 	CGI_10023657	superfamily	131388	34	252	2.86E-12	66.8469	cl17985	hydr_PhnA superfamily	C	 - 	"phosphonoacetate hydrolase; This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile that the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for pther specific phosphonatases."
Q#11875 - 	CGI_10023658	superfamily	247866	46	274	5.65E-16	76.7224	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#11875 - 	CGI_10023658	superfamily	243179	422	557	4.57E-11	60.2391	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#11878 - 	CGI_10023661	superfamily	241607	94	129	2.73E-08	47.6498	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#11878 - 	CGI_10023661	superfamily	241607	135	169	1.19E-05	40.331	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#11878 - 	CGI_10023661	superfamily	241607	166	199	0.000512261	36.1282	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#11884 - 	CGI_10023667	superfamily	247057	554	622	1.35E-20	87.7428	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#11884 - 	CGI_10023667	superfamily	247057	623	686	2.90E-22	92.3571	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#11884 - 	CGI_10023667	superfamily	248012	715	826	3.51E-17	78.7736	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#11886 - 	CGI_10023669	superfamily	220395	26	200	6.34E-43	144.832	cl10757	Guanylate_cyc_2 superfamily	 - 	 - 	"Guanylylate cyclase; Members of this family of proteins catalyze the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate."
Q#11887 - 	CGI_10023670	superfamily	241555	5	97	8.15E-38	126.505	cl00020	GAT_1 superfamily	C	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#11888 - 	CGI_10023671	superfamily	247724	25	181	3.07E-47	154.921	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11889 - 	CGI_10023672	superfamily	247724	21	179	1.38E-49	160.699	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11890 - 	CGI_10023673	superfamily	248458	95	204	0.00017449	42.3009	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11893 - 	CGI_10023676	superfamily	245201	674	913	2.41E-39	146.228	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11896 - 	CGI_10023679	superfamily	241832	52	255	5.42E-66	210.225	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#11896 - 	CGI_10023679	superfamily	241832	253	371	9.58E-49	165.157	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#11898 - 	CGI_10023681	superfamily	243066	40	115	6.62E-09	49.1529	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#11901 - 	CGI_10023684	superfamily	216063	868	1046	1.53E-44	160.862	cl02929	Cation_ATPase_C superfamily	 - 	 - 	"Cation transporting ATPase, C-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices."
Q#11901 - 	CGI_10023684	superfamily	215733	141	274	9.40E-32	125.37	cl02811	E1-E2_ATPase superfamily	C	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#11901 - 	CGI_10023684	superfamily	222006	503	590	1.57E-20	88.8186	cl16182	Hydrolase_like2 superfamily	 - 	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#11901 - 	CGI_10023684	superfamily	215733	357	469	2.22E-15	76.4498	cl02811	E1-E2_ATPase superfamily	N	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#11901 - 	CGI_10023684	superfamily	152858	1088	1121	2.61E-12	64.3976	cl13811	ATP_Ca_trans_C superfamily	C	 - 	"Plasma membrane calcium transporter ATPase C terminal; This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam00689, pfam00122, pfam00702, pfam00690. There is a conserved QTQ sequence motif. This family is the C terminal of a calcium transporting ATPase located in the plasma membrane."
Q#11901 - 	CGI_10023684	superfamily	243244	43	102	2.43E-08	52.923	cl02930	Cation_ATPase_N superfamily	 - 	 - 	"Cation transporter/ATPase, N-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport."
Q#11902 - 	CGI_10023685	superfamily	245864	39	501	1.15E-102	318.068	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#11903 - 	CGI_10023686	superfamily	241596	67	108	6.86E-10	52.9867	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#11906 - 	CGI_10023689	superfamily	241563	60	95	0.000953966	37.3167	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11911 - 	CGI_10023694	superfamily	243035	29	151	2.35E-05	39.9106	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11912 - 	CGI_10023695	superfamily	243035	110	226	4.77E-08	49.5406	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#11913 - 	CGI_10023696	superfamily	222429	13	56	0.00456991	31.8273	cl18676	Myb_DNA-bind_5 superfamily	C	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#11914 - 	CGI_10014965	superfamily	241823	21	183	8.71E-90	268.677	cl00376	Ribosomal_L10_P0 superfamily	 - 	 - 	"Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2."
Q#11915 - 	CGI_10014966	superfamily	242880	6	285	2.05E-103	304.499	cl02098	14-3-3 superfamily	 - 	 - 	"14-3-3 domain; 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 14-3-3 proteins play important roles in many biological processes that are regulated by phosphorylation, including cell cycle regulation, cell proliferation, protein trafficking, metabolic regulation and apoptosis.  More than 300 binding partners of the 14-3-3 domain have been identified in all subcellular compartments and include transcription factors, signaling molecules, tumor suppressors, biosynthetic enzymes, cytoskeletal proteins and apoptosis factors. 14-3-3 binding can alter the conformation, localization, stability, phosphorylation state, activity as well as molecular interactions of a target protein. They function only as dimers, some preferring strictly homodimeric interaction, while others form heterodimers. Binding of the 14-3-3 domain to its target occurs in a phosphospecific manner where it binds to one of two consensus sequences of their target proteins; RSXpSXP (mode-1) and RXXXpSXP (mode-2). In some instances, 14-3-3 domain containing proteins are involved in regulation and signaling of a number of cellular processes in phosphorylation-independent manner. Many organisms express multiple isoforms: there are seven mammalian 14-3-3 family members (beta, gamma, eta, theta, epsilon, sigma, zeta), each encoded by a distinct gene, while plants contain up to 13 isoforms. The flexible C-terminal segment of 14-3-3 isoforms shows the highest sequence variability and may significantly contribute to individual isoform uniqueness by playing an important regulatory role by occupying the ligand binding groove and blocking the binding of inappropriate ligands in a distinct manner. Elevated amounts of 14-3-3 proteins are found in the cerebrospinal fluid of patients with Creutzfeldt-Jakob disease. In protozoa, like Plasmodium or Cryptosporidium parvum 14-3-3 proteins play an important role in key steps of parasite development."
Q#11916 - 	CGI_10014967	superfamily	248458	541	685	1.81E-10	61.9461	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11916 - 	CGI_10014967	superfamily	248458	76	137	0.000731749	41.1453	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#11917 - 	CGI_10014968	superfamily	245596	75	287	2.30E-59	195.82	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#11918 - 	CGI_10014969	superfamily	247792	234	274	7.55E-06	42.4328	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11918 - 	CGI_10014969	superfamily	245716	167	196	0.00410321	34.4563	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#11919 - 	CGI_10014970	superfamily	247724	57	425	1.59E-118	351.058	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11920 - 	CGI_10014971	superfamily	247724	57	424	1.19E-118	351.444	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11922 - 	CGI_10014973	superfamily	247724	445	803	1.05E-115	356.066	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11922 - 	CGI_10014973	superfamily	247724	57	410	1.24E-102	321.783	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11923 - 	CGI_10014974	superfamily	247724	82	336	2.54E-62	203.142	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11923 - 	CGI_10014974	superfamily	247724	57	79	6.55E-08	52.1436	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#11925 - 	CGI_10014976	superfamily	243088	95	219	2.65E-46	158.309	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#11925 - 	CGI_10014976	superfamily	149621	356	459	6.36E-19	82.3324	cl07303	Nexin_C superfamily	 - 	 - 	Sorting nexin C terminal; This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787.
Q#11926 - 	CGI_10014977	superfamily	243089	66	238	1.10E-40	143.168	cl02564	PXA superfamily	 - 	 - 	PXA domain; This domain is associated with PX domains pfam00787.
Q#11926 - 	CGI_10014977	superfamily	243090	279	357	7.19E-28	106.271	cl02565	RGS superfamily	C	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#11928 - 	CGI_10014979	superfamily	243092	339	626	2.87E-87	276.138	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#11929 - 	CGI_10014980	superfamily	222150	282	307	6.73E-05	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11929 - 	CGI_10014980	superfamily	222150	198	222	0.00142145	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11929 - 	CGI_10014980	superfamily	222150	338	363	0.00260379	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#11932 - 	CGI_10014983	superfamily	247068	60	154	4.04E-12	62.3309	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11932 - 	CGI_10014983	superfamily	247068	262	340	1.08E-09	55.3974	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11932 - 	CGI_10014983	superfamily	247068	173	254	1.13E-05	43.4562	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#11935 - 	CGI_10018371	superfamily	241570	43	180	3.50E-13	66.9658	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#11935 - 	CGI_10018371	superfamily	241570	198	248	0.00474797	36.1498	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#11937 - 	CGI_10018373	superfamily	115027	123	349	2.16E-14	72.0957	cl17947	DUF1057 superfamily	C	 - 	Alpha/beta hydrolase of unknown function (DUF1057); This family consists of several Caenorhabditis elegans specific proteins of unknown function. Members of this family have an alpha/beta hydrolase fold.
Q#11938 - 	CGI_10018374	superfamily	247792	26	71	1.90E-05	42.818	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11938 - 	CGI_10018374	superfamily	128778	217	342	4.03E-08	52.2671	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#11938 - 	CGI_10018374	superfamily	216033	396	469	2.87E-05	43.0912	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#11938 - 	CGI_10018374	superfamily	241563	171	209	0.00406147	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11938 - 	CGI_10018374	superfamily	241563	104	141	0.00795071	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11940 - 	CGI_10018376	superfamily	247941	131	267	2.53E-08	51.1825	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#11941 - 	CGI_10018377	superfamily	243034	102	134	0.00160445	33.6419	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#11942 - 	CGI_10018378	superfamily	243074	12	63	1.61E-06	45.9605	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#11946 - 	CGI_10018382	superfamily	113205	196	321	4.60E-51	172.582	cl04510	DUF544 superfamily	 - 	 - 	Protein of unknown function (DUF544); Eukaryotic protein of unknown function.
Q#11947 - 	CGI_10018383	superfamily	117815	342	491	4.60E-81	255.127	cl07780	BTD superfamily	 - 	 - 	"Beta-trefoil DNA-binding domain; Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR)."
Q#11947 - 	CGI_10018383	superfamily	220160	210	341	1.08E-60	200.349	cl07781	LAG1-DNAbind superfamily	 - 	 - 	"LAG1, DNA binding; Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding. This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins."
Q#11947 - 	CGI_10018383	superfamily	247038	521	609	9.96E-43	149.145	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#11948 - 	CGI_10018384	superfamily	247792	130	179	0.0016251	35.114	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11949 - 	CGI_10018385	superfamily	218280	1	111	2.38E-52	176.641	cl04781	Rad21_Rec8_N superfamily	 - 	 - 	"N terminus of Rad21 / Rec8 like protein; This family represents a conserved N-terminal region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Members of this family mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation."
Q#11949 - 	CGI_10018385	superfamily	113590	586	638	3.80E-11	59.2718	cl04780	Rad21_Rec8 superfamily	 - 	 - 	"Conserved region of Rad21 / Rec8 like protein; This family represents a conserved region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Members of this family mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation."
Q#11950 - 	CGI_10018386	superfamily	248388	311	381	0.000422178	39.6193	cl17834	Ser_hydrolase superfamily	N	 - 	"Serine hydrolase; Members of this family have serine hydrolase activity. They contain a conserved serine hydrolase motif, GXSXG/A, where the serine is a putative nucleophile. This family has an alpha-beta hydrolase fold. Eukaryotic members of this family have a conserved LXCXE motif, which binds to retinoblastomas. This motif is absent from prokaryotic members of this family."
Q#11952 - 	CGI_10018388	superfamily	217293	15	149	5.73E-19	84.2215	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11954 - 	CGI_10018390	superfamily	216554	421	563	4.32E-26	105.254	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#11954 - 	CGI_10018390	superfamily	216554	113	250	2.64E-24	100.247	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#11955 - 	CGI_10018391	superfamily	217355	239	615	0	582.872	cl03873	GCS superfamily	 - 	 - 	"Glutamate-cysteine ligase; This family represents the catalytic subunit of glutamate-cysteine ligase (E.C. 6.3.2.2), also known as gamma-glutamylcysteine synthetase (GCS). This enzyme catalyzes the rate limiting step in the biosynthesis of glutathione. The eukaryotic enzyme is a dimer of a heavy chain and a light chain with all the catalytic activity exhibited by the heavy chain (this family)."
Q#11958 - 	CGI_10018394	superfamily	243061	96	197	2.20E-41	138.629	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11958 - 	CGI_10018394	superfamily	243061	37	90	1.72E-17	74.6858	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11959 - 	CGI_10018395	superfamily	243061	67	168	2.04E-37	127.073	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11959 - 	CGI_10018395	superfamily	243061	8	61	6.09E-14	64.2854	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#11960 - 	CGI_10018396	superfamily	246940	64	258	1.21E-19	84.6925	cl15377	Radical_SAM superfamily	 - 	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#11961 - 	CGI_10018397	superfamily	247792	18	69	3.58E-07	47.8256	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#11961 - 	CGI_10018397	superfamily	241563	209	238	0.000382903	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#11962 - 	CGI_10018398	superfamily	241599	97	151	1.40E-23	91.536	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#11962 - 	CGI_10018398	superfamily	146451	265	285	5.36E-07	45.4279	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#11964 - 	CGI_10018400	superfamily	217293	27	226	1.89E-31	119.275	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#11964 - 	CGI_10018400	superfamily	202474	234	316	6.20E-17	78.0793	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#11966 - 	CGI_10018402	superfamily	247743	12	142	0.00032896	40.9775	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#11966 - 	CGI_10018402	superfamily	221913	211	410	3.93E-47	168.103	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#11967 - 	CGI_10018403	superfamily	245716	172	194	0.00434474	35.6119	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#11968 - 	CGI_10018404	superfamily	217613	164	282	2.72E-42	143.084	cl04154	Cullin_binding superfamily	 - 	 - 	"Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices."
Q#11970 - 	CGI_10003419	superfamily	246675	1	293	5.47E-88	274.878	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#11971 - 	CGI_10013115	superfamily	247794	1	264	1.52E-149	432.61	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#11973 - 	CGI_10013117	superfamily	245819	612	788	3.44E-67	221.684	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#11973 - 	CGI_10013117	superfamily	245225	101	269	6.57E-32	128.198	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#11973 - 	CGI_10013117	superfamily	245201	320	536	1.07E-30	121.875	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11973 - 	CGI_10013117	superfamily	219526	553	598	5.90E-07	49.5399	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#11974 - 	CGI_10013119	superfamily	247772	157	207	1.15E-07	47.2396	cl17218	Cupin_2 superfamily	C	 - 	Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).
Q#11975 - 	CGI_10013120	superfamily	245596	3	150	3.09E-43	153.618	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#11976 - 	CGI_10013121	superfamily	215647	91	330	1.52E-58	193.209	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#11976 - 	CGI_10013121	superfamily	243029	16	71	4.31E-13	63.9089	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#11978 - 	CGI_10013123	superfamily	219541	302	440	1.05E-26	106.013	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#11978 - 	CGI_10013123	superfamily	215896	77	187	9.75E-15	71.9424	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#11979 - 	CGI_10013124	superfamily	241585	407	453	1.84E-06	47.5136	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#11979 - 	CGI_10013124	superfamily	241585	549	596	1.84E-05	44.8172	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#11979 - 	CGI_10013124	superfamily	241585	697	741	0.000219121	41.3504	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#11979 - 	CGI_10013124	superfamily	241585	454	494	0.000419621	40.58	cl00066	FU superfamily	C	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#11979 - 	CGI_10013124	superfamily	241585	502	545	0.000517832	40.1948	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#11979 - 	CGI_10013124	superfamily	207627	1746	1840	1.42E-15	75.3639	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#11979 - 	CGI_10013124	superfamily	248289	107	164	5.42E-11	60.9007	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#11979 - 	CGI_10013124	superfamily	248289	299	354	7.68E-10	57.8191	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#11979 - 	CGI_10013124	superfamily	207627	1641	1718	7.80E-08	52.2567	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#11979 - 	CGI_10013124	superfamily	248289	43	100	9.64E-08	51.6559	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#11979 - 	CGI_10013124	superfamily	248289	169	229	7.20E-07	49.0516	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#11979 - 	CGI_10013124	superfamily	248289	246	293	4.39E-06	46.6483	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#11979 - 	CGI_10013124	superfamily	219541	1910	1937	0.000191528	42.4555	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#11979 - 	CGI_10013124	superfamily	241585	644	683	0.00240395	38.2598	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#11980 - 	CGI_10013125	superfamily	245213	92	122	5.95E-06	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#11980 - 	CGI_10013125	superfamily	241611	135	242	4.62E-07	47.3832	cl00102	PTX superfamily	C	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#11981 - 	CGI_10000658	superfamily	222429	6	82	1.86E-16	70.7324	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#11984 - 	CGI_10000694	superfamily	219542	61	89	8.38E-06	39.5324	cl18517	Cu-oxidase_3 superfamily	C	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#11986 - 	CGI_10000918	superfamily	241900	10	182	2.11E-23	93.8674	cl00490	EEP superfamily	C	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#11987 - 	CGI_10001018	superfamily	245201	134	295	2.85E-21	94.1404	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11987 - 	CGI_10001018	superfamily	245201	428	532	2.78E-15	75.6508	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#11991 - 	CGI_10001367	superfamily	215647	3	212	9.65E-06	44.5217	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#11994 - 	CGI_10008824	superfamily	220231	3	165	1.24E-12	62.0675	cl09664	Nop16 superfamily	 - 	 - 	Ribosome biogenesis protein Nop16; Nop16 is a protein involved in ribosome biogenesis.
Q#11998 - 	CGI_10008828	superfamily	241573	17	344	2.82E-106	326.981	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#11998 - 	CGI_10008828	superfamily	246669	518	640	5.26E-42	148.195	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#11998 - 	CGI_10008828	superfamily	241653	355	495	3.01E-37	135.889	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#12000 - 	CGI_10008830	superfamily	243082	950	1162	7.94E-53	186.339	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#12000 - 	CGI_10008830	superfamily	243082	526	564	5.60E-13	68.8534	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#12000 - 	CGI_10008830	superfamily	243082	48	205	1.36E-05	47.6985	cl02553	Peptidase_C19 superfamily	NC	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#12000 - 	CGI_10008830	superfamily	247792	876	924	0.000397184	39.6836	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12003 - 	CGI_10001455	superfamily	248097	114	235	2.64E-16	72.2978	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12003 - 	CGI_10001455	superfamily	248097	54	123	7.09E-10	54.1934	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12004 - 	CGI_10011054	superfamily	248012	344	443	2.75E-23	94.5668	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12006 - 	CGI_10011056	superfamily	243058	405	499	1.73E-08	53.0871	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#12006 - 	CGI_10011056	superfamily	248012	534	619	6.25E-23	94.952	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12007 - 	CGI_10011057	superfamily	241578	600	754	2.77E-14	73.0946	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12007 - 	CGI_10011057	superfamily	241578	1739	1898	7.98E-11	62.6942	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12007 - 	CGI_10011057	superfamily	241578	38	148	7.40E-17	81.1202	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12007 - 	CGI_10011057	superfamily	243119	1951	2007	3.94E-05	43.5765	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#12007 - 	CGI_10011057	superfamily	241578	1523	1672	0.000231772	42.8268	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12007 - 	CGI_10011057	superfamily	243119	260	316	0.000853288	39.7346	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#12010 - 	CGI_10011060	superfamily	243090	344	464	5.44E-65	211.051	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#12010 - 	CGI_10011060	superfamily	243090	185	328	2.92E-24	100.22	cl02565	RGS superfamily	N	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#12010 - 	CGI_10011060	superfamily	243090	51	110	3.92E-15	73.6408	cl02565	RGS superfamily	C	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#12015 - 	CGI_10011065	superfamily	245864	43	502	2.88E-84	270.304	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12018 - 	CGI_10011068	superfamily	222429	5	69	2.88E-06	44.5388	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#12019 - 	CGI_10011069	superfamily	247723	64	129	1.26E-30	106.538	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#12022 - 	CGI_10001944	superfamily	245596	6	286	4.54E-140	406.577	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12022 - 	CGI_10001944	superfamily	247772	332	473	1.33E-88	269.915	cl17218	Cupin_2 superfamily	 - 	 - 	Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).
Q#12023 - 	CGI_10001945	superfamily	243519	6	454	0	574.846	cl03757	phosphohexomutase superfamily	 - 	 - 	"The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model."
Q#12024 - 	CGI_10001946	superfamily	242207	234	464	6.25E-103	309.167	cl00939	Bac_transf superfamily	 - 	 - 	"Bacterial sugar transferase; This Pfam family represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways."
Q#12025 - 	CGI_10001948	superfamily	245023	1	426	0	854.211	cl09156	PS_pyruv_trans superfamily	 - 	 - 	Polysaccharide pyruvyl transferase; Pyruvyl-transferases involved in peptidoglycan-associated polymer biosynthesis. CsaB in Bacillus anthracis is necessary for the non-covalent anchoring of proteins containing an SLH (S-layer homology) domain to peptidoglycan-associated pyruvylated polysaccharides. WcaK and AmsJ are involved in the biosynthesis of colanic acid in Escherichia coli and of amylovoran in Erwinia amylovora.
Q#12026 - 	CGI_10001949	superfamily	245227	69	372	2.72E-109	327.204	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#12027 - 	CGI_10001952	superfamily	246713	114	273	1.35E-27	105.016	cl14786	ENDO3c superfamily	 - 	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#12027 - 	CGI_10001952	superfamily	244116	6	92	1.57E-28	106.508	cl05528	AlkA_N superfamily	C	 - 	AlkA N-terminal domain; AlkA N-terminal domain.  
Q#12028 - 	CGI_10001953	superfamily	245819	82	196	6.90E-29	110.724	cl11967	Nucleotidyl_cyc_III superfamily	N	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#12028 - 	CGI_10001953	superfamily	241757	274	450	1.04E-13	69.1115	cl00290	EAL superfamily	N	 - 	"EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2).  The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria."
Q#12028 - 	CGI_10001953	superfamily	247824	1	84	2.98E-36	134.304	cl17270	APH_ChoK_like superfamily	N	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#12030 - 	CGI_10001955	superfamily	247744	10	208	1.88E-98	287.143	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#12031 - 	CGI_10001957	superfamily	222180	357	569	4.17E-17	80.1252	cl18644	AsmA_2 superfamily	 - 	 - 	AsmA-like C-terminal region; This family is similar to the C-terminal of the AsmA protein of E. coli.
Q#12032 - 	CGI_10001959	superfamily	202285	46	138	2.83E-26	99.9751	cl03645	Poly_export superfamily	 - 	 - 	Polysaccharide biosynthesis/export protein; This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export.
Q#12032 - 	CGI_10001959	superfamily	220798	146	188	0.00245715	35.2756	cl14799	SLBB superfamily	 - 	 - 	SLBB domain; SLBB domain.  
Q#12033 - 	CGI_10001960	superfamily	241614	3	140	3.94E-54	169.368	cl00105	LMWPc superfamily	 - 	 - 	Low molecular weight phosphatase family;
Q#12034 - 	CGI_10001961	superfamily	247074	16	111	1.30E-23	97.8065	cl15801	Wzz superfamily	C	 - 	Chain length determinant protein; This family includes proteins involved in lipopolysaccharide (lps) biosynthesis. This family comprises the whole length of chain length determinant protein (or wzz protein) that confers a modal distribution of chain length on the O-antigen component of lps. This region is also found as part of bacterial tyrosine kinases.
Q#12034 - 	CGI_10001961	superfamily	222392	367	417	2.17E-19	84.173	cl18670	GNVR superfamily	C	 - 	"G-rich domain on putative tyrosine kinase; This domain is found between two families, Wzz, pfam02706 and CbiA pfam01656. There is a highly conserved GNVR sequence motif which characterizes this domain. The function is not known."
Q#12034 - 	CGI_10001961	superfamily	247757	538	564	0.000200327	40.5962	cl17203	Fer4_NifH superfamily	C	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#12034 - 	CGI_10001961	superfamily	247074	212	252	0.00034123	40.0265	cl15801	Wzz superfamily	N	 - 	Chain length determinant protein; This family includes proteins involved in lipopolysaccharide (lps) biosynthesis. This family comprises the whole length of chain length determinant protein (or wzz protein) that confers a modal distribution of chain length on the O-antigen component of lps. This region is also found as part of bacterial tyrosine kinases.
Q#12035 - 	CGI_10001962	superfamily	245596	8	171	2.32E-32	118.334	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12036 - 	CGI_10001964	superfamily	245227	36	274	1.49E-35	133.14	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#12036 - 	CGI_10001964	superfamily	245227	243	342	1.33E-06	47.9817	cl10013	Glycosyltransferase_GTB_type superfamily	N	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#12037 - 	CGI_10001965	superfamily	189184	1	273	1.58E-172	495.593	cl08075	wcaD superfamily	 - 	 - 	putative colanic acid biosynthesis protein; Provisional
Q#12037 - 	CGI_10001965	superfamily	245596	272	505	9.04E-163	464.384	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12038 - 	CGI_10001967	superfamily	245206	4	352	0	545.655	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12039 - 	CGI_10001968	superfamily	245206	5	313	0	515.979	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12040 - 	CGI_10004123	superfamily	202886	370	510	3.84E-56	188.201	cl04399	Nucleoporin2 superfamily	 - 	 - 	Nucleoporin autopeptidase; Nucleoporin autopeptidase.  
Q#12041 - 	CGI_10004124	superfamily	205121	822	846	2.54E-05	42.8764	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#12041 - 	CGI_10004124	superfamily	205121	393	415	0.00306025	36.7132	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#12041 - 	CGI_10004124	superfamily	205121	165	188	0.00857435	35.1724	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#12046 - 	CGI_10002178	superfamily	243263	25	536	9.62E-69	231.528	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#12047 - 	CGI_10002179	superfamily	220635	5	191	2.55E-45	159.237	cl12380	DUF2151 superfamily	C	 - 	"Cell cycle and development regulator; This is a set of proteins conserved from worms to humans. The proteins are a PAN GU kinase substrate, Mat89Bb, essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells."
Q#12048 - 	CGI_10002180	superfamily	213107	16	57	0.00129469	33.7828	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#12049 - 	CGI_10016637	superfamily	218406	4	74	3.00E-16	72.077	cl04914	MGAT2 superfamily	NC	 - 	"N-acetylglucosaminyltransferase II (MGAT2); UDP-N-acetyl-D-glucosamine:alpha-6-D-mannoside beta-1,2-N- acetylglucosaminyltransferase II (EC 2.4.1.143) (GnT II/MGAT2) is a Golgi resident enzyme that catalyzes an essential step in the biosynthetic pathway leading from high mannose to complex N-linked oligosaccharides. Mutations in the MGAT2 gene lead to congenital disorder of glycosylation (CDG IIa). CDG IIa patients have an increased bleeding tendency, unrelated to coagulation factors."
Q#12051 - 	CGI_10016639	superfamily	245864	204	573	4.09E-50	184.019	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12051 - 	CGI_10016639	superfamily	245864	747	940	1.04E-48	179.782	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12051 - 	CGI_10016639	superfamily	245864	585	653	0.00156501	40.5649	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12052 - 	CGI_10016640	superfamily	245864	3	195	8.71E-51	181.708	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12052 - 	CGI_10016640	superfamily	245864	238	431	4.39E-48	174.004	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12052 - 	CGI_10016640	superfamily	245864	424	534	1.02E-20	93.8822	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12055 - 	CGI_10016643	superfamily	241624	147	283	4.23E-29	112.035	cl00120	PP2Cc superfamily	N	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#12055 - 	CGI_10016643	superfamily	241624	81	179	7.80E-15	71.2035	cl00120	PP2Cc superfamily	C	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#12059 - 	CGI_10016647	superfamily	246962	67	327	5.63E-45	157.2	cl15430	Nucleoside_tran superfamily	 - 	 - 	"Nucleoside transporter; This is a family of nucleoside transporters. In mammalian cells nucleoside transporters transport nucleoside across the plasma membrane and are essential for nucleotide synthesis via the salvage pathways for cells that lack their own de novo synthesis pathways. Also in this family is mouse and human nucleolar protein HNP36, a protein of unknown function; although it has been hypothesised to be a plasma membrane nucleoside transporter."
Q#12060 - 	CGI_10016648	superfamily	246961	68	461	6.86E-40	146.43	cl15429	ABD superfamily	 - 	 - 	"Alpha-Mannosidase Binding Domain of Atg19/34; These proteins are related to the Alpha-mannosidase (Ams1) Binding Domain of Atg19/Atg34, a key component in the targeting pathway that directs alpha-mannosidase and aminopeptidase I to the vacuole, either through cytoplasm-to-vacuole trafficking or via autophagy in starvation conditions. Autophagy in a eukaryotic mechanism in which cytoplasm is enclosed in double-membraned autophagosomes which fuse with a vacuole for transport into the lumen. In Saccharomyces cerevisiae, alpha-mannosidase is selectively directed to the vacuole via the direct interaction with Atg19 (and paralog Atg34) in the Cvt pathway. Ams1 binding domains (ABD) Atg19/34 have a immunoglobulin fold with eight beta-strands. The ABD is responsible for Ams1 recognition, but its deletion does not affect the fusion of Atg19 with prApe1, and the transport of prApe1 to the vacuole. The Atg19 N-terminal region is a distinct coiled-coil domain."
Q#12064 - 	CGI_10003236	superfamily	110440	85	111	0.00437395	32.7649	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#12066 - 	CGI_10003238	superfamily	243091	171	276	1.35E-08	53.8775	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#12066 - 	CGI_10003238	superfamily	222150	409	433	3.42E-05	42.3789	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12066 - 	CGI_10003238	superfamily	222150	380	404	0.000162664	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12066 - 	CGI_10003238	superfamily	197676	366	388	0.00988818	35.1342	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#12067 - 	CGI_10002647	superfamily	245595	482	737	1.33E-178	537.719	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#12070 - 	CGI_10001438	superfamily	242274	3	155	9.09E-11	56.2666	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#12071 - 	CGI_10001439	superfamily	242274	15	171	0.000423242	38.5474	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#12073 - 	CGI_10002381	superfamily	193607	572	702	3.05E-57	191.246	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#12073 - 	CGI_10002381	superfamily	247792	525	566	4.33E-10	56.3	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12073 - 	CGI_10002381	superfamily	241554	23	181	1.86E-23	98.4967	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#12074 - 	CGI_10002382	superfamily	193607	1126	1255	3.03E-70	231.692	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#12074 - 	CGI_10002382	superfamily	247792	1077	1120	4.43E-11	60.152	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12074 - 	CGI_10002382	superfamily	241554	723	897	2.37E-47	168.603	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#12074 - 	CGI_10002382	superfamily	241554	7	168	1.39E-43	157.817	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#12075 - 	CGI_10009247	superfamily	216981	12	82	0.00542224	34.8158	cl17087	OTU superfamily	N	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#12077 - 	CGI_10009249	superfamily	245596	149	446	3.22E-148	433.169	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12077 - 	CGI_10009249	superfamily	247085	488	612	4.32E-12	63.6786	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#12078 - 	CGI_10009250	superfamily	152105	5	59	2.67E-05	37.8975	cl13169	WBP-1 superfamily	C	 - 	"WW domain-binding protein 1; This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain."
Q#12079 - 	CGI_10009251	superfamily	245596	312	554	4.96E-26	107.182	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12082 - 	CGI_10009254	superfamily	247724	5	180	2.75E-77	233.094	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12083 - 	CGI_10009255	superfamily	243034	703	802	4.27E-19	84.7391	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#12083 - 	CGI_10009255	superfamily	243034	483	587	5.54E-12	63.9384	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#12083 - 	CGI_10009255	superfamily	243034	151	229	1.94E-09	56.6196	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#12083 - 	CGI_10009255	superfamily	222431	1033	1133	3.74E-21	90.3593	cl16447	RPAP3_C superfamily	 - 	 - 	Potential Monad-binding region of RPAP3; This domain is found at the C-terminus of RNA-polymerase II-associated proteins. These proteins bind to Monad and are involved in regulating apoptosis. They contain TPR-repeats towards the N_terminus.
Q#12084 - 	CGI_10009256	superfamily	214545	462	604	1.84E-58	196.002	cl10551	CULLIN superfamily	 - 	 - 	Cullin; Cullin.  
Q#12084 - 	CGI_10009256	superfamily	245539	708	774	1.48E-28	109.951	cl11186	Cullin_Nedd8 superfamily	 - 	 - 	"Cullin protein neddylation domain; This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue."
Q#12089 - 	CGI_10021542	superfamily	205516	305	457	1.14E-82	254.252	cl18271	AcetylCoA_hyd_C superfamily	 - 	 - 	"Acetyl-CoA hydrolase/transferase C-terminal domain; This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 utilises acyl-CoA and acetate to form acetyl-CoA."
Q#12089 - 	CGI_10021542	superfamily	217098	42	213	3.12E-19	85.2806	cl15896	AcetylCoA_hydro superfamily	 - 	 - 	"Acetyl-CoA hydrolase/transferase N-terminal domain; This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 utilises acyl-CoA and acetate to form acetyl-CoA."
Q#12090 - 	CGI_10021543	superfamily	243175	6	134	7.41E-19	77.3707	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#12091 - 	CGI_10021544	superfamily	241832	4	79	2.62E-22	87.2001	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#12091 - 	CGI_10021544	superfamily	243175	84	215	2.85E-19	80.4523	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#12092 - 	CGI_10021545	superfamily	247724	32	87	1.45E-18	76.1616	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12093 - 	CGI_10021546	superfamily	247724	32	192	6.29E-55	175.158	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12094 - 	CGI_10021547	superfamily	247724	19	195	9.33E-65	200.966	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12095 - 	CGI_10021548	superfamily	245206	17	304	1.66E-78	243.286	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12097 - 	CGI_10021550	superfamily	150446	20	141	1.39E-10	56.6952	cl10756	OSTMP1 superfamily	N	 - 	"Osteopetrosis-associated transmembrane protein 1 precursor; Members of this family of proteins are required for osteoclast and melanocyte maturation and function. Mutations give rise to autosomal recessive osteopetrosis, also called autosomal recessive Albers-Schonberg disease."
Q#12098 - 	CGI_10021551	superfamily	247755	398	495	5.17E-40	144.919	cl17201	ABC_ATPase superfamily	NC	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#12098 - 	CGI_10021551	superfamily	216049	65	324	8.56E-18	83.1042	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#12099 - 	CGI_10021552	superfamily	243053	909	1139	6.77E-67	225.98	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#12099 - 	CGI_10021552	superfamily	243067	770	877	5.63E-14	70.5191	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#12102 - 	CGI_10021555	superfamily	241646	23	65	2.49E-08	45.9046	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#12103 - 	CGI_10021556	superfamily	222150	99	124	9.98E-05	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12104 - 	CGI_10021557	superfamily	247683	1435	1490	4.71E-27	107.098	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#12104 - 	CGI_10021557	superfamily	248279	285	401	6.14E-42	151.335	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#12104 - 	CGI_10021557	superfamily	245835	909	1068	1.44E-30	123.463	cl12013	BAR superfamily	C	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#12104 - 	CGI_10021557	superfamily	220792	59	208	1.19E-13	70.5127	cl11150	EPL1 superfamily	 - 	 - 	Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.
Q#12104 - 	CGI_10021557	superfamily	247999	234	279	1.03E-11	62.508	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#12104 - 	CGI_10021557	superfamily	247683	1324	1378	5.40E-10	57.7219	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#12106 - 	CGI_10021559	superfamily	244843	1	71	1.49E-10	55.7	cl08040	Ggt superfamily	N	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#12107 - 	CGI_10021560	superfamily	213438	6	42	2.04E-12	56.4974	cl04635	F1-ATPase_epsilon superfamily	 - 	 - 	"eukaryotic mitochondrial ATP synthase epsilon subunit; The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes, and in chloroplast thylakoid membranes. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta, and epsilon subunits (only found in eukaryotes, lacking in bacteria) with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain.The epsilon subunit is thought to be involved in the regulation of ATP synthase, since a null mutation increased oligomycin sensitivity and decreased inhibition by inhibitor protein IF1."
Q#12108 - 	CGI_10021561	superfamily	245835	1089	1198	0.00162779	39.9991	cl12013	BAR superfamily	C	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#12109 - 	CGI_10021562	superfamily	247725	869	978	1.34E-10	61.0203	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12109 - 	CGI_10021562	superfamily	243056	1592	1805	1.46E-60	209.47	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#12109 - 	CGI_10021562	superfamily	247725	1147	1195	3.19E-11	63.4654	cl17171	PH-like superfamily	NC	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12109 - 	CGI_10021562	superfamily	152266	1462	1510	2.38E-07	50.3127	cl13297	DUF3350 superfamily	 - 	 - 	Domain of unknown function (DUF3350); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 50 to 64 amino acids in length.
Q#12110 - 	CGI_10021563	superfamily	243072	2211	2337	2.89E-30	119.025	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12110 - 	CGI_10021563	superfamily	243077	1252	1305	1.06E-13	69.1113	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#12110 - 	CGI_10021563	superfamily	206405	926	971	3.12E-12	64.5503	cl16735	DUF4339 superfamily	 - 	 - 	"Domain of unknown function (DUF4339); This domain is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. There are two completely conserved residues (G and W) that may be functionally important."
Q#12111 - 	CGI_10021564	superfamily	246925	68	240	5.62E-05	44.2686	cl15309	LRR_RI superfamily	C	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#12114 - 	CGI_10004430	superfamily	247684	1	201	1.95E-45	161.676	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#12116 - 	CGI_10004432	superfamily	245304	3	177	1.44E-55	185.456	cl10459	Peptidases_S8_S53 superfamily	N	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#12116 - 	CGI_10004432	superfamily	201820	262	345	3.72E-19	80.7474	cl08326	P_proprotein superfamily	 - 	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#12117 - 	CGI_10004433	superfamily	245010	65	154	0.000486063	39.5983	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#12117 - 	CGI_10004433	superfamily	192987	128	227	0.000644895	39.0927	cl13724	TMF_TATA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family."
Q#12117 - 	CGI_10004433	superfamily	247068	437	512	0.00308975	36.9078	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12120 - 	CGI_10003886	superfamily	247724	201	468	4.17E-156	452.77	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12122 - 	CGI_10016549	superfamily	245364	107	186	4.00E-23	90.4904	cl10717	CactinC_cactus superfamily	C	 - 	"Cactus-binding C-terminus of cactin protein; CactinC_cactus is the C-terminal 200 residues of the cactin protein which are necessary for the association of cactin with IkappaB-cactus as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo. Most members of the family also have a Cactin_mid domain pfam10312 further upstream."
Q#12122 - 	CGI_10016549	superfamily	197732	52	82	4.41E-07	44.5507	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#12123 - 	CGI_10016550	superfamily	248264	2	67	0.000145409	39.1426	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#12124 - 	CGI_10016551	superfamily	247905	4	79	2.18E-16	71.8852	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#12128 - 	CGI_10016556	superfamily	241645	640	710	4.42E-10	57.3547	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#12128 - 	CGI_10016556	superfamily	222150	29	54	1.02E-05	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12128 - 	CGI_10016556	superfamily	222150	57	80	0.000196297	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12128 - 	CGI_10016556	superfamily	246975	16	37	0.00447763	36.1709	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#12130 - 	CGI_10016559	superfamily	248097	101	228	5.94E-20	82.313	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12131 - 	CGI_10016560	superfamily	248012	67	206	3.48E-24	93.9272	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12132 - 	CGI_10016561	superfamily	248012	61	200	4.47E-24	93.542	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12133 - 	CGI_10016562	superfamily	248012	19	158	1.15E-24	93.9272	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12134 - 	CGI_10016563	superfamily	241593	240	374	2.13E-11	60.353	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#12134 - 	CGI_10016563	superfamily	220754	30	191	1.01E-53	178.57	cl11087	BCDHK_Adom3 superfamily	 - 	 - 	"Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase; Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. This is the butyryl-CoA dehydrogenase, subunit A domain 3, a largely alpha-helical bundle of the enzyme BCDHK. This enzyme is the regulator of the dehydrogenase complex that breaks branched-chain amino-acids down, by phosphorylating and thereby inactivating it when synthesis is required. The domain is associated with family HATPase_c pfam02518 which is towards the C-terminal."
Q#12137 - 	CGI_10016568	superfamily	243146	318	367	1.16E-06	45.7431	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12137 - 	CGI_10016568	superfamily	243146	369	414	1.27E-05	42.6615	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12137 - 	CGI_10016568	superfamily	243146	158	210	1.45E-05	42.6615	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12137 - 	CGI_10016568	superfamily	243146	216	261	0.000605681	37.6539	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12137 - 	CGI_10016568	superfamily	243146	253	296	0.00595203	34.7314	cl02701	Kelch_3 superfamily	C	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12138 - 	CGI_10016569	superfamily	245008	496	573	6.04E-26	101.907	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#12143 - 	CGI_10005307	superfamily	215733	89	153	1.39E-07	47.5599	cl02811	E1-E2_ATPase superfamily	C	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#12143 - 	CGI_10005307	superfamily	243244	9	50	1.81E-06	42.1374	cl02930	Cation_ATPase_N superfamily	N	 - 	"Cation transporter/ATPase, N-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport."
Q#12144 - 	CGI_10005308	superfamily	241571	27	136	1.68E-28	107.883	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#12144 - 	CGI_10005308	superfamily	241571	215	328	6.80E-27	103.261	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#12144 - 	CGI_10005308	superfamily	241571	156	231	5.92E-06	43.918	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#12145 - 	CGI_10004495	superfamily	243161	4	69	0.000545321	35.0626	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#12146 - 	CGI_10013672	superfamily	246680	24	106	3.10E-14	66.9636	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#12146 - 	CGI_10013672	superfamily	248012	171	281	1.08E-09	55.4072	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12148 - 	CGI_10013674	superfamily	248264	78	242	2.89E-51	166.258	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#12148 - 	CGI_10013674	superfamily	222263	1	89	1.37E-05	41.9197	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#12149 - 	CGI_10013675	superfamily	241600	1	73	2.99E-23	88.4514	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12150 - 	CGI_10013676	superfamily	243096	11	200	2.84E-36	133.192	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#12150 - 	CGI_10013676	superfamily	247725	302	391	3.89E-20	86.2344	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12150 - 	CGI_10013676	superfamily	247725	237	276	8.77E-13	65.0484	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12150 - 	CGI_10013676	superfamily	247725	400	537	2.30E-11	62.0134	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12152 - 	CGI_10013678	superfamily	241754	56	766	0	1223.87	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#12156 - 	CGI_10006336	superfamily	221612	159	299	6.10E-20	91.3516	cl13889	DUF3715 superfamily	 - 	 - 	"Protein of unknown function (DUF3715); This domain family is found in eukaryotes, and is approximately 170 amino acids in length."
Q#12157 - 	CGI_10006337	superfamily	241628	5	164	9.74E-48	157.929	cl00130	PseudoU_synth superfamily	N	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#12159 - 	CGI_10006339	superfamily	212639	121	831	0	721.018	cl17018	FANC superfamily	C	 - 	"Fanconi anemia ID complex proteins FANCI and FANCD2; The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA at the ICL site, recognizing branched DNA structures. Defects in the complex cause Fanconi anemia, a cancer predisposition syndrome."
Q#12159 - 	CGI_10006339	superfamily	212639	920	1406	1.24E-139	461.008	cl17018	FANC superfamily	N	 - 	"Fanconi anemia ID complex proteins FANCI and FANCD2; The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA at the ICL site, recognizing branched DNA structures. Defects in the complex cause Fanconi anemia, a cancer predisposition syndrome."
Q#12160 - 	CGI_10006340	superfamily	241974	697	765	7.97E-13	66.111	cl00604	STAS superfamily	N	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#12160 - 	CGI_10006340	superfamily	241974	577	612	1.09E-05	44.5399	cl00604	STAS superfamily	C	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#12160 - 	CGI_10006340	superfamily	216188	238	519	2.03E-53	186.655	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#12160 - 	CGI_10006340	superfamily	205965	70	153	4.46E-34	125.988	cl18285	Sulfate_tra_GLY superfamily	 - 	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#12167 - 	CGI_10004678	superfamily	247727	100	223	1.55E-09	54.3583	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#12168 - 	CGI_10004679	superfamily	247085	301	418	6.07E-15	70.9974	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#12168 - 	CGI_10004679	superfamily	245596	18	288	1.67E-101	306.823	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12169 - 	CGI_10006874	superfamily	244881	245	546	6.15E-133	403.112	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#12169 - 	CGI_10006874	superfamily	215788	21	111	1.80E-27	108.035	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#12169 - 	CGI_10006874	superfamily	203720	655	747	1.12E-25	103.012	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#12169 - 	CGI_10006874	superfamily	147487	73	170	0.000858572	38.923	cl05075	SVA superfamily	N	 - 	"Seminal vesicle autoantigen (SVA); This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19-kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP, has several known functions. In saliva, this protein plays a role in host defence by binding to microorganisms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4."
Q#12170 - 	CGI_10006875	superfamily	241754	80	114	6.77E-17	75.7003	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#12171 - 	CGI_10006876	superfamily	241754	74	108	2.28E-15	71.0779	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#12171 - 	CGI_10006876	superfamily	111612	26	68	2.28E-06	40.5422	cl03686	Myosin_N superfamily	 - 	 - 	Myosin N-terminal SH3-like domain; This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown.
Q#12174 - 	CGI_10006879	superfamily	242828	74	337	1.08E-34	132.847	cl01996	Glyco_hydro_76 superfamily	 - 	 - 	"Glycosyl hydrolase family 76; Family of alpha-1,6-mannanases."
Q#12175 - 	CGI_10006880	superfamily	246918	292	348	4.14E-06	44.8851	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12175 - 	CGI_10006880	superfamily	246918	24	76	0.000137437	40.6479	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12175 - 	CGI_10006880	superfamily	245814	386	447	0.00137688	37.3864	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12175 - 	CGI_10006880	superfamily	246918	513	533	0.00769173	35.2551	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12176 - 	CGI_10006881	superfamily	220757	318	362	2.07E-09	54.9847	cl11093	FIST_C superfamily	N	 - 	"FIST C domain; The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids."
Q#12176 - 	CGI_10006881	superfamily	243074	24	55	9.68E-05	39.7274	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#12176 - 	CGI_10006881	superfamily	245358	222	323	0.00348847	37.2593	cl10701	FIST superfamily	C	 - 	"FIST N domain; The FIST N domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids."
Q#12177 - 	CGI_10006882	superfamily	183292	82	250	7.60E-20	88.7251	cl18135	PRK11728 superfamily	NC	 - 	hydroxyglutarate oxidase; Provisional
Q#12181 - 	CGI_10006886	superfamily	247907	12	166	2.35E-10	59.3541	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#12181 - 	CGI_10006886	superfamily	241645	466	559	0.0020239	37.5628	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#12186 - 	CGI_10005399	superfamily	245206	32	269	1.01E-54	181.318	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12188 - 	CGI_10005401	superfamily	241563	70	107	0.000217026	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12189 - 	CGI_10009981	superfamily	241874	68	629	0	682.753	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#12190 - 	CGI_10009982	superfamily	241607	536	592	2.75E-19	83.8929	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#12191 - 	CGI_10009983	superfamily	241646	20	64	0.000109813	35.119	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#12192 - 	CGI_10009984	superfamily	248097	129	228	3.84E-17	76.1498	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12193 - 	CGI_10009985	superfamily	248097	6	131	2.07E-20	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12195 - 	CGI_10009987	superfamily	241607	209	265	4.39E-16	70.7961	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#12196 - 	CGI_10009988	superfamily	245819	255	391	3.68E-55	184.32	cl11967	Nucleotidyl_cyc_III superfamily	C	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#12196 - 	CGI_10009988	superfamily	245201	22	178	1.50E-21	93.37	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12196 - 	CGI_10009988	superfamily	219526	194	241	7.21E-06	45.6879	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#12197 - 	CGI_10009989	superfamily	245225	1	264	1.69E-61	202.477	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#12198 - 	CGI_10009990	superfamily	245225	24	103	7.97E-07	44.9949	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#12199 - 	CGI_10009991	superfamily	245603	59	385	0	567.172	cl11403	pepsin_retropepsin_like superfamily	 - 	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#12199 - 	CGI_10009991	superfamily	245603	409	434	3.45E-07	50.1164	cl11403	pepsin_retropepsin_like superfamily	N	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#12199 - 	CGI_10009991	superfamily	116576	20	47	3.24E-05	41.186	cl06833	A1_Propeptide superfamily	 - 	 - 	"A1 Propeptide; Most eukaryotic endopeptidases (Merops Family A1) are synthesised with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residues in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions."
Q#12201 - 	CGI_10009993	superfamily	241565	407	479	2.99E-08	51.9387	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#12201 - 	CGI_10009993	superfamily	241565	509	573	5.10E-08	51.1683	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#12201 - 	CGI_10009993	superfamily	241565	620	686	2.92E-07	48.8571	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#12201 - 	CGI_10009993	superfamily	241565	82	134	1.94E-06	46.5459	cl00038	BRCT superfamily	N	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#12201 - 	CGI_10009993	superfamily	241565	9	72	0.000926379	38.4567	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#12201 - 	CGI_10009993	superfamily	241565	723	805	0.00124241	38.1262	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#12202 - 	CGI_10005290	superfamily	241555	34	282	2.16E-38	138.959	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#12203 - 	CGI_10005291	superfamily	247068	358	454	1.88E-10	58.4789	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12203 - 	CGI_10005291	superfamily	247068	483	556	4.02E-06	45.4183	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12203 - 	CGI_10005291	superfamily	247068	562	652	0.00262186	36.9078	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12205 - 	CGI_10003063	superfamily	241600	50	258	4.33E-84	252.932	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12206 - 	CGI_10003064	superfamily	245206	38	251	6.08E-51	169.713	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12207 - 	CGI_10007535	superfamily	241563	117	150	2.65E-06	44.9707	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12208 - 	CGI_10007536	superfamily	241577	27	187	1.04E-74	225.963	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#12209 - 	CGI_10007537	superfamily	219542	89	187	3.20E-37	130.439	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12209 - 	CGI_10007537	superfamily	215896	200	306	1.98E-15	71.172	cl18351	Cu-oxidase superfamily	C	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#12211 - 	CGI_10007539	superfamily	219541	191	339	1.46E-24	97.1538	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12211 - 	CGI_10007539	superfamily	215896	2	68	2.08E-08	51.912	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#12214 - 	CGI_10002815	superfamily	215754	185	273	6.15E-24	93.0868	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12214 - 	CGI_10002815	superfamily	215754	82	182	7.03E-16	70.7452	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12214 - 	CGI_10002815	superfamily	215754	1	74	7.05E-11	57.2632	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12216 - 	CGI_10002817	superfamily	243072	101	220	9.10E-32	119.796	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12216 - 	CGI_10002817	superfamily	243072	199	319	3.10E-30	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12216 - 	CGI_10002817	superfamily	243072	293	418	6.62E-30	114.403	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12216 - 	CGI_10002817	superfamily	243072	363	484	9.43E-26	102.847	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12216 - 	CGI_10002817	superfamily	243072	35	154	2.03E-25	102.077	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12216 - 	CGI_10002817	superfamily	243073	559	601	4.37E-06	44.4087	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#12217 - 	CGI_10002818	superfamily	245205	31	106	3.25E-05	40.2989	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#12219 - 	CGI_10002395	superfamily	241573	90	410	1.46E-115	354.716	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#12219 - 	CGI_10002395	superfamily	241653	421	571	1.45E-43	154.764	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#12221 - 	CGI_10008237	superfamily	245847	120	192	5.77E-05	40.6178	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12222 - 	CGI_10008238	superfamily	241574	406	632	3.99E-97	306.435	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#12222 - 	CGI_10008238	superfamily	241574	706	886	6.33E-14	71.4629	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#12223 - 	CGI_10008239	superfamily	248097	122	247	1.35E-18	78.8462	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12224 - 	CGI_10008240	superfamily	241750	52	329	1.76E-40	144.263	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#12225 - 	CGI_10008241	superfamily	243035	227	268	1.01E-05	42.9922	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#12226 - 	CGI_10008242	superfamily	245206	27	192	5.09E-42	143.583	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12227 - 	CGI_10008243	superfamily	245206	44	105	2.72E-05	40.2109	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12229 - 	CGI_10008245	superfamily	215724	1	257	6.86E-140	398.531	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#12230 - 	CGI_10005193	superfamily	248012	52	129	1.84E-18	78.134	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12231 - 	CGI_10005194	superfamily	248012	615	758	3.71E-18	82.3712	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12233 - 	CGI_10005196	superfamily	247727	215	348	5.37E-12	62.0622	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#12236 - 	CGI_10005199	superfamily	243138	117	350	1.78E-109	324.141	cl02675	DZF superfamily	 - 	 - 	DZF domain; The function of this domain is unknown. It is often found associated with pfam00098 or pfam00035. This domain has been predicted to belong to the nucleotidyltransferase superfamily.
Q#12238 - 	CGI_10003461	superfamily	221540	318	452	8.37E-63	201.551	cl13742	DUF3641 superfamily	 - 	 - 	"Protein of unknown function (DUF3641); This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam04055. This family consists of proteins which are commonly annotated as Radical SAM domains but there is little annotation to back this up."
Q#12239 - 	CGI_10003462	superfamily	243050	23	75	4.20E-23	88.0358	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#12239 - 	CGI_10003462	superfamily	243050	127	179	6.36E-18	74.1686	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#12241 - 	CGI_10022231	superfamily	242730	162	240	0.00811369	35.6999	cl01825	Phage_Mu_Gam superfamily	C	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#12242 - 	CGI_10022232	superfamily	244083	41	147	2.87E-36	124.284	cl05417	PLA2_like superfamily	 - 	 - 	"PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers."
Q#12243 - 	CGI_10022233	superfamily	246597	84	337	1.26E-123	370.017	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#12243 - 	CGI_10022233	superfamily	217260	364	512	7.48E-45	156.646	cl03752	5_nucleotid_C superfamily	 - 	 - 	"5'-nucleotidase, C-terminal domain; 5'-nucleotidase, C-terminal domain.  "
Q#12244 - 	CGI_10022234	superfamily	242715	7	179	2.20E-81	242.808	cl01799	Ribosomal_L13e superfamily	 - 	 - 	Ribosomal protein L13e; Ribosomal protein L13e.  
Q#12247 - 	CGI_10022237	superfamily	248469	183	273	2.12E-14	72.0175	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#12247 - 	CGI_10022237	superfamily	248469	438	545	3.43E-14	71.2471	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#12247 - 	CGI_10022237	superfamily	218493	935	1073	3.16E-44	157.904	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#12248 - 	CGI_10022238	superfamily	221917	111	198	3.80E-17	74.1875	cl16089	CENP-L superfamily	 - 	 - 	"Kinetochore complex Sim4 subunit Fta1; CENP-L is one of the components that assembles onto the CENP-A-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. Fta1 is the equivalent component of the fission yeast Sim4 complex. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals."
Q#12249 - 	CGI_10022239	superfamily	216144	221	277	3.23E-12	63.5769	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	737	789	1.45E-08	53.1765	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	999	1048	3.65E-08	52.0209	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	852	915	4.66E-08	51.6357	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	419	477	6.37E-08	51.2505	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	96	154	4.75E-07	48.5541	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	554	612	1.86E-05	43.9317	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	677	716	0.000102437	41.6205	cl02981	Cys_rich_FGFR superfamily	C	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	349	399	0.000124507	41.2353	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	481	547	0.000153557	41.2353	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	795	848	0.00019617	40.8501	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	614	674	0.000880486	38.9241	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	282	345	0.00124697	38.5389	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	918	991	0.00228726	37.3833	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12249 - 	CGI_10022239	superfamily	216144	157	219	0.00258465	37.3833	cl02981	Cys_rich_FGFR superfamily	 - 	 - 	Cysteine rich repeat; This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Q#12252 - 	CGI_10022242	superfamily	243263	263	502	9.13E-29	117.509	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#12252 - 	CGI_10022242	superfamily	243263	2	203	1.58E-16	80.915	cl02990	ASC superfamily	C	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#12253 - 	CGI_10022243	superfamily	247727	54	150	6.46E-12	62.0622	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#12254 - 	CGI_10022244	superfamily	246940	101	299	2.93E-05	43.091	cl15377	Radical_SAM superfamily	 - 	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#12255 - 	CGI_10022245	superfamily	219969	722	1017	4.02E-33	130.225	cl07345	ASD2 superfamily	 - 	 - 	Apx/Shroom domain ASD2; This region is found in the actin binding protein Shroom which mediates apical contriction in epithelial cells and is required for neural tube closure.
Q#12256 - 	CGI_10022246	superfamily	241622	29	105	4.66E-13	59.8878	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#12257 - 	CGI_10022247	superfamily	241584	174	251	5.68E-10	55.1951	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#12257 - 	CGI_10022247	superfamily	241568	13	69	0.00100691	36.672	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12259 - 	CGI_10022249	superfamily	241677	166	226	6.74E-28	105.417	cl00197	cyclophilin superfamily	N	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#12260 - 	CGI_10022250	superfamily	128469	570	665	8.57E-12	62.858	cl17971	VPS9 superfamily	 - 	 - 	Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
Q#12261 - 	CGI_10022251	superfamily	247723	473	556	2.07E-41	147.75	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#12261 - 	CGI_10022251	superfamily	243035	758	869	2.22E-06	47.2294	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#12261 - 	CGI_10022251	superfamily	207684	13	44	2.00E-05	43.1363	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#12262 - 	CGI_10022252	superfamily	241568	621	681	3.16E-08	52.8504	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	821	883	1.07E-07	51.3096	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	562	616	2.18E-07	50.154	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	1707	1752	2.58E-07	50.154	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	503	557	4.42E-07	49.3836	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	381	435	1.34E-06	47.8428	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	745	816	2.35E-06	47.0724	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	686	740	2.84E-06	47.0724	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	888	943	5.36E-06	46.302	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	1479	1533	5.46E-06	46.302	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	322	376	1.04E-05	45.5316	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	460	498	2.36E-05	44.376	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12262 - 	CGI_10022252	superfamily	241568	1757	1811	3.73E-05	43.6056	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12263 - 	CGI_10022253	superfamily	241754	4	365	0	546.91	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#12263 - 	CGI_10022253	superfamily	241581	461	564	2.07E-10	59.3222	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#12263 - 	CGI_10022253	superfamily	246669	810	846	0.00488812	36.6611	cl14603	C2 superfamily	NC	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12263 - 	CGI_10022253	superfamily	221571	677	718	1.14E-07	50.1939	cl13810	KIF1B superfamily	 - 	 - 	"Kinesin protein 1B; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00225, pfam00498. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells."
Q#12264 - 	CGI_10022254	superfamily	241754	4	47	5.00E-13	61.9439	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#12265 - 	CGI_10022255	superfamily	241550	38	231	1.37E-72	241.383	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#12265 - 	CGI_10022255	superfamily	241550	388	550	2.10E-48	173.588	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#12265 - 	CGI_10022255	superfamily	245839	550	671	3.78E-16	75.7193	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#12265 - 	CGI_10022255	superfamily	241550	317	332	0.00686039	37.7833	cl00015	nt_trans superfamily	NC	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#12266 - 	CGI_10022256	superfamily	241983	22	329	3.28E-54	182.172	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#12267 - 	CGI_10022257	superfamily	245839	17	52	6.05E-05	38.3549	cl12020	Anticodon_Ia_like superfamily	N	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#12268 - 	CGI_10022258	superfamily	241983	1	246	2.93E-36	132.096	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#12269 - 	CGI_10022259	superfamily	242043	28	66	2.46E-11	55.8112	cl00713	Auto_anti-p27 superfamily	 - 	 - 	Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
Q#12270 - 	CGI_10022260	superfamily	247692	797	1291	1.52E-137	436.49	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#12270 - 	CGI_10022260	superfamily	245206	1447	1738	5.35E-70	239.09	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12270 - 	CGI_10022260	superfamily	241838	218	382	5.74E-60	205.57	cl00395	FMT_core superfamily	 - 	 - 	"Formyltransferase, catalytic core domain; Formyltransferase, catalytic core domain. The proteins of this superfamily contain a formyltransferase domain that hydrolyzes the removal of a formyl group from its substrate as part of a multistep transfer mechanism, and this alignment model represents the catalytic core of the formyltransferase domain.  This family includes the following known members; Glycinamide Ribonucleotide Transformylase (GART), Formyl-FH4 Hydrolase, Methionyl-tRNA Formyltransferase, ArnA, and 10-Formyltetrahydrofolate Dehydrogenase (FDH).  Glycinamide Ribonucleotide Transformylase  (GART) catalyzes the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Methionyl-tRNA Formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA, which plays important role in translation initiation. ArnA is required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. 10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. Members of this family are multidomain proteins. The formyltransferase domain is located at the N-terminus of FDH, Methionyl-tRNA Formyltransferase and ArnA, and at the C-terminus of Formyl-FH4 Hydrolase.  Prokaryotic Glycinamide Ribonucleotide Transformylase (GART) is a single domain protein while eukaryotic GART is a trifunctional protein that catalyzes the second, third and fifth steps in de novo purine biosynthesis."
Q#12270 - 	CGI_10022260	superfamily	246712	410	500	1.22E-09	57.6274	cl14785	FMT_C_like superfamily	 - 	 - 	"Carboxy-terminal domain of Formyltransferase and similar domains; This family represents the C-terminal domain of formyltransferase and similar proteins. This domain is found in a variety of enzymes with formyl transferase and alkyladenine DNA glycosylase activities. The proteins with formyltransferase function include methionyl-tRNA formyltransferase, ArnA, 10-formyltetrahydrofolate dehydrogenase and HypX proteins. Although most proteins with formyl transferase activity contain this C-terminal domain, prokaryotic glycinamide ribonucleotide transformylase (GART), a single domain protein, only contains the core catalytic domain. Thus, the C-terminal domain is not required for formyl transferase catalytic activity and may be involved in substrate binding. Some members of this family have shown nucleic acid binding capacity. The C-terminal domain of methionyl-tRNA formyltransferase is involved in tRNA binding. Alkyladenine DNA glycosylase is a distant member of this family with very low sequence similarity to other members. It catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site and shows ability to bind to DNA."
Q#12270 - 	CGI_10022260	superfamily	245209	1315	1380	3.04E-08	52.9422	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#12271 - 	CGI_10022261	superfamily	241600	214	425	2.76E-94	285.288	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12271 - 	CGI_10022261	superfamily	243092	4	156	1.31E-16	78.5308	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12272 - 	CGI_10022262	superfamily	242406	1	70	2.79E-07	46.0453	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#12274 - 	CGI_10022264	superfamily	245819	1155	1332	2.26E-65	220.914	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#12274 - 	CGI_10022264	superfamily	245201	837	1082	5.02E-29	117.723	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12275 - 	CGI_10005778	superfamily	218200	81	309	2.08E-81	256.525	cl04660	Glyco_transf_54 superfamily	 - 	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#12276 - 	CGI_10005779	superfamily	202000	29	131	1.64E-09	55.5577	cl03375	XRCC1_N superfamily	 - 	 - 	XRCC1 N terminal domain; XRCC1 N terminal domain.  
Q#12278 - 	CGI_10005781	superfamily	243035	1	67	6.86E-18	72.6525	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#12280 - 	CGI_10007543	superfamily	220691	34	157	0.000640171	39.1382	cl18569	7TM_GPCR_Srv superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#12282 - 	CGI_10007545	superfamily	245847	5	168	1.19E-05	42.1586	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12283 - 	CGI_10007546	superfamily	118308	1	50	2.38E-10	50.9082	cl10755	Mitoc_L55 superfamily	N	 - 	Mitochondrial ribosomal protein L55; Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Q#12285 - 	CGI_10007548	superfamily	248100	14	70	2.79E-11	57.164	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#12285 - 	CGI_10007548	superfamily	248100	155	212	5.62E-10	53.6972	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#12286 - 	CGI_10007549	superfamily	241748	110	154	9.17E-09	51.8224	cl00279	APP_MetAP superfamily	C	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#12287 - 	CGI_10021433	superfamily	248241	1	309	1.05E-93	287.617	cl17687	5_nucleotid superfamily	N	 - 	"5' nucleotidase family; This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5."
Q#12288 - 	CGI_10021434	superfamily	241563	60	102	4.46E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12289 - 	CGI_10021435	superfamily	241780	263	673	0	636.105	cl00319	Gn_AT_II superfamily	 - 	 - 	"Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate.  Asparagine synthetase B  synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the formation of the beta-lactam ring in the beta-lactamase inhibitor clavulanic acid. GltS synthesizes L-glutamate from 2-oxoglutarate and L-glutamine. These enzymes are generally dimers, but GPATase also exists as a homotetramer."
Q#12289 - 	CGI_10021435	superfamily	247740	1067	1437	8.91E-156	487.819	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#12289 - 	CGI_10021435	superfamily	218318	717	1004	5.88E-150	466.637	cl04830	Glu_syn_central superfamily	 - 	 - 	Glutamate synthase central domain; The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology. This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP.
Q#12289 - 	CGI_10021435	superfamily	241716	1494	1685	3.11E-93	304.835	cl00239	GXGXG superfamily	 - 	 - 	"GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS),  in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC). It is also found in a primarily archeal group of proteins predicted to encode part of the large subunit of GltS. It is characterized by a repeated GXXGXXXG motif. GltS is a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites occur in other domains within the protein or or encoded by separate genes, and are not present in the domain in this CD. FwdC and FmdC are reversible ion pumps that catalyze the formylation and deformylation of methanofuran in hyperthermophiles and bacteria.  They require the presence of either tungstun (FwdC) or molybdenum (FmdC). The specific function of this domain also remains unidentified in the formylmethanofuran dehydrogenases."
Q#12289 - 	CGI_10021435	superfamily	248054	1860	1895	2.24E-09	56.3264	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#12291 - 	CGI_10021437	superfamily	242385	179	476	0	537.406	cl01244	arom_aa_hydroxylase superfamily	 - 	 - 	"Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers."
Q#12291 - 	CGI_10021437	superfamily	245020	38	166	7.43E-13	65.1116	cl09141	ACT superfamily	 - 	 - 	"ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but  the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times."
Q#12292 - 	CGI_10021438	superfamily	149674	153	190	0.000199077	40.3929	cl07350	SKG6 superfamily	 - 	 - 	Transmembrane alpha-helix domain; SKG6/Axl2 are membrane proteins that show polarised intracellular localisation. SKG6_Tmem is the highly conserved transmembrane alpha-helical domain of SKG6 and Axl2 proteins. The full-length fungal protein has a negative regulatory function in cytokinesis.
Q#12293 - 	CGI_10021439	superfamily	241564	410	477	5.87E-28	106.966	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#12293 - 	CGI_10021439	superfamily	241564	211	270	1.46E-15	72.2983	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#12293 - 	CGI_10021439	superfamily	247792	524	562	5.07E-05	41.2772	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12294 - 	CGI_10021440	superfamily	190261	169	220	0.00890361	34.4466	cl03504	RFX_DNA_binding superfamily	C	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#12296 - 	CGI_10021442	superfamily	241563	71	109	4.31E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12296 - 	CGI_10021442	superfamily	241563	28	59	0.00479427	35.5328	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12298 - 	CGI_10021444	superfamily	217064	7	119	2.14E-20	84.4684	cl03617	CLN3 superfamily	N	 - 	CLN3 protein; This is a family of proteins from the CLN3 gene. A missense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease).
Q#12299 - 	CGI_10021445	superfamily	241563	68	109	4.71E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12299 - 	CGI_10021445	superfamily	241563	28	59	0.000790062	37.844	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12299 - 	CGI_10021445	superfamily	246954	122	207	0.00290547	38.9386	cl15415	Sec1 superfamily	NC	 - 	Sec1 family; Sec1 family.  
Q#12303 - 	CGI_10021449	superfamily	248097	147	274	2.37E-20	84.239	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12304 - 	CGI_10021450	superfamily	245213	145	183	5.93E-08	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12304 - 	CGI_10021450	superfamily	245213	109	143	8.53E-07	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12304 - 	CGI_10021450	superfamily	222049	10	94	1.36E-06	46.1779	cl16239	Mucin2_WxxW superfamily	 - 	 - 	"Mucin-2 protein WxxW repeating region; This family is repeating region found on mucins 2 and 5. The function is not known, but the repeat can be present in up to 32 copies, as in a member from Branchiostoma floridae. The region carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues."
Q#12307 - 	CGI_10021453	superfamily	242274	6	70	1.69E-06	42.2226	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#12309 - 	CGI_10021456	superfamily	241574	551	700	1.08E-56	193.571	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#12309 - 	CGI_10021456	superfamily	243035	185	298	4.22E-06	45.6886	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#12309 - 	CGI_10021456	superfamily	245226	112	148	0.00127752	38.8209	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#12310 - 	CGI_10021457	superfamily	216363	32	97	8.24E-12	56.7098	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#12312 - 	CGI_10004303	superfamily	243072	76	200	4.45E-25	98.995	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12312 - 	CGI_10004303	superfamily	243072	179	312	1.11E-18	81.661	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12312 - 	CGI_10004303	superfamily	243072	8	129	4.37E-18	80.1202	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12312 - 	CGI_10004303	superfamily	243073	395	428	0.00694432	34.3935	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#12317 - 	CGI_10019563	superfamily	243074	620	660	3.60E-11	60.2129	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#12318 - 	CGI_10019564	superfamily	241995	7	347	2.08E-111	328.081	cl00635	Ntn_Asparaginase_2_like superfamily	 - 	 - 	"Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and  L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue."
Q#12319 - 	CGI_10019565	superfamily	201806	53	285	5.17E-21	94.8581	cl18220	Peptidase_M8 superfamily	NC	 - 	Leishmanolysin; Leishmanolysin.  
Q#12321 - 	CGI_10019567	superfamily	215754	175	266	7.83E-26	99.6352	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12321 - 	CGI_10019567	superfamily	215754	270	356	9.91E-22	88.0792	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12321 - 	CGI_10019567	superfamily	215754	69	162	2.21E-21	86.9236	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12322 - 	CGI_10019568	superfamily	243085	158	209	1.65E-13	65.0758	cl02557	DM superfamily	 - 	 - 	"DM DNA binding domain; The DM domain is named after dsx and mab-3. dsx contains a single amino-terminal DM domain, whereas mab-3 contains two amino-terminal domains. The DM domain has a pattern of conserved zinc chelating residues C2H2C4. The dsx DM domain has been shown to dimerise and bind palindromic DNA."
Q#12324 - 	CGI_10019570	superfamily	247724	1	157	1.68E-80	238.983	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12326 - 	CGI_10019572	superfamily	243072	93	241	3.49E-22	92.8318	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12326 - 	CGI_10019572	superfamily	243072	19	143	3.40E-14	70.105	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12326 - 	CGI_10019572	superfamily	243072	482	592	1.80E-06	46.6078	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12327 - 	CGI_10019573	superfamily	215648	362	582	7.50E-21	91.8883	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#12327 - 	CGI_10019573	superfamily	217211	179	225	0.00608493	35.3378	cl03691	Cache_1 superfamily	C	 - 	Cache domain; Cache domain.  
Q#12328 - 	CGI_10019574	superfamily	245213	329	365	5.21E-09	53.4094	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12328 - 	CGI_10019574	superfamily	245213	240	268	5.31E-05	41.4682	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12329 - 	CGI_10019575	superfamily	222269	118	234	1.21E-06	48.4738	cl18657	Cupin_8 superfamily	N	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#12330 - 	CGI_10019576	superfamily	242406	69	219	9.51E-51	164.302	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#12331 - 	CGI_10019577	superfamily	243072	788	913	5.01E-36	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12331 - 	CGI_10019577	superfamily	243072	710	847	1.41E-27	109.395	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12331 - 	CGI_10019577	superfamily	247743	225	379	0.00061202	39.8756	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#12332 - 	CGI_10019578	superfamily	216901	1638	1812	1.59E-62	213.987	cl03466	Rap_GAP superfamily	 - 	 - 	Rap/ran-GAP; Rap/ran-GAP.  
Q#12333 - 	CGI_10019579	superfamily	242443	78	480	5.55E-160	462.761	cl01342	Peptidase_A22B superfamily	 - 	 - 	"Signal peptide peptidase; The members of this family are membrane proteins. In some proteins this region is found associated with pfam02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with pfam01080."
Q#12334 - 	CGI_10019581	superfamily	241749	42	175	1.75E-10	55.0845	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#12335 - 	CGI_10019582	superfamily	247724	18	200	5.94E-63	196.226	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12336 - 	CGI_10019583	superfamily	206009	341	387	6.35E-17	76.4378	cl16430	Clathrin_H_link superfamily	C	 - 	"Clathrin-H-link; This short domain is found on clathrins, and often appears on proteins directly downstream from the Clathrin-link domain pfam09268."
Q#12337 - 	CGI_10019584	superfamily	247743	170	336	5.25E-19	82.9643	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#12338 - 	CGI_10019585	superfamily	241578	406	571	1.50E-40	149.686	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12338 - 	CGI_10019585	superfamily	241578	731	875	9.16E-29	115.467	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12338 - 	CGI_10019585	superfamily	241578	594	721	7.25E-28	112.77	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12338 - 	CGI_10019585	superfamily	241578	27	190	3.15E-42	154.752	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12338 - 	CGI_10019585	superfamily	241578	905	1078	7.05E-36	136.749	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12338 - 	CGI_10019585	superfamily	241578	218	387	1.08E-32	127.504	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12338 - 	CGI_10019585	superfamily	248012	1428	1504	6.68E-11	61.4397	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12338 - 	CGI_10019585	superfamily	248012	1271	1370	2.48E-09	57.3332	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12339 - 	CGI_10019586	superfamily	245202	25	102	3.87E-43	139.872	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#12340 - 	CGI_10019587	superfamily	247684	19	188	0.000455431	39.8796	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#12341 - 	CGI_10019588	superfamily	245201	1189	1403	1.36E-33	131.59	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12341 - 	CGI_10019588	superfamily	241739	1473	1788	5.75E-27	113.081	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#12341 - 	CGI_10019588	superfamily	216167	8	173	2.26E-34	131.94	cl02999	DNA_photolyase superfamily	 - 	 - 	DNA photolyase; This domain binds a light harvesting cofactor.
Q#12341 - 	CGI_10019588	superfamily	243141	521	639	1.92E-21	92.7646	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#12341 - 	CGI_10019588	superfamily	245201	803	1016	6.46E-17	82.2197	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12341 - 	CGI_10019588	superfamily	241738	1801	1895	0.000337746	40.986	cl00266	HGTP_anticodon superfamily	 - 	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#12342 - 	CGI_10019589	superfamily	241599	65	120	1.76E-15	69.1944	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#12345 - 	CGI_10019592	superfamily	241750	174	374	7.18E-39	140.401	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#12346 - 	CGI_10019593	superfamily	241588	28	131	6.10E-21	81.9449	cl00070	GHB_like superfamily	 - 	 - 	"Glycoprotein hormone beta chain homologues; This family of cystine-knot hormones includes the beta chains of gonadotropins, thyrotropins, follitropins, choriogonadotropins and more. The members are reproductive hormones that consist of two glycosylated chains (alpha and beta), which form a tightly bound dimer."
Q#12353 - 	CGI_10019600	superfamily	246910	38	85	0.00645085	31.567	cl15257	GIY-YIG_SF superfamily	N	 - 	"GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions."
Q#12354 - 	CGI_10001746	superfamily	245814	173	240	4.07E-07	47.0987	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12354 - 	CGI_10001746	superfamily	245814	98	152	0.000598067	37.5566	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12356 - 	CGI_10004698	superfamily	241547	4	100	1.79E-33	117.649	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#12358 - 	CGI_10004700	superfamily	241599	152	211	3.08E-13	64.9572	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#12365 - 	CGI_10004978	superfamily	216363	51	134	1.25E-12	59.7914	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#12369 - 	CGI_10004982	superfamily	110440	340	366	3.35E-05	41.2393	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#12372 - 	CGI_10002584	superfamily	241754	20	701	0	812.652	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#12372 - 	CGI_10002584	superfamily	247725	1504	1619	6.64E-41	149.472	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12372 - 	CGI_10002584	superfamily	247725	2013	2123	2.36E-31	121.752	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12372 - 	CGI_10002584	superfamily	243052	1700	1854	6.39E-26	107.061	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#12372 - 	CGI_10002584	superfamily	243052	1157	1300	3.21E-20	90.4975	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#12372 - 	CGI_10002584	superfamily	215882	1420	1528	6.99E-14	70.7726	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#12372 - 	CGI_10002584	superfamily	241645	1304	1372	0.00170721	39.0428	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#12372 - 	CGI_10002584	superfamily	215882	1947	2036	0.00537274	37.6455	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#12373 - 	CGI_10013333	superfamily	215647	296	497	0.000188851	41.8253	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#12374 - 	CGI_10013334	superfamily	241578	942	1083	2.89E-13	70.1157	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12374 - 	CGI_10013334	superfamily	241578	26	193	5.43E-09	56.6337	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12374 - 	CGI_10013334	superfamily	219821	849	888	1.62E-06	48.5214	cl07136	VWA_N superfamily	N	 - 	"VWA N-terminal; This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits."
Q#12374 - 	CGI_10013334	superfamily	217211	257	322	4.82E-06	46.5086	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#12374 - 	CGI_10013334	superfamily	217211	1136	1201	1.80E-05	44.9678	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#12376 - 	CGI_10013336	superfamily	241874	59	589	1.61E-121	376.921	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#12377 - 	CGI_10013338	superfamily	220692	25	332	4.30E-32	123.468	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#12379 - 	CGI_10013340	superfamily	245213	461	497	1.06E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	245213	537	573	2.48E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	245213	347	383	3.82E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	245213	309	345	4.23E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	245213	499	535	5.72E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	245213	271	307	6.97E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	245213	423	459	1.34E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	245213	385	421	1.48E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12379 - 	CGI_10013340	superfamily	205157	234	269	4.09E-05	42.1395	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#12380 - 	CGI_10013341	superfamily	245213	436	472	2.67E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	170	206	4.23E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	398	434	5.73E-07	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	284	320	7.71E-07	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	208	244	1.88E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	360	396	3.42E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	132	168	6.25E-06	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	246	282	8.64E-06	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	322	358	2.73E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	245213	94	130	0.000169549	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12380 - 	CGI_10013341	superfamily	243060	479	536	3.69E-06	45.4476	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#12381 - 	CGI_10013342	superfamily	245213	311	347	9.99E-08	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	245213	425	461	9.99E-08	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	245213	235	271	1.85E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	245213	273	309	3.17E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	245213	387	423	3.17E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	245213	349	384	7.49E-07	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	245213	463	498	7.49E-07	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	245213	501	536	6.97E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12381 - 	CGI_10013342	superfamily	243035	204	231	0.00539695	35.8148	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#12383 - 	CGI_10013344	superfamily	245201	64	232	1.17E-10	59.9429	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12384 - 	CGI_10020759	superfamily	248264	270	438	3.45E-19	88.8333	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#12385 - 	CGI_10020760	superfamily	241583	116	197	3.97E-13	65.6702	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#12387 - 	CGI_10020762	superfamily	246680	235	293	6.34E-05	40.0114	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#12389 - 	CGI_10020764	superfamily	246597	7	299	0	674.462	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#12393 - 	CGI_10020769	superfamily	246613	23	246	9.79E-147	422.889	cl14058	lectin_L-type superfamily	 - 	 - 	"legume lectins; The L-type (legume-type) lectins are a highly diverse family of carbohydrate binding proteins that generally display no enzymatic activity toward the sugars they bind.  This family includes arcelin, concanavalinA, the lectin-like receptor kinases, the ERGIC-53/VIP36/EMP46 type1 transmembrane proteins, and an alpha-amylase inhibitor.  L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face".  This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers.  Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely."
Q#12394 - 	CGI_10020770	superfamily	247724	30	295	4.41E-141	412.409	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12394 - 	CGI_10020770	superfamily	216255	217	511	6.26E-126	374.188	cl03076	Dynamin_M superfamily	 - 	 - 	"Dynamin central region; This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169."
Q#12395 - 	CGI_10020771	superfamily	243061	134	234	8.24E-42	139.785	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12400 - 	CGI_10020776	superfamily	248458	304	431	1.08E-05	46.5381	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#12401 - 	CGI_10020777	superfamily	207411	100	136	3.37E-10	54.3729	cl01438	zf-AN1 superfamily	 - 	 - 	"AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues."
Q#12401 - 	CGI_10020777	superfamily	207411	10	52	5.24E-10	53.6025	cl01438	zf-AN1 superfamily	 - 	 - 	"AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues."
Q#12401 - 	CGI_10020777	superfamily	145783	209	226	0.00145513	35.4856	cl03724	UIM superfamily	 - 	 - 	Ubiquitin interaction motif; This motif is called the ubiquitin interaction motif. One of the proteins containing this motif is a receptor for poly-ubiquitination chains for the proteasome. This motif has a pattern of conservation characteristic of an alpha helix.
Q#12402 - 	CGI_10020778	superfamily	203593	130	250	4.59E-21	86.5854	cl18243	Mod_r superfamily	 - 	 - 	"Modifier of rudimentary (Mod(r)) protein; This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic, and both of these regions are represented in this family. Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB). The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37). The mammalian homologue of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors."
Q#12403 - 	CGI_10020779	superfamily	248145	11	264	5.14E-118	344.211	cl17591	CAF1 superfamily	 - 	 - 	CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Q#12404 - 	CGI_10020780	superfamily	243092	36	287	1.72E-24	100.872	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12404 - 	CGI_10020780	superfamily	192471	285	325	5.53E-07	46.9906	cl10872	DUF2372 superfamily	C	 - 	Uncharacterized conserved protein (DUF2372); This family consists of proteins found from plants to humans. The function is not known.
Q#12405 - 	CGI_10020781	superfamily	241609	566	647	1.36E-37	137.124	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#12405 - 	CGI_10020781	superfamily	245201	736	1016	1.10E-151	455.06	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12405 - 	CGI_10020781	superfamily	243092	1	197	6.34E-31	124.37	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12405 - 	CGI_10020781	superfamily	243040	423	552	2.52E-22	95.1649	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#12405 - 	CGI_10020781	superfamily	245814	214	292	3.08E-05	43.2629	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12406 - 	CGI_10020782	superfamily	199940	6	148	1.22E-100	288.006	cl03715	Mago_nashi superfamily	 - 	 - 	"Mago nashi proteins, integral members of the exon junction complex; Members of this family, which was originally identified in Drosophila and called mago nashi, are integral members of the exon junction complex (EJC). The EJC is a multiprotein complex that is deposited on spliced mRNAs after intron removal at a conserved position upstream of the exon-exon junction, and transported to the cytoplasm where it has been shown to influence translation, surveillance, and localization of the spliced mRNA. It consists of four core proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP and is supposed to be a binding platform for more peripherally and transiently associated factors along mRNA travel. Mago and Y14 form a stable heterodimer that stabilizes the complex by inhibiting eIF4AIII's ATPase activity. In humans, but not Drosophila, EJC is involved in nonsense-mediated mRNA decay (NMD) via binding to Upf3b, a central NMD effector. EJC is stripped off the mRNA during the first round of translation and then the complex components are transported back into the nucleus and recycled. The Mago-Y14 heterodimer has been shown to interact with the cytoplasmic protein PYM, an EJC disassembly factor, and specifically binds to the karyopherin nuclear receptor importin 13."
Q#12409 - 	CGI_10020785	superfamily	218611	246	409	1.54E-54	182.368	cl05191	DMAP1 superfamily	 - 	 - 	"DNA methyltransferase 1-associated protein 1 (DMAP1); DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic amino terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication."
Q#12409 - 	CGI_10020785	superfamily	212556	155	202	4.55E-14	67.0478	cl18296	SANT_DMAP1_like superfamily	 - 	 - 	"SANT/myb-like domain of Human Dna Methyltransferase 1 Associated Protein 1-like; These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#12410 - 	CGI_10020786	superfamily	247899	126	233	2.41E-05	45.3327	cl17345	AccA superfamily	NC	 - 	Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]
Q#12413 - 	CGI_10020789	superfamily	248193	12	352	4.73E-74	239.85	cl17639	MiaA superfamily	 - 	 - 	"tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]"
Q#12414 - 	CGI_10020790	superfamily	241596	343	402	1.07E-11	60.3055	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#12414 - 	CGI_10020790	superfamily	216269	62	228	1.04E-20	91.1496	cl03082	Myc_N superfamily	C	 - 	"Myc amino-terminal region; The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see pfam00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication. Mutations in the C-terminal 20 residues of this domain cause unique changes in the induction of apoptosis, transformation, and G2 arrest."
Q#12415 - 	CGI_10020791	superfamily	247725	1	100	7.67E-12	60.3862	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12416 - 	CGI_10020792	superfamily	241884	669	759	1.50E-59	200.549	cl00467	Ntn_hydrolase superfamily	N	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#12416 - 	CGI_10020792	superfamily	247792	16	59	6.76E-07	47.4404	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12416 - 	CGI_10020792	superfamily	241563	129	163	3.63E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12417 - 	CGI_10020793	superfamily	241592	303	373	5.69E-06	43.8559	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#12417 - 	CGI_10020793	superfamily	247999	12	57	0.000136625	39.5026	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#12419 - 	CGI_10001710	superfamily	241563	89	124	0.000493591	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12420 - 	CGI_10017354	superfamily	243086	237	284	7.90E-16	72.0225	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#12420 - 	CGI_10017354	superfamily	215647	331	438	7.17E-12	64.1668	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#12421 - 	CGI_10017355	superfamily	245201	630	877	3.73E-113	350.584	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12421 - 	CGI_10017355	superfamily	243051	414	506	0.000207782	41.2094	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#12421 - 	CGI_10017355	superfamily	241613	311	329	0.00645382	35.7346	cl00104	LDLa superfamily	C	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#12422 - 	CGI_10017356	superfamily	220744	170	307	8.84E-30	115.407	cl11075	OAS1_C superfamily	 - 	 - 	"2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus; This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between 320 and 344 at the extreme C-terminal end. Oligoadenylate synthetases are antiviral enzymes that counteract vial attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication. This domain is often associated with NTP_transf_2 pfam01909."
Q#12422 - 	CGI_10017356	superfamily	245818	105	156	5.54E-05	42.0017	cl11966	Rel-Spo_like superfamily	C	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#12423 - 	CGI_10017357	superfamily	247744	2	45	2.17E-07	45.2965	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#12423 - 	CGI_10017357	superfamily	247744	42	85	5.31E-07	44.1409	cl17190	NK superfamily	N	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#12427 - 	CGI_10017361	superfamily	241624	131	478	8.56E-38	138.999	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#12428 - 	CGI_10017362	superfamily	243146	80	134	8.77E-06	44.5875	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12428 - 	CGI_10017362	superfamily	243146	206	252	9.71E-05	41.5059	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12428 - 	CGI_10017362	superfamily	243146	135	197	0.000192922	40.7355	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12428 - 	CGI_10017362	superfamily	243146	253	319	0.00038138	39.5799	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12428 - 	CGI_10017362	superfamily	243146	21	58	0.000388436	39.567	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#12430 - 	CGI_10017364	superfamily	248097	48	171	6.85E-15	67.2902	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12431 - 	CGI_10017365	superfamily	248097	48	149	1.27E-12	61.127	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12432 - 	CGI_10017366	superfamily	243066	46	151	5.53E-17	76.5021	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#12432 - 	CGI_10017366	superfamily	198867	189	267	0.000103347	40.4025	cl06652	BACK superfamily	N	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#12436 - 	CGI_10017370	superfamily	241577	213	403	1.88E-148	422.415	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#12436 - 	CGI_10017370	superfamily	241576	8	130	1.35E-75	233.576	cl00055	MH1 superfamily	 - 	 - 	"N-terminal Mad Homology 1 (MH1) domain; The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure.  It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. Receptor-regulated SMAD proteins (R-SMADs, including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by phosphorylation by transforming growth factor (TGF)-beta type I receptors. The active R-SMAD associates with a common mediator SMAD (Co-SMAD or SMAD4) and other cofactors, which together translocate to the nucleus to regulate gene expression. The inhibitory or antagonistic SMADs (I-SMADs, including SMAD6 and SMAD7) negatively regulate TGF-beta signaling by competing with R-SMADs for type I receptor or Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a nuclear localization signal as well as DNA-binding activity. The activated R-SMAD/SMAD4 complex then binds with very low affinity to a DNA sequence CAGAC called SMAD-binding element (SBE) via the MH1 domain."
Q#12437 - 	CGI_10017371	superfamily	219542	39	139	1.08E-37	135.062	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12437 - 	CGI_10017371	superfamily	215896	153	299	1.06E-19	85.8096	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#12437 - 	CGI_10017371	superfamily	219541	381	521	8.62E-11	59.7895	cl18516	Cu-oxidase_2 superfamily	C	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12438 - 	CGI_10017372	superfamily	219542	39	139	2.69E-38	127.743	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12440 - 	CGI_10017374	superfamily	241577	12	192	4.52E-79	236.892	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#12441 - 	CGI_10017375	superfamily	219542	150	253	8.50E-36	131.595	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12441 - 	CGI_10017375	superfamily	219541	512	660	7.41E-26	104.087	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12441 - 	CGI_10017375	superfamily	215896	261	390	2.20E-12	65.394	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#12442 - 	CGI_10017376	superfamily	216363	69	153	4.60E-19	77.8958	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#12443 - 	CGI_10017377	superfamily	219542	87	187	1.44E-38	139.299	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12443 - 	CGI_10017377	superfamily	219541	436	606	1.63E-21	91.7611	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12443 - 	CGI_10017377	superfamily	215896	201	323	1.90E-15	74.2536	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#12444 - 	CGI_10004147	superfamily	241583	365	405	0.00278564	37.6031	cl00064	ZnMc superfamily	NC	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#12446 - 	CGI_10004149	superfamily	241568	16	59	4.06E-09	50.154	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12446 - 	CGI_10004149	superfamily	241568	72	121	2.28E-07	45.5316	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12449 - 	CGI_10005590	superfamily	245864	488	834	4.02E-61	214.45	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12449 - 	CGI_10005590	superfamily	241567	24	290	9.76E-20	89.2198	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#12450 - 	CGI_10005591	superfamily	215733	179	410	3.56E-55	192.01	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#12450 - 	CGI_10005591	superfamily	216063	832	1035	5.72E-28	112.327	cl02929	Cation_ATPase_C superfamily	 - 	 - 	"Cation transporting ATPase, C-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices."
Q#12450 - 	CGI_10005591	superfamily	222006	470	547	1.28E-24	99.9894	cl16182	Hydrolase_like2 superfamily	 - 	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#12450 - 	CGI_10005591	superfamily	243244	84	158	3.14E-22	92.6458	cl02930	Cation_ATPase_N superfamily	 - 	 - 	"Cation transporter/ATPase, N-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport."
Q#12450 - 	CGI_10005591	superfamily	226572	658	779	0.000294953	41.0052	cl18761	COG4087 superfamily	 - 	 - 	Soluble P-type ATPase [General function prediction only]
Q#12451 - 	CGI_10005592	superfamily	243179	212	276	4.64E-06	44.2794	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#12451 - 	CGI_10005592	superfamily	243179	310	374	4.64E-06	44.2794	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#12452 - 	CGI_10005593	superfamily	243179	158	272	1.53E-11	59.8539	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#12455 - 	CGI_10011622	superfamily	216347	401	819	8.28E-130	397.677	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#12455 - 	CGI_10011622	superfamily	202361	253	353	1.93E-09	56.1697	cl03680	Cu_amine_oxidN3 superfamily	 - 	 - 	"Copper amine oxidase, N3 domain; This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ)."
Q#12458 - 	CGI_10011625	superfamily	241632	4	368	5.00E-134	390.46	cl00137	SERPIN superfamily	 - 	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#12459 - 	CGI_10011626	superfamily	241594	415	468	9.92E-10	58.7304	cl00077	HECTc superfamily	C	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#12460 - 	CGI_10011627	superfamily	241632	4	368	1.99E-132	386.223	cl00137	SERPIN superfamily	 - 	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#12461 - 	CGI_10011628	superfamily	245814	85	142	1.34E-07	49.3275	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12461 - 	CGI_10011628	superfamily	245814	164	230	5.66E-06	44.654	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12461 - 	CGI_10011628	superfamily	245814	12	49	0.00562112	35.4604	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12462 - 	CGI_10011629	superfamily	245814	240	308	5.92E-07	46.2154	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12463 - 	CGI_10011630	superfamily	245213	1483	1516	0.000205827	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	2114	2145	0.000216586	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	1711	1746	0.000608165	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	813	855	0.000667189	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	2344	2386	0.00125994	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	664	697	0.00287456	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	1213	1248	0.00320881	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	395	426	0.00390404	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	1626	1661	0.00635158	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	1836	1866	0.00734443	37.231	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	519	552	0.0093357	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	216290	2598	2691	1.11E-27	111.997	cl03089	Cu2_monooxygen superfamily	N	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#12463 - 	CGI_10011630	superfamily	205157	1258	1293	4.58E-07	49.4583	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#12463 - 	CGI_10011630	superfamily	241578	2262	2302	1.80E-06	50.076	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12463 - 	CGI_10011630	superfamily	241578	2300	2341	1.97E-06	50.076	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12463 - 	CGI_10011630	superfamily	201391	869	910	2.50E-05	44.6298	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#12463 - 	CGI_10011630	superfamily	201391	111	153	3.60E-05	43.8594	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#12463 - 	CGI_10011630	superfamily	241578	352	392	0.000117855	44.6832	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12463 - 	CGI_10011630	superfamily	241578	2032	2070	0.000137264	44.6832	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12463 - 	CGI_10011630	superfamily	241578	1084	1124	0.000159379	44.298	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12463 - 	CGI_10011630	superfamily	201391	761	796	0.000237859	41.5482	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#12463 - 	CGI_10011630	superfamily	201391	1546	1583	0.000282849	41.163	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#12463 - 	CGI_10011630	superfamily	245213	918	958	0.000429486	40.7952	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	241578	204	245	0.000744109	42.372	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12463 - 	CGI_10011630	superfamily	201391	1891	1934	0.00105576	39.6222	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#12463 - 	CGI_10011630	superfamily	201391	2168	2209	0.001144	39.6222	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#12463 - 	CGI_10011630	superfamily	245213	1044	1084	0.00223751	38.484	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	1951	1992	0.00238577	38.382	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	201391	572	616	0.00324116	38.0814	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#12463 - 	CGI_10011630	superfamily	245213	1752	1793	0.00347936	37.9968	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	241578	999	1039	0.00359476	40.0608	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12463 - 	CGI_10011630	superfamily	221695	334	357	0.00448407	37.8198	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#12463 - 	CGI_10011630	superfamily	245213	706	734	0.00557619	37.6116	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	2222	2262	0.0061924	37.3284	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	1794	1834	0.0082691	36.9432	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12463 - 	CGI_10011630	superfamily	245213	623	662	0.00836722	36.9432	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12464 - 	CGI_10011631	superfamily	241580	78	155	1.70E-47	156.175	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#12466 - 	CGI_10011633	superfamily	246669	507	640	1.03E-18	83.4016	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12466 - 	CGI_10011633	superfamily	246669	373	493	1.98E-18	82.3047	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12467 - 	CGI_10011634	superfamily	241659	55	120	7.57E-11	55.6039	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#12467 - 	CGI_10011634	superfamily	241659	153	221	2.94E-09	51.3667	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#12469 - 	CGI_10011636	superfamily	245206	6	266	2.67E-99	294.879	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12472 - 	CGI_10011639	superfamily	248097	207	329	3.55E-19	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12473 - 	CGI_10011640	superfamily	201383	116	215	1.15E-29	107.574	cl02923	Ribosomal_L5_C superfamily	 - 	 - 	ribosomal L5P family C-terminus; This region is found associated with pfam00281.
Q#12473 - 	CGI_10011640	superfamily	109342	59	112	5.34E-16	69.2676	cl08254	Ribosomal_L5 superfamily	 - 	 - 	Ribosomal protein L5; Ribosomal protein L5.  
Q#12476 - 	CGI_10010327	superfamily	241575	72	137	4.57E-09	53.8155	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#12476 - 	CGI_10010327	superfamily	241575	182	242	1.14E-07	49.5783	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#12476 - 	CGI_10010327	superfamily	243132	306	645	6.08E-74	243.02	cl02661	A_deamin superfamily	 - 	 - 	"Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc."
Q#12478 - 	CGI_10010329	superfamily	243092	312	427	9.54E-11	61.1968	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12479 - 	CGI_10010330	superfamily	242406	153	300	5.69E-25	98.4324	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#12481 - 	CGI_10010332	superfamily	241563	40	80	7.05E-07	46.7036	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12482 - 	CGI_10010333	superfamily	243092	19	259	7.72E-43	155.186	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12482 - 	CGI_10010333	superfamily	222150	388	412	8.72E-05	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12482 - 	CGI_10010333	superfamily	222150	416	438	9.36E-05	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12482 - 	CGI_10010333	superfamily	222150	445	468	0.000104732	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12483 - 	CGI_10010334	superfamily	247916	115	172	1.84E-05	43.9107	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#12484 - 	CGI_10010335	superfamily	247916	127	185	1.10E-06	47.7627	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#12485 - 	CGI_10010336	superfamily	247916	131	193	1.03E-08	53.9259	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#12486 - 	CGI_10010337	superfamily	247916	129	187	1.08E-05	44.6811	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#12490 - 	CGI_10010342	superfamily	199166	64	205	9.42E-30	112.036	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#12491 - 	CGI_10010343	superfamily	243047	14	118	7.01E-44	152.11	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#12493 - 	CGI_10008109	superfamily	247866	37	253	6.20E-48	162.237	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#12494 - 	CGI_10008110	superfamily	246669	110	220	1.35E-54	181.61	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12494 - 	CGI_10008110	superfamily	246669	1	98	1.27E-38	137.701	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12494 - 	CGI_10008110	superfamily	241578	232	486	1.58E-102	312.769	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12496 - 	CGI_10001409	superfamily	241574	227	369	1.34E-10	59.5217	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#12496 - 	CGI_10001409	superfamily	238012	29	61	0.00387515	35.0226	cl11390	EGF_Lam superfamily	N	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#12497 - 	CGI_10010732	superfamily	213107	27	61	8.62E-07	44.1881	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#12498 - 	CGI_10010733	superfamily	216966	23	159	8.06E-24	93.9278	cl03523	HORMA superfamily	N	 - 	"HORMA domain; The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity."
Q#12503 - 	CGI_10010738	superfamily	245201	53	300	6.08E-56	183.592	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12505 - 	CGI_10010740	superfamily	241805	70	145	1.54E-25	94.107	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#12505 - 	CGI_10010740	superfamily	191937	1	60	3.71E-33	113.057	cl06898	Ribosomal_S13_N superfamily	 - 	 - 	Ribosomal S13/S15 N-terminal domain; This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021.
Q#12506 - 	CGI_10010741	superfamily	245206	1	309	1.34E-138	405.143	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12506 - 	CGI_10010741	superfamily	176932	334	425	1.49E-34	124.975	cl03838	FAR_C superfamily	 - 	 - 	"C-terminal domain of fatty acyl CoA reductases; C-terminal domain of fatty acyl CoA reductases, a family of SDR-like proteins. SDRs or short-chain dehydrogenases/reductases are Rossmann-fold NAD(P)H-binding proteins. Many proteins in this FAR_C family may function as fatty acyl-CoA reductases (FARs), acting on medium and long chain fatty acids, and have been reported to be involved in diverse processes such as the biosynthesis of insect pheromones, plant cuticular wax production, and mammalian wax biosynthesis. In Arabidopsis thaliana, proteins with this particular architecture have also been identified as the MALE STERILITY 2 (MS2) gene product, which is implicated in male gametogenesis. Mutations in MS2 inhibit the synthesis of exine (sporopollenin), rendering plants unable to reduce pollen wall fatty acids to corresponding alcohols. The function of this C-terminal domain is unclear."
Q#12507 - 	CGI_10010742	superfamily	247824	36	271	1.16E-76	237.961	cl17270	APH_ChoK_like superfamily	 - 	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#12508 - 	CGI_10010743	superfamily	247069	6	158	1.09E-14	72.7614	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#12513 - 	CGI_10001294	superfamily	219542	37	149	6.77E-36	130.825	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12513 - 	CGI_10001294	superfamily	219541	465	602	5.07E-22	92.5315	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#12513 - 	CGI_10001294	superfamily	215896	157	340	3.44E-18	81.9576	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#12516 - 	CGI_10019783	superfamily	241622	935	1035	2.12E-19	85.311	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#12516 - 	CGI_10019783	superfamily	241622	833	916	3.61E-17	78.7626	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#12516 - 	CGI_10019783	superfamily	241622	1127	1184	2.05E-16	76.4514	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#12516 - 	CGI_10019783	superfamily	241622	410	487	8.15E-08	51.4135	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#12516 - 	CGI_10019783	superfamily	241622	237	314	1.30E-06	47.9467	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#12516 - 	CGI_10019783	superfamily	241647	137	164	2.82E-05	42.9002	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#12517 - 	CGI_10019784	superfamily	241622	32	96	1.90E-06	44.4799	cl00117	PDZ superfamily	C	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#12517 - 	CGI_10019784	superfamily	247744	133	207	5.75E-24	95.8227	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#12519 - 	CGI_10019786	superfamily	241563	68	104	5.44E-06	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12519 - 	CGI_10019786	superfamily	241563	10	47	0.000117813	38.8575	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12523 - 	CGI_10019790	superfamily	247044	9	119	2.21E-42	138.153	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#12524 - 	CGI_10019791	superfamily	246669	127	254	7.91E-11	60.495	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12529 - 	CGI_10019796	superfamily	198898	2	59	2.36E-24	95.1274	cl07406	c-SKI_SMAD_bind superfamily	N	 - 	c-SKI Smad4 binding domain; c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins. This domain binds to Smad4
Q#12530 - 	CGI_10019797	superfamily	245213	544	583	2.84E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12530 - 	CGI_10019797	superfamily	246918	397	452	1.52E-10	58.7523	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12530 - 	CGI_10019797	superfamily	245814	464	541	3.09E-07	49.8113	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12530 - 	CGI_10019797	superfamily	246918	331	374	3.22E-05	43.3443	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12532 - 	CGI_10019799	superfamily	241706	97	178	2.43E-35	120.74	cl00229	eIF1_SUI1_like superfamily	 - 	 - 	"Eukaryotic initiation factor 1 and related proteins; Members of the eIF1/SUI1 (eukaryotic initiation factor 1) family are found in eukaryotes, archaea, and some bacteria; eukaryotic members are understood to play an important role in accurate initiator codon recognition during translation initiation. eIF1 interacts with 18S rRNA in the 40S ribosomal subunit during eukaryotic translation initiation. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown. The function of non-eukaryotic family members is also unclear."
Q#12534 - 	CGI_10019801	superfamily	247741	48	378	0	622.347	cl17187	Aldolase_Class_I superfamily	 - 	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#12535 - 	CGI_10019802	superfamily	242670	11	148	3.95E-60	185.499	cl01729	VKOR superfamily	 - 	 - 	"Vitamin K epoxide reductase (VKOR) family; VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. This family includes enzymes that are present in vertebrates, Drosophila, plants, bacteria, and archaea. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some plant and bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. Warfarin, a widely used oral anticoagulant used in medicine as well as rodenticides, inhibits the activity of VKOR, resulting in decreased levels of reduced vitamin K, which is required for the function of several clotting factors. However, anticoagulation effect of warfarin is significantly associated with polymorphism of certain genes, including VKORC1. Interestingly, in rodents, an adaptive trait appears to have evolved convergently by selection on new or standing genetic polymorphisms in VKORC1 as well as by adaptive introgressive hybridization between species, likely brought about by human-mediated dispersal."
Q#12536 - 	CGI_10019803	superfamily	243175	40	133	1.06E-24	93.0467	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#12536 - 	CGI_10019803	superfamily	241832	4	38	3.79E-16	69.194	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#12537 - 	CGI_10019804	superfamily	243175	93	219	8.38E-44	145.434	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#12537 - 	CGI_10019804	superfamily	241832	4	79	9.81E-34	117.729	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#12540 - 	CGI_10019807	superfamily	247724	66	268	3.86E-75	236.663	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12541 - 	CGI_10019808	superfamily	245814	803	876	9.92E-11	60.1955	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12541 - 	CGI_10019808	superfamily	245814	619	672	2.84E-05	44.0171	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12541 - 	CGI_10019808	superfamily	245814	900	979	4.74E-20	87.5495	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12541 - 	CGI_10019808	superfamily	245814	700	779	1.29E-19	86.1148	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12541 - 	CGI_10019808	superfamily	245814	375	461	5.59E-09	55.1442	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12542 - 	CGI_10019809	superfamily	241563	71	109	7.08E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12543 - 	CGI_10019810	superfamily	241563	68	101	0.000855702	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12544 - 	CGI_10019811	superfamily	245847	43	184	4.32E-20	82.6045	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12546 - 	CGI_10019813	superfamily	217473	61	291	1.01E-23	101.288	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#12547 - 	CGI_10019814	superfamily	241832	126	215	1.40E-08	50.3846	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#12551 - 	CGI_10004586	superfamily	241564	77	146	1.38E-23	88.4767	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#12553 - 	CGI_10012268	superfamily	192535	49	235	7.03E-05	41.8126	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#12555 - 	CGI_10012270	superfamily	215866	38	153	1.11E-05	43.468	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#12556 - 	CGI_10012271	superfamily	245716	64	86	0.000737638	36.4533	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#12556 - 	CGI_10012271	superfamily	245716	120	144	0.00346063	34.5273	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#12558 - 	CGI_10012273	superfamily	241640	65	292	1.58E-100	296.88	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#12559 - 	CGI_10012274	superfamily	241640	67	312	1.22E-73	230.626	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#12560 - 	CGI_10012275	superfamily	245864	146	378	9.04E-65	215.99	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12560 - 	CGI_10012275	superfamily	245864	43	195	0.00386589	37.643	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12562 - 	CGI_10012277	superfamily	247724	71	261	1.21E-113	327.593	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12563 - 	CGI_10012278	superfamily	247724	41	79	5.03E-17	72.5907	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12566 - 	CGI_10003862	superfamily	243098	1434	1479	2.02E-12	64.5415	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#12566 - 	CGI_10003862	superfamily	243098	1105	1168	2.49E-08	52.6003	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#12567 - 	CGI_10003863	superfamily	243092	3	321	2.26E-68	217.588	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12568 - 	CGI_10003864	superfamily	246925	55	196	0.00052423	39.261	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#12569 - 	CGI_10003865	superfamily	248300	265	322	1.79E-05	41.4497	cl17746	RAP superfamily	 - 	 - 	"RAP domain; This domain is found in various eukaryotic species, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain. The domain is involved in plant defence in response to bacterial infection."
Q#12570 - 	CGI_10003866	superfamily	241862	379	617	2.37E-24	102.82	cl00437	COG0428 superfamily	 - 	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#12572 - 	CGI_10005750	superfamily	241568	907	962	1.68E-11	61.3248	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12572 - 	CGI_10005750	superfamily	243124	98	256	5.30E-41	149.114	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#12572 - 	CGI_10005750	superfamily	155088	477	618	5.32E-17	79.9474	cl02758	AMOP superfamily	 - 	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#12572 - 	CGI_10005750	superfamily	243065	636	783	0.000322497	41.2333	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#12573 - 	CGI_10005751	superfamily	218493	443	590	9.40E-50	173.312	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#12577 - 	CGI_10000986	superfamily	241600	19	229	9.79E-100	291.837	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12578 - 	CGI_10000713	superfamily	247756	6	243	5.20E-80	242.663	cl17202	HAD superfamily	 - 	 - 	haloacid dehalogenase-like hydrolase; haloacid dehalogenase-like hydrolase.  
Q#12580 - 	CGI_10024202	superfamily	241563	59	98	1.51E-05	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12580 - 	CGI_10024202	superfamily	110440	483	509	0.00171223	37.3873	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#12580 - 	CGI_10024202	superfamily	128778	109	215	0.00310615	37.6295	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#12582 - 	CGI_10024204	superfamily	245201	13	255	1.91E-106	311.778	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12583 - 	CGI_10024205	superfamily	245201	93	262	6.28E-74	228.501	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12583 - 	CGI_10024205	superfamily	246908	17	45	4.59E-09	51.7595	cl15255	SH2 superfamily	C	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#12585 - 	CGI_10024207	superfamily	241600	101	272	4.33E-71	220.19	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12586 - 	CGI_10024208	superfamily	241782	23	251	5.98E-105	324.719	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#12586 - 	CGI_10024208	superfamily	241782	255	325	7.08E-29	117.482	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#12588 - 	CGI_10024210	superfamily	222150	907	932	8.43E-06	44.3049	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12588 - 	CGI_10024210	superfamily	222150	879	902	8.07E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12588 - 	CGI_10024210	superfamily	197676	865	887	0.00200998	37.4453	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#12588 - 	CGI_10024210	superfamily	222150	787	810	0.00977989	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12589 - 	CGI_10024211	superfamily	243035	754	870	1.82E-24	100.387	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#12589 - 	CGI_10024211	superfamily	216897	498	576	7.33E-21	88.8924	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#12589 - 	CGI_10024211	superfamily	245847	625	741	1.35E-13	69.3033	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12589 - 	CGI_10024211	superfamily	243119	931	979	0.000213554	40.505	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#12589 - 	CGI_10024211	superfamily	203209	19	169	0.000260232	42.0657	cl12305	STOP superfamily	C	 - 	"STOP protein; Neurons contain abundant subsets of highly stable microtubules that resist de-polymerising conditions such as exposure to the cold. Stable microtubules are thought to be essential for neuronal development, maintenance, and function. STOP is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity. Additionally knowledge of STOPs function and properties may help in the treatment of neuroleptics in illnesses such as schizophrenia, currently thought to result from synaptic defects."
Q#12590 - 	CGI_10024212	superfamily	215866	4	141	0.00236167	36.5344	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#12591 - 	CGI_10024213	superfamily	248469	177	227	1.55E-08	51.2167	cl17915	HAD_like superfamily	N	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#12591 - 	CGI_10024213	superfamily	248469	8	120	0.000185851	39.2755	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#12596 - 	CGI_10024218	superfamily	247736	364	445	3.83E-07	47.7094	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#12597 - 	CGI_10024219	superfamily	245206	1315	1546	1.46E-59	212.53	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12597 - 	CGI_10024219	superfamily	244888	176	461	1.45E-64	224.204	cl08282	Acyl_transf_1 superfamily	 - 	 - 	Acyl transferase domain; Acyl transferase domain.  
Q#12597 - 	CGI_10024219	superfamily	245210	1	62	2.02E-15	79.9094	cl09938	cond_enzymes superfamily	N	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#12597 - 	CGI_10024219	superfamily	245209	1585	1662	0.000265039	41.4669	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#12598 - 	CGI_10024220	superfamily	245210	2	297	2.74E-120	357.638	cl09938	cond_enzymes superfamily	C	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#12600 - 	CGI_10024222	superfamily	243061	44	88	4.65E-21	80.849	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12601 - 	CGI_10024223	superfamily	243091	68	177	2.34E-12	65.0483	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#12601 - 	CGI_10024223	superfamily	222150	549	574	1.80E-05	43.1493	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12601 - 	CGI_10024223	superfamily	222150	577	602	1.86E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12601 - 	CGI_10024223	superfamily	222150	605	630	5.81E-05	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12601 - 	CGI_10024223	superfamily	222150	633	656	0.00172066	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12603 - 	CGI_10024225	superfamily	243072	100	224	1.00E-31	117.099	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12603 - 	CGI_10024225	superfamily	243072	35	149	1.80E-28	107.855	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12603 - 	CGI_10024225	superfamily	243073	333	369	3.37E-05	40.9165	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#12604 - 	CGI_10024226	superfamily	248338	14	126	1.95E-26	111.154	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#12604 - 	CGI_10024226	superfamily	248338	366	447	3.08E-12	64.8274	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#12605 - 	CGI_10024227	superfamily	241832	57	228	2.06E-117	335.629	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#12608 - 	CGI_10024230	superfamily	248097	120	241	3.78E-13	63.4382	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12609 - 	CGI_10024231	superfamily	248097	82	210	4.33E-11	57.3121	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12610 - 	CGI_10024232	superfamily	248097	133	261	1.28E-09	54.2305	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#12612 - 	CGI_10024234	superfamily	217473	133	324	5.00E-24	102.443	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#12619 - 	CGI_10016651	superfamily	245213	310	346	5.64E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	245213	538	574	7.23E-07	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	245213	462	498	8.60E-07	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	245213	386	422	1.97E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	245213	277	307	1.52E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	245213	356	383	0.000197272	40.6978	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	245213	432	459	0.000371403	39.9274	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	245213	508	535	0.00577163	36.4606	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12619 - 	CGI_10016651	superfamily	243061	688	789	7.58E-35	130.155	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12619 - 	CGI_10016651	superfamily	243061	1118	1219	3.53E-34	128.229	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12619 - 	CGI_10016651	superfamily	243061	579	680	1.44E-33	126.688	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12619 - 	CGI_10016651	superfamily	243061	902	1003	1.96E-33	126.303	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12619 - 	CGI_10016651	superfamily	243061	1010	1111	5.02E-33	125.147	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12619 - 	CGI_10016651	superfamily	243061	796	895	1.78E-31	120.525	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#12620 - 	CGI_10016652	superfamily	245213	1500	1539	6.64E-08	51.4834	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	245213	1581	1615	1.83E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	245213	1459	1494	2.20E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	245213	1332	1367	7.91E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	245213	1791	1825	0.000126707	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	245213	1663	1703	0.000690042	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	245213	891	924	0.00113937	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	245213	1624	1662	0.00114961	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	243124	90	184	2.52E-12	67.0669	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#12620 - 	CGI_10016652	superfamily	205157	1544	1579	9.23E-08	50.9991	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#12620 - 	CGI_10016652	superfamily	243065	276	403	5.98E-07	50.1329	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#12620 - 	CGI_10016652	superfamily	241578	720	763	0.000152789	43.9128	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12620 - 	CGI_10016652	superfamily	241578	1197	1239	0.000349743	42.7572	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12620 - 	CGI_10016652	superfamily	245213	685	724	0.00335919	37.6116	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12620 - 	CGI_10016652	superfamily	241578	974	1014	0.00345407	40.0608	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12620 - 	CGI_10016652	superfamily	221695	790	812	0.00554919	37.0494	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#12620 - 	CGI_10016652	superfamily	245213	1064	1096	0.00743446	36.8412	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12621 - 	CGI_10016653	superfamily	241599	119	213	7.03E-08	48.7789	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#12623 - 	CGI_10016657	superfamily	219593	93	158	1.16E-22	94.0646	cl06721	Abi_HHR superfamily	C	 - 	"Abl-interactor HHR; The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases. More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins. Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganisation, but their precise role remains unclear."
Q#12623 - 	CGI_10016657	superfamily	247683	374	406	1.94E-13	66.576	cl17036	SH3 superfamily	C	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#12623 - 	CGI_10016657	superfamily	241624	504	683	1.09E-09	58.1006	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#12624 - 	CGI_10016658	superfamily	191103	18	135	1.56E-36	140.477	cl04777	TIMELESS superfamily	C	 - 	Timeless protein; The timeless gene in Drosophila melanogaster and its homologues in a number of other insects and mammals (including human) are involved in circadian rhythm control. This family includes a related proteins from a number of fungal species.
Q#12624 - 	CGI_10016658	superfamily	191103	142	197	7.53E-11	63.0523	cl04777	TIMELESS superfamily	N	 - 	Timeless protein; The timeless gene in Drosophila melanogaster and its homologues in a number of other insects and mammals (including human) are involved in circadian rhythm control. This family includes a related proteins from a number of fungal species.
Q#12625 - 	CGI_10016659	superfamily	246925	97	252	6.67E-06	47.3502	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#12625 - 	CGI_10016659	superfamily	214507	485	527	7.13E-05	41.2616	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#12625 - 	CGI_10016659	superfamily	243030	22	48	0.000471221	38.3823	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#12627 - 	CGI_10016661	superfamily	245201	14	42	1.87E-07	45.1675	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12628 - 	CGI_10016662	superfamily	245201	201	517	1.06E-42	159.03	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12629 - 	CGI_10016663	superfamily	243176	368	628	4.60E-109	349.598	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#12629 - 	CGI_10016663	superfamily	248318	108	161	1.22E-19	85.9505	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#12629 - 	CGI_10016663	superfamily	243097	1678	1948	8.06E-97	316.927	cl02572	PIPKc superfamily	 - 	 - 	"Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs."
Q#12629 - 	CGI_10016663	superfamily	243038	208	251	2.02E-08	53.9859	cl02442	DEP superfamily	N	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#12630 - 	CGI_10016664	superfamily	218241	8	222	1.57E-56	181.711	cl04723	Far-17a_AIG1 superfamily	 - 	 - 	"FAR-17a/AIG1-like protein; This family includes the hamster androgen-induced FAR-17a protein, and its human homologue, the AIG1 protein. The function of these proteins is unknown. This family also includes homologous regions from a number of other metazoan proteins."
Q#12636 - 	CGI_10016670	superfamily	241648	102	144	1.39E-17	75.487	cl00158	ZnF_GATA superfamily	C	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#12636 - 	CGI_10016670	superfamily	241648	17	49	5.28E-11	57.3826	cl00158	ZnF_GATA superfamily	C	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#12638 - 	CGI_10016672	superfamily	236582	104	280	4.10E-24	99.8231	cl18895	PRK09599 superfamily	C	 - 	6-phosphogluconate dehydrogenase-like protein; Reviewed
Q#12639 - 	CGI_10016673	superfamily	246918	1189	1239	1.49E-06	47.9667	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12639 - 	CGI_10016673	superfamily	246918	673	728	0.00376201	37.5663	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12642 - 	CGI_10016676	superfamily	245226	81	248	1.13E-17	78.4964	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#12643 - 	CGI_10015924	superfamily	246925	111	378	5.73E-22	94.3445	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#12644 - 	CGI_10015925	superfamily	216939	55	120	6.59E-30	104.282	cl03492	PC4 superfamily	 - 	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#12645 - 	CGI_10015926	superfamily	245836	303	480	1.91E-55	188.23	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#12645 - 	CGI_10015926	superfamily	245836	58	194	2.58E-53	182.452	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#12646 - 	CGI_10015927	superfamily	246918	171	222	0.000193423	38.3367	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12646 - 	CGI_10015927	superfamily	204025	232	263	0.000782474	36.0753	cl07344	PLAC superfamily	 - 	 - 	PLAC (protease and lacunin) domain; The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins. It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin.
Q#12646 - 	CGI_10015927	superfamily	246918	112	139	0.00767071	33.533	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#12649 - 	CGI_10015930	superfamily	243050	4	50	2.90E-26	99.7224	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#12649 - 	CGI_10015930	superfamily	241645	221	307	1.51E-18	79.9347	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#12650 - 	CGI_10015931	superfamily	247724	8	181	8.87E-89	260.617	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12651 - 	CGI_10015932	superfamily	247724	23	178	1.45E-80	239.015	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12652 - 	CGI_10015933	superfamily	247724	24	166	8.74E-60	185.473	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12653 - 	CGI_10015934	superfamily	247724	22	173	2.32E-84	248.645	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12656 - 	CGI_10015937	superfamily	247941	7	146	6.01E-05	40.0117	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#12662 - 	CGI_10015943	superfamily	248264	58	135	3.85E-13	62.2546	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#12663 - 	CGI_10015944	superfamily	247805	24	137	6.26E-10	52.7248	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#12664 - 	CGI_10015945	superfamily	247905	1	43	5.24E-09	50.6993	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#12669 - 	CGI_10015950	superfamily	247856	26	88	5.32E-06	41.7645	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12669 - 	CGI_10015950	superfamily	247856	67	119	0.00015061	37.9125	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12669 - 	CGI_10015950	superfamily	247856	99	167	0.000716299	35.9865	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12670 - 	CGI_10015951	superfamily	247856	30	87	4.72E-08	46.0017	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12670 - 	CGI_10015951	superfamily	247856	62	121	0.00106976	34.0605	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12671 - 	CGI_10015952	superfamily	243085	25	62	2.99E-19	80.0287	cl02557	DM superfamily	 - 	 - 	"DM DNA binding domain; The DM domain is named after dsx and mab-3. dsx contains a single amino-terminal DM domain, whereas mab-3 contains two amino-terminal domains. The DM domain has a pattern of conserved zinc chelating residues C2H2C4. The dsx DM domain has been shown to dimerise and bind palindromic DNA."
Q#12671 - 	CGI_10015952	superfamily	112299	198	235	3.11E-11	57.8042	cl04098	DMA superfamily	 - 	 - 	DMRTA motif; This region is found to the C-terminus of the pfam00751. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Q#12673 - 	CGI_10002933	superfamily	115634	1	226	2.03E-154	431.153	cl06169	Phage_lambda_P superfamily	 - 	 - 	"Replication protein P; This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin."
Q#12675 - 	CGI_10004409	superfamily	241600	15	160	9.34E-39	132.749	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12676 - 	CGI_10004410	superfamily	220659	2	46	5.15E-16	65.4236	cl10943	SAYSvFN superfamily	N	 - 	Uncharacterized conserved domain (SAYSvFN); This domain of approximately 75 residues contains a highly conserved SATSv/iFN motif. The function is unknown but the domain is conserved from plants to humans.
Q#12679 - 	CGI_10001597	superfamily	241574	190	350	1.10E-55	189.719	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#12679 - 	CGI_10001597	superfamily	241574	418	575	2.62E-13	68.7665	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#12681 - 	CGI_10001808	superfamily	247743	162	329	8.10E-25	98.7575	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#12683 - 	CGI_10008280	superfamily	217293	215	406	1.18E-39	144.313	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#12683 - 	CGI_10008280	superfamily	217280	113	194	3.15E-19	87.2609	cl14953	Fe_hyd_lg_C superfamily	C	 - 	"Iron only hydrogenase large subunit, C-terminal domain; Iron only hydrogenase large subunit, C-terminal domain.  "
Q#12684 - 	CGI_10008281	superfamily	243092	12	289	2.86E-48	164.815	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12687 - 	CGI_10008284	superfamily	215754	196	286	2.73E-18	77.6788	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12687 - 	CGI_10008284	superfamily	215754	14	94	1.66E-17	75.3676	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12687 - 	CGI_10008284	superfamily	215754	95	190	3.10E-16	71.9008	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#12688 - 	CGI_10008285	superfamily	248011	790	870	0.00132557	40.1726	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#12688 - 	CGI_10008285	superfamily	241546	2671	2788	2.05E-38	143.185	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#12688 - 	CGI_10008285	superfamily	243086	2563	2607	4.94E-08	53.1478	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#12688 - 	CGI_10008285	superfamily	248011	1421	1490	1.54E-05	45.8662	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#12688 - 	CGI_10008285	superfamily	248011	1505	1567	6.85E-05	43.9402	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#12688 - 	CGI_10008285	superfamily	248011	891	951	0.000555783	41.2438	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#12688 - 	CGI_10008285	superfamily	222537	3677	3804	0.00470176	40.2779	cl16609	DUF4271 superfamily	N	 - 	Domain of unknown function (DUF4271); This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 221 and 326 amino acids in length.
Q#12689 - 	CGI_10008286	superfamily	246976	3	645	0	728.394	cl15483	Dymeclin superfamily	N	 - 	"Dyggve-Melchior-Clausen syndrome protein; Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 residues long and present in plants and animals. Mutations in the gene coding for this protein in humans give rise to the disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM 223800) which is an autosomal-recessive disorder characterized by the association of a spondylo-epi-metaphyseal dysplasia and mental retardation. DYM transcripts are widely expressed throughout human development and Dymeclin is not an integral membrane protein of the ER, but rather a peripheral membrane protein dynamically associated with the Golgi apparatus."
Q#12690 - 	CGI_10001867	superfamily	245213	73	108	1.55E-10	54.1798	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12690 - 	CGI_10001867	superfamily	245213	111	146	8.61E-08	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12690 - 	CGI_10001867	superfamily	245847	152	218	1.58E-09	53.3294	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12692 - 	CGI_10002048	superfamily	241583	55	209	7.45E-42	146.365	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#12693 - 	CGI_10002049	superfamily	241642	109	166	2.38E-05	40.5885	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#12698 - 	CGI_10004512	superfamily	245213	849	881	0.000170522	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12698 - 	CGI_10004512	superfamily	245213	138	173	0.000311411	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12698 - 	CGI_10004512	superfamily	245213	345	377	0.00228084	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12698 - 	CGI_10004512	superfamily	245213	606	637	0.00268633	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12698 - 	CGI_10004512	superfamily	245213	262	294	0.00571227	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12698 - 	CGI_10004512	superfamily	192997	2350	2443	3.02E-23	99.9635	cl18184	Sterol-sensing superfamily	C	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#12698 - 	CGI_10004512	superfamily	243060	1280	1366	7.94E-11	62.0112	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#12698 - 	CGI_10004512	superfamily	241578	640	684	4.50E-08	55.0835	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	241578	928	971	3.16E-07	52.3871	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	241578	160	216	1.05E-06	50.8464	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	241578	1145	1188	6.83E-06	48.5352	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	245213	429	468	0.00030313	41.1804	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12698 - 	CGI_10004512	superfamily	241578	685	719	0.000336794	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	241578	1022	1062	0.000613028	42.372	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	241578	1186	1228	0.000988803	41.9868	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	241578	517	559	0.00165354	41.2164	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#12698 - 	CGI_10004512	superfamily	221695	242	265	0.00177986	38.9754	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#12699 - 	CGI_10004513	superfamily	247856	103	156	1.74E-09	51.7797	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12699 - 	CGI_10004513	superfamily	247856	70	127	1.45E-06	43.6905	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12699 - 	CGI_10004513	superfamily	247856	134	191	0.00759315	33.2901	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12700 - 	CGI_10002685	superfamily	247792	17	58	1.58E-07	43.5884	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12701 - 	CGI_10002686	superfamily	247792	783	827	1.07E-11	61.3076	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12704 - 	CGI_10013194	superfamily	241584	327	400	4.32E-05	41.7131	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#12704 - 	CGI_10013194	superfamily	214531	114	144	4.33E-05	41.0481	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#12704 - 	CGI_10013194	superfamily	214531	146	188	0.000602635	37.5813	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#12705 - 	CGI_10013195	superfamily	247856	142	196	2.10E-16	75.2769	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12705 - 	CGI_10013195	superfamily	247856	64	125	9.71E-14	67.5729	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12705 - 	CGI_10013195	superfamily	241584	467	548	2.42E-09	55.5803	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#12705 - 	CGI_10013195	superfamily	241584	767	843	0.000251461	40.1723	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#12705 - 	CGI_10013195	superfamily	214531	310	351	5.78E-07	47.5965	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#12705 - 	CGI_10013195	superfamily	214531	277	307	8.20E-06	44.1297	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#12705 - 	CGI_10013195	superfamily	241584	669	750	0.000265761	40.2905	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#12707 - 	CGI_10013197	superfamily	243066	9	99	1.74E-41	146.544	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#12707 - 	CGI_10013197	superfamily	219619	334	401	7.36E-10	56.4471	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#12708 - 	CGI_10013198	superfamily	247792	809	849	0.000114495	40.892	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12708 - 	CGI_10013198	superfamily	204923	850	898	1.01E-17	78.7452	cl13837	VPS11_C superfamily	 - 	 - 	"Vacuolar protein sorting protein 11 C terminal; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion."
Q#12711 - 	CGI_10013201	superfamily	247856	130	183	3.51E-10	53.7057	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12711 - 	CGI_10013201	superfamily	247856	54	116	4.66E-10	53.3205	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12712 - 	CGI_10013202	superfamily	247856	22	84	1.99E-12	59.0985	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12712 - 	CGI_10013202	superfamily	247856	100	151	1.53E-09	51.0093	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12713 - 	CGI_10013203	superfamily	247856	60	122	4.80E-09	49.8537	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12713 - 	CGI_10013203	superfamily	247856	96	160	5.77E-07	44.4609	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12713 - 	CGI_10013203	superfamily	247856	134	189	2.04E-05	40.2237	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12714 - 	CGI_10013204	superfamily	247856	49	111	1.31E-11	56.7873	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12714 - 	CGI_10013204	superfamily	247856	85	149	1.97E-08	48.3129	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12714 - 	CGI_10013204	superfamily	247856	126	177	2.75E-08	47.9277	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12715 - 	CGI_10013205	superfamily	247856	27	89	4.17E-15	66.0321	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12715 - 	CGI_10013205	superfamily	247856	103	156	1.41E-13	61.7949	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12716 - 	CGI_10013206	superfamily	246664	1	64	1.55E-22	93.4082	cl14561	An_peroxidase_like superfamily	N	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#12717 - 	CGI_10013207	superfamily	248264	1048	1215	4.67E-13	68.8029	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#12717 - 	CGI_10013207	superfamily	222263	955	1025	0.00152599	38.4529	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#12720 - 	CGI_10003155	superfamily	245847	5	83	0.000439169	35.6102	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12721 - 	CGI_10007244	superfamily	245201	10	218	3.32E-125	360.928	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12722 - 	CGI_10007245	superfamily	241571	33	144	8.01E-18	75.5266	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#12723 - 	CGI_10007246	superfamily	202748	141	190	1.33E-16	70.9831	cl04238	DUF307 superfamily	 - 	 - 	Domain of unknown function (DUF307); Domain occurs as one or more copies in a small family of putative membrane proteins.
Q#12724 - 	CGI_10007247	superfamily	243166	84	199	6.35E-07	50.3698	cl02759	TRAM_LAG1_CLN8 superfamily	C	 - 	TLC domain; TLC domain.  
Q#12724 - 	CGI_10007247	superfamily	245874	837	928	0.000274129	41.2578	cl12111	TNFR superfamily	 - 	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#12724 - 	CGI_10007247	superfamily	245874	1205	1296	0.000583988	40.1022	cl12111	TNFR superfamily	 - 	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#12725 - 	CGI_10007248	superfamily	245835	7	237	4.75E-123	374.094	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#12726 - 	CGI_10007249	superfamily	247723	209	280	4.68E-14	67.5823	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#12726 - 	CGI_10007249	superfamily	247723	75	149	7.03E-14	66.8119	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#12726 - 	CGI_10007249	superfamily	247723	412	483	1.72E-06	45.7589	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#12727 - 	CGI_10007250	superfamily	220394	11	701	3.38E-146	450.373	cl10752	Meckelin superfamily	 - 	 - 	"Meckelin (Transmembrane protein 67); Members of this family are thought to be related to the ciliary basal body. Defects result in Meckel syndrome type 3, an autosomal recessive disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. Joubert syndrome type 6 is also a manifestation of certain mutations; it is an autosomal recessive congenital malformation of the cerebellar vermis and brainstem with abnormalities of axonal decussation (crossing in the brain) affecting the corticospinal tract and superior cerebellar peduncles. Individuals with Joubert syndrome have motor and behavioral abnormalities, including an inability to walk due to severe clumsiness and 'mirror' movements, and cognitive and behavioural disturbances."
Q#12729 - 	CGI_10004622	superfamily	243072	4	81	3.69E-20	78.5794	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12730 - 	CGI_10006612	superfamily	217574	4	119	8.19E-39	136.584	cl04089	eRF1_1 superfamily	 - 	 - 	"eRF1 domain 1; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#12730 - 	CGI_10006612	superfamily	217575	124	256	1.33E-37	133.169	cl04090	eRF1_2 superfamily	 - 	 - 	"eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#12730 - 	CGI_10006612	superfamily	146221	259	358	1.07E-36	129.595	cl04091	eRF1_3 superfamily	 - 	 - 	"eRF1 domain 3; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#12731 - 	CGI_10006613	superfamily	247999	53	96	9.31E-13	64.8192	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#12731 - 	CGI_10006613	superfamily	247999	214	259	7.43E-10	56.0662	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#12731 - 	CGI_10006613	superfamily	241581	731	786	0.00105152	38.5214	cl00062	FHA superfamily	NC	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#12733 - 	CGI_10006615	superfamily	241872	8	177	4.72E-14	66.2416	cl00453	CDP-OH_P_transf superfamily	 - 	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#12734 - 	CGI_10006616	superfamily	128469	207	303	3.06E-25	99.4519	cl17971	VPS9 superfamily	 - 	 - 	Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
Q#12736 - 	CGI_10006618	superfamily	242534	67	146	1.34E-15	70.7255	cl01495	Glyco_hydro_10 superfamily	C	 - 	Glycosyl hydrolase family 10; Glycosyl hydrolase family 10.  
Q#12737 - 	CGI_10006619	superfamily	242534	717	963	2.82E-46	168.566	cl01495	Glyco_hydro_10 superfamily	 - 	 - 	Glycosyl hydrolase family 10; Glycosyl hydrolase family 10.  
Q#12737 - 	CGI_10006619	superfamily	242534	222	467	1.87E-45	166.255	cl01495	Glyco_hydro_10 superfamily	 - 	 - 	Glycosyl hydrolase family 10; Glycosyl hydrolase family 10.  
Q#12737 - 	CGI_10006619	superfamily	221377	1158	1250	2.09E-08	54.0118	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#12737 - 	CGI_10006619	superfamily	216848	591	675	3.10E-06	47.046	cl03406	CBM_4_9 superfamily	C	 - 	Carbohydrate binding domain; This family includes diverse carbohydrate binding domains.
Q#12741 - 	CGI_10003732	superfamily	243267	20	386	3.55E-148	427.03	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#12745 - 	CGI_10005968	superfamily	241599	268	325	2.85E-16	72.6612	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#12745 - 	CGI_10005968	superfamily	198730	183	249	3.28E-46	155.289	cl02582	Pou superfamily	 - 	 - 	Pou domain - N-terminal to homeobox domain; Pou domain - N-terminal to homeobox domain.  
Q#12746 - 	CGI_10017007	superfamily	215529	1	122	4.18E-62	194.188	cl18336	PLN02978 superfamily	C	 - 	pyridoxal kinase
Q#12747 - 	CGI_10017008	superfamily	241672	4	127	8.71E-13	62.4056	cl00192	ribokinase_pfkB_like superfamily	N	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#12748 - 	CGI_10017009	superfamily	246681	2	259	3.21E-118	342.553	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#12750 - 	CGI_10017011	superfamily	242889	9	452	5.44E-117	352.711	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#12751 - 	CGI_10017012	superfamily	220078	44	168	6.19E-26	100.662	cl07513	DUF1917 superfamily	N	 - 	Domain of unknown function (DUF1917); This domain is found in various hypothetical and basophilic leukaemia proteins. It has no known function.
Q#12752 - 	CGI_10017013	superfamily	243179	266	362	0.000338873	38.6679	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#12753 - 	CGI_10017014	superfamily	248458	112	233	1.82E-05	43.0245	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#12754 - 	CGI_10017015	superfamily	243179	132	244	3.86E-10	55.2315	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#12755 - 	CGI_10017016	superfamily	243179	140	246	1.19E-13	65.2467	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#12756 - 	CGI_10017017	superfamily	247856	35	92	1.09E-07	47.1573	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12756 - 	CGI_10017017	superfamily	247856	104	165	1.22E-06	44.0757	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12756 - 	CGI_10017017	superfamily	247856	175	234	0.00026601	37.5273	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12757 - 	CGI_10017018	superfamily	245716	93	119	3.65E-06	43.7721	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#12758 - 	CGI_10017019	superfamily	245596	4	261	8.16E-164	464.034	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12758 - 	CGI_10017019	superfamily	193687	289	355	5.57E-19	81.0447	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#12759 - 	CGI_10017020	superfamily	241592	1	136	1.63E-82	240.962	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#12760 - 	CGI_10017021	superfamily	241704	69	210	1.00E-33	119.786	cl00227	PEBP superfamily	 - 	 - 	"PhosphatidylEthanolamine-Binding Protein (PEBP) domain; PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer)."
Q#12761 - 	CGI_10017022	superfamily	245835	80	283	3.11E-115	345.615	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#12761 - 	CGI_10017022	superfamily	147001	467	626	1.57E-25	105.483	cl04636	ICA69 superfamily	N	 - 	"Islet cell autoantigen ICA69, C-terminal domain; This family includes a 69 kD protein which has been identified as an islet cell autoantigen in type I diabetes mellitus. Its precise function is unknown."
Q#12762 - 	CGI_10017023	superfamily	241563	177	212	2.55E-05	42.2744	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12762 - 	CGI_10017023	superfamily	247792	17	80	0.00357673	35.8844	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#12762 - 	CGI_10017023	superfamily	128778	228	347	0.00023094	40.3259	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#12763 - 	CGI_10017024	superfamily	248022	67	387	3.84E-34	130.861	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#12764 - 	CGI_10017025	superfamily	247724	87	185	3.69E-17	74.8147	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12766 - 	CGI_10017027	superfamily	245201	2	248	1.15E-74	231.271	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12768 - 	CGI_10017029	superfamily	247057	305	362	2.08E-11	60.3869	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#12769 - 	CGI_10017030	superfamily	241550	553	784	2.94E-69	235.605	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#12769 - 	CGI_10017030	superfamily	245839	783	902	9.29E-40	144.656	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#12769 - 	CGI_10017030	superfamily	241550	48	231	8.09E-21	94.2366	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#12769 - 	CGI_10017030	superfamily	241550	195	270	1.39E-06	50.1097	cl00015	nt_trans superfamily	NC	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#12770 - 	CGI_10017031	superfamily	241659	11	103	3.14E-37	124.876	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#12771 - 	CGI_10017032	superfamily	247804	66	109	4.99E-07	46.4146	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#12771 - 	CGI_10017032	superfamily	203011	363	434	2.39E-12	62.6097	cl04515	SWIRM superfamily	 - 	 - 	SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
Q#12771 - 	CGI_10017032	superfamily	241760	8	56	6.14E-07	46.5168	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#12774 - 	CGI_10017037	superfamily	245847	25	147	0.00132411	37.0968	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12775 - 	CGI_10017038	superfamily	247941	7	89	1.03E-05	41.7293	cl17387	Methyltransf_21 superfamily	N	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#12778 - 	CGI_10003016	superfamily	149104	7	101	9.89E-28	98.3154	cl06748	Renin_r superfamily	 - 	 - 	"Renin receptor-like protein; The sequences featured in this family are similar to a region of the human renin receptor that bears a putative transmembrane spanning segment. The renin receptor is involved in intracellular signal transduction by the activation of the ERK1/ERK2 pathway, and it also serves to increase the efficiency of angiotensinogen cleavage by receptor-bound renin, therefore facilitating angiotensin II generation and action on a cell surface."
Q#12779 - 	CGI_10007999	superfamily	247068	467	562	3.47E-25	102.007	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12779 - 	CGI_10007999	superfamily	247068	571	669	4.26E-25	102.007	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12779 - 	CGI_10007999	superfamily	247068	249	344	6.23E-18	81.2057	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12779 - 	CGI_10007999	superfamily	247068	130	238	1.25E-14	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12779 - 	CGI_10007999	superfamily	247068	365	458	2.17E-14	70.8053	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12779 - 	CGI_10007999	superfamily	247068	682	779	3.99E-10	58.4789	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12779 - 	CGI_10007999	superfamily	247068	14	121	1.47E-06	47.6934	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12782 - 	CGI_10008002	superfamily	247724	169	340	2.44E-99	302.942	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12782 - 	CGI_10008002	superfamily	191952	395	447	1.58E-21	88.8798	cl06963	NOGCT superfamily	 - 	 - 	NOGCT (NUC087) domain; This C terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins.
Q#12783 - 	CGI_10008003	superfamily	246925	79	211	2.26E-06	48.1206	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#12783 - 	CGI_10008003	superfamily	245814	289	370	9.88E-06	43.6481	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12784 - 	CGI_10008004	superfamily	245814	297	351	7.49E-05	40.9517	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12784 - 	CGI_10008004	superfamily	243030	26	51	0.00639232	34.9155	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#12785 - 	CGI_10008005	superfamily	245814	300	370	0.000288057	39.0876	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12786 - 	CGI_10008006	superfamily	245814	210	264	7.41E-05	40.5665	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12786 - 	CGI_10008006	superfamily	246925	18	101	0.00630834	36.5646	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#12786 - 	CGI_10008006	superfamily	214507	146	191	0.00969674	33.9428	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#12787 - 	CGI_10008007	superfamily	247068	466	564	7.06E-26	103.932	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12787 - 	CGI_10008007	superfamily	247068	250	346	2.08E-24	99.6953	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12787 - 	CGI_10008007	superfamily	247068	576	667	5.28E-21	90.0653	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12787 - 	CGI_10008007	superfamily	247068	365	458	4.28E-20	87.3689	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12787 - 	CGI_10008007	superfamily	247068	139	242	3.81E-16	75.8129	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12787 - 	CGI_10008007	superfamily	247068	680	769	2.11E-14	70.8053	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12787 - 	CGI_10008007	superfamily	247068	25	131	1.06E-09	56.9382	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12788 - 	CGI_10008008	superfamily	247068	464	560	7.14E-23	95.4581	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12788 - 	CGI_10008008	superfamily	247068	248	345	9.64E-22	91.9913	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12788 - 	CGI_10008008	superfamily	247068	569	658	1.01E-19	86.2133	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12788 - 	CGI_10008008	superfamily	247068	140	240	5.63E-18	81.2057	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12788 - 	CGI_10008008	superfamily	247068	671	764	7.62E-18	80.8205	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12788 - 	CGI_10008008	superfamily	247068	363	456	3.41E-14	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12788 - 	CGI_10008008	superfamily	247068	22	129	7.31E-07	48.4638	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12789 - 	CGI_10008009	superfamily	247068	462	558	3.51E-27	107.784	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12789 - 	CGI_10008009	superfamily	247068	566	661	4.33E-22	93.1469	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12789 - 	CGI_10008009	superfamily	247068	247	342	9.04E-22	92.3765	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12789 - 	CGI_10008009	superfamily	247068	674	767	4.92E-17	78.5093	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12789 - 	CGI_10008009	superfamily	247068	360	453	2.81E-15	73.5017	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12789 - 	CGI_10008009	superfamily	247068	138	238	1.30E-14	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12789 - 	CGI_10008009	superfamily	247068	23	127	2.36E-07	50.0046	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#12791 - 	CGI_10003262	superfamily	243069	24	173	1.54E-53	171.561	cl02525	Band_7 superfamily	N	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#12792 - 	CGI_10003263	superfamily	243072	49	144	1.38E-17	75.4978	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12793 - 	CGI_10003264	superfamily	241583	118	289	1.06E-49	172.558	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#12794 - 	CGI_10003265	superfamily	248458	342	513	6.03E-12	65.7981	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#12794 - 	CGI_10003265	superfamily	248458	152	282	1.81E-09	58.0941	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#12795 - 	CGI_10003266	superfamily	243035	277	358	9.54E-17	75.7141	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#12796 - 	CGI_10003267	superfamily	248012	502	624	1.72E-25	103.122	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#12796 - 	CGI_10003267	superfamily	245814	395	461	7.47E-06	44.7368	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#12797 - 	CGI_10005664	superfamily	217473	96	216	1.58E-08	53.5229	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#12798 - 	CGI_10005665	superfamily	217473	49	216	7.86E-09	54.2933	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#12799 - 	CGI_10005666	superfamily	219877	175	281	6.19E-49	171.769	cl11719	STAG superfamily	 - 	 - 	"STAG domain; STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version."
Q#12799 - 	CGI_10005666	superfamily	217473	1300	1523	8.06E-32	127.866	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#12800 - 	CGI_10005667	superfamily	247856	86	147	1.23E-09	51.0093	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12801 - 	CGI_10005668	superfamily	202715	30	127	2.45E-38	126.924	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#12802 - 	CGI_10005669	superfamily	247069	154	291	3.43E-20	87.0138	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#12803 - 	CGI_10005670	superfamily	243096	301	480	2.64E-45	160.926	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#12803 - 	CGI_10005670	superfamily	247683	720	773	3.99E-14	68.4319	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#12803 - 	CGI_10005670	superfamily	243054	49	199	5.55E-09	55.5296	cl02488	SPEC superfamily	N	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#12803 - 	CGI_10005670	superfamily	247725	487	612	2.05E-50	173.176	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#12805 - 	CGI_10000157	superfamily	220015	19	116	2.72E-19	77.3734	cl07407	RPA_C superfamily	 - 	 - 	"Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints."
Q#12805 - 	CGI_10000157	superfamily	245205	3	22	3.06E-06	41.0457	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#12806 - 	CGI_10003163	superfamily	220249	67	128	5.60E-10	51.4521	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#12808 - 	CGI_10003165	superfamily	243087	9	69	1.37E-06	44.508	cl02562	PWI superfamily	 - 	 - 	PWI domain; PWI domain.  
Q#12808 - 	CGI_10003165	superfamily	219911	222	257	0.000716297	38.497	cl07255	PRP3 superfamily	C	 - 	pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa.
Q#12809 - 	CGI_10001627	superfamily	243689	70	99	0.00167695	32.6005	cl04271	IBN_N superfamily	C	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#12811 - 	CGI_10017134	superfamily	245847	89	205	0.000632194	37.5362	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#12813 - 	CGI_10017136	superfamily	245596	81	256	3.51E-77	235.939	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#12814 - 	CGI_10017138	superfamily	241563	61	100	0.000239909	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12815 - 	CGI_10017139	superfamily	241958	48	165	3.91E-18	81.0225	cl00573	SDF superfamily	NC	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#12816 - 	CGI_10017140	superfamily	241958	49	377	6.71E-43	155.751	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#12817 - 	CGI_10017141	superfamily	245208	79	511	4.27E-142	422.935	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#12818 - 	CGI_10017142	superfamily	246908	1252	1336	1.65E-39	143.532	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#12818 - 	CGI_10017142	superfamily	246908	1345	1436	1.67E-24	100.762	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#12818 - 	CGI_10017142	superfamily	245202	1148	1201	1.23E-06	48.1455	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#12818 - 	CGI_10017142	superfamily	150144	309	555	6.48E-09	56.3275	cl09624	Tex_N superfamily	 - 	 - 	Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Bordetella pertussis tex. This protein defines a novel family of prokaryotic transcriptional accessory factors.
Q#12818 - 	CGI_10017142	superfamily	247832	699	812	8.38E-09	55.2657	cl17278	UPF0081 superfamily	 - 	 - 	Uncharacterized protein family (UPF0081); Uncharacterized protein family (UPF0081).  
Q#12821 - 	CGI_10017145	superfamily	245605	14	143	6.36E-47	149.665	cl11409	RNAP_RPB11_RPB3 superfamily	 - 	 - 	"RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts."
Q#12822 - 	CGI_10017146	superfamily	245201	90	210	2.55E-05	44.9202	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#12823 - 	CGI_10017147	superfamily	214507	395	453	0.000130488	40.106	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#12824 - 	CGI_10017148	superfamily	218140	202	643	2.84E-155	458.986	cl04579	Anoctamin superfamily	 - 	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#12825 - 	CGI_10017149	superfamily	243072	189	298	3.95E-21	90.1354	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12825 - 	CGI_10017149	superfamily	243072	78	233	1.85E-20	88.2094	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12827 - 	CGI_10017151	superfamily	245226	90	250	3.10E-64	200.497	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#12828 - 	CGI_10017152	superfamily	216082	75	263	7.88E-30	119.86	cl08284	Glyco_hydro_15 superfamily	C	 - 	Glycosyl hydrolases family 15; In higher organisms this family is represented by phosphorylase kinase subunits.
Q#12828 - 	CGI_10017152	superfamily	213147	296	323	0.00686604	35.6889	cl17040	ADDz superfamily	NC	 - 	"ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain; The ADDz zinc finger domain is present in the chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2 type transcription factor protein. The Dnmt3 family includes two active DNA methyltransferases, Dnmt3a and -3b, and one regulatory factor Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif."
Q#12836 - 	CGI_10017160	superfamily	220695	108	232	0.00762629	36.4027	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#12837 - 	CGI_10000440	superfamily	247856	28	80	1.43E-07	44.4609	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12839 - 	CGI_10009804	superfamily	241718	61	181	3.07E-59	189.945	cl00241	IF6 superfamily	N	 - 	"Ribosome anti-association factor IF6 binds the large ribosomal subunit and prevents the two subunits from associating during translation initiation. IF6 comprises a family of translation factors that includes both eukaryotic (eIF6) and archeal (aIF6) members.  All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved C-terminal extension which is not required for ribosomal binding, and may have an alternative function."
Q#12842 - 	CGI_10009807	superfamily	245213	1603	1639	0.000237706	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12842 - 	CGI_10009807	superfamily	245213	1717	1753	0.00078648	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12842 - 	CGI_10009807	superfamily	245213	157	192	0.00163323	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12842 - 	CGI_10009807	superfamily	245213	783	818	0.00192965	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12842 - 	CGI_10009807	superfamily	245213	600	635	0.00307838	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12843 - 	CGI_10009809	superfamily	220692	109	254	6.81E-07	49.1249	cl18570	7TM_GPCR_Srw superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#12844 - 	CGI_10009810	superfamily	244843	1	119	2.89E-20	84.9752	cl08040	Ggt superfamily	N	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#12845 - 	CGI_10009811	superfamily	192535	165	251	2.75E-05	43.3534	cl18179	7TM_GPCR_Srsx superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#12846 - 	CGI_10009812	superfamily	241832	9	128	1.06E-56	175.552	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#12847 - 	CGI_10009813	superfamily	241832	29	170	2.51E-48	155.136	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#12848 - 	CGI_10009814	superfamily	202668	477	576	3.58E-30	116.995	cl04110	BK_channel_a superfamily	 - 	 - 	Calcium-activated BK potassium channel alpha subunit; Calcium-activated BK potassium channel alpha subunit.  
Q#12848 - 	CGI_10009814	superfamily	219619	247	322	1.29E-11	62.6103	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#12849 - 	CGI_10009815	superfamily	247984	47	232	9.88E-51	165.476	cl17430	FtsJ superfamily	 - 	 - 	"FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping."
Q#12850 - 	CGI_10009816	superfamily	207654	246	317	2.76E-22	88.2686	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#12850 - 	CGI_10009816	superfamily	207654	88	152	3.05E-20	82.4906	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#12850 - 	CGI_10009816	superfamily	207654	21	80	2.28E-18	77.483	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#12850 - 	CGI_10009816	superfamily	207654	172	236	1.42E-12	61.6898	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#12852 - 	CGI_10004212	superfamily	241577	24	188	1.19E-82	245.116	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#12855 - 	CGI_10004215	superfamily	245867	9	94	0.00217274	35.2406	cl12090	DUF2156 superfamily	NC	 - 	"Uncharacterized conserved protein (DUF2156); This domain, found in various hypothetical prokaryotic proteins, has no known function."
Q#12856 - 	CGI_10011484	superfamily	245225	207	667	2.20E-49	182.828	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#12857 - 	CGI_10011485	superfamily	245225	58	147	0.00012627	40.6891	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#12858 - 	CGI_10011486	superfamily	219078	32	127	1.33E-05	40.9575	cl12333	DUF1113 superfamily	 - 	 - 	Protein of unknown function (DUF1113); This family consists of several bacterial proteins of unknown function.
Q#12859 - 	CGI_10011487	superfamily	243034	95	188	7.49E-19	81.6575	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#12859 - 	CGI_10011487	superfamily	222431	327	416	6.08E-22	89.5889	cl16447	RPAP3_C superfamily	 - 	 - 	Potential Monad-binding region of RPAP3; This domain is found at the C-terminus of RNA-polymerase II-associated proteins. These proteins bind to Monad and are involved in regulating apoptosis. They contain TPR-repeats towards the N_terminus.
Q#12860 - 	CGI_10011488	superfamily	241563	68	104	2.64E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#12862 - 	CGI_10011490	superfamily	245864	149	261	9.72E-27	111.987	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12863 - 	CGI_10011491	superfamily	245864	88	360	8.95E-59	198.656	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#12866 - 	CGI_10011494	superfamily	243134	134	254	4.19E-39	133.929	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#12866 - 	CGI_10011494	superfamily	243134	2	120	9.16E-26	98.4903	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#12869 - 	CGI_10011497	superfamily	243064	24	198	2.59E-11	58.1958	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#12870 - 	CGI_10011498	superfamily	243064	22	202	3.19E-16	72.4482	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#12871 - 	CGI_10011499	superfamily	243092	2	235	3.52E-38	136.696	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12872 - 	CGI_10011500	superfamily	110440	523	550	0.00682929	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#12873 - 	CGI_10011501	superfamily	222150	163	188	6.44E-05	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12873 - 	CGI_10011501	superfamily	222150	219	244	0.000793315	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12873 - 	CGI_10011501	superfamily	222150	191	215	0.00286382	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12876 - 	CGI_10002962	superfamily	214531	20	62	8.61E-09	47.5965	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#12876 - 	CGI_10002962	superfamily	214531	64	105	1.43E-06	41.4333	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#12877 - 	CGI_10004601	superfamily	243051	173	295	8.45E-22	90.1297	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#12877 - 	CGI_10004601	superfamily	241571	7	123	8.70E-08	49.3331	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#12877 - 	CGI_10004601	superfamily	245213	131	155	0.000286409	38.2266	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#12879 - 	CGI_10004603	superfamily	218200	28	259	1.12E-71	229.561	cl04660	Glyco_transf_54 superfamily	 - 	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#12881 - 	CGI_10004605	superfamily	222150	401	426	0.00561638	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#12882 - 	CGI_10004606	superfamily	248458	30	409	9.53E-24	100.466	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#12886 - 	CGI_10010161	superfamily	248022	1	122	5.13E-09	51.8947	cl17468	Aa_trans superfamily	N	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#12887 - 	CGI_10010162	superfamily	199166	237	421	7.24E-10	57.7224	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#12887 - 	CGI_10010162	superfamily	199166	144	315	4.76E-08	52.3296	cl15308	AMN1 superfamily	N	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#12887 - 	CGI_10010162	superfamily	243074	89	129	0.000409218	38.2565	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#12888 - 	CGI_10010163	superfamily	245230	2	426	0	951.72	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#12889 - 	CGI_10010164	superfamily	243082	438	834	6.84E-89	288.236	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#12890 - 	CGI_10010165	superfamily	241799	30	267	1.49E-132	378.751	cl00339	SugarP_isomerase superfamily	 - 	 - 	"SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway."
Q#12891 - 	CGI_10010166	superfamily	247743	198	321	2.21E-12	64.4747	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#12891 - 	CGI_10010166	superfamily	243072	71	178	3.91E-12	63.5566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12891 - 	CGI_10010166	superfamily	209247	393	472	3.43E-09	53.9397	cl11083	ClpB_D2-small superfamily	 - 	 - 	"C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighboring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724."
Q#12892 - 	CGI_10010167	superfamily	248458	1196	1282	0.000683428	42.3009	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#12892 - 	CGI_10010167	superfamily	222006	677	753	2.85E-08	52.995	cl16182	Hydrolase_like2 superfamily	N	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#12892 - 	CGI_10010167	superfamily	215733	96	289	0.000271947	42.5523	cl02811	E1-E2_ATPase superfamily	C	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#12892 - 	CGI_10010167	superfamily	241762	814	881	0.00107796	38.8447	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#12892 - 	CGI_10010167	superfamily	226572	976	1024	0.00458332	37.9236	cl18761	COG4087 superfamily	N	 - 	Soluble P-type ATPase [General function prediction only]
Q#12893 - 	CGI_10010168	superfamily	244363	22	126	6.77E-30	107.499	cl06336	Commd superfamily	N	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#12896 - 	CGI_10010171	superfamily	241659	61	129	7.84E-10	55.2187	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#12897 - 	CGI_10010172	superfamily	247856	163	215	4.12E-07	47.1573	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12897 - 	CGI_10010172	superfamily	246925	1	141	4.24E-11	62.7582	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#12898 - 	CGI_10010173	superfamily	221416	62	223	2.46E-27	110.58	cl13517	Spt20 superfamily	 - 	 - 	Spt20 family; This presumed domain is found in the Spt20 proteins from both human and yeast. The Spt20 protein is part of the SAGA complex which is a large cmplex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.
Q#12900 - 	CGI_10027190	superfamily	243089	94	258	1.80E-42	153.953	cl02564	PXA superfamily	 - 	 - 	PXA domain; This domain is associated with PX domains pfam00787.
Q#12900 - 	CGI_10027190	superfamily	149621	839	946	2.50E-33	125.475	cl07303	Nexin_C superfamily	 - 	 - 	Sorting nexin C terminal; This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787.
Q#12900 - 	CGI_10027190	superfamily	243088	642	765	7.94E-30	115.934	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#12900 - 	CGI_10027190	superfamily	243090	390	463	1.48E-16	77.4541	cl02565	RGS superfamily	N	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#12901 - 	CGI_10027191	superfamily	247941	4	123	8.77E-06	41.9377	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#12902 - 	CGI_10027192	superfamily	241825	41	180	5.08E-22	91.0623	cl00379	Ribosomal_L18_L5e superfamily	 - 	 - 	"Ribosomal L18/L5e:  L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified."
Q#12902 - 	CGI_10027192	superfamily	241825	242	381	5.08E-22	91.0623	cl00379	Ribosomal_L18_L5e superfamily	 - 	 - 	"Ribosomal L18/L5e:  L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified."
Q#12902 - 	CGI_10027192	superfamily	222592	403	483	6.27E-35	126.128	cl16705	Ribosomal_L18_c superfamily	 - 	 - 	Ribosomal L18 C-terminal region; This domain is the C-terminal end of ribosomal L18/L5 proteins.
Q#12904 - 	CGI_10027194	superfamily	247856	47	133	2.47E-05	39.0681	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#12909 - 	CGI_10027199	superfamily	245604	17	91	2.01E-32	111.086	cl11404	Biotinyl_lipoyl_domains superfamily	N	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#12911 - 	CGI_10027201	superfamily	245226	16	83	6.85E-08	46.5249	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#12912 - 	CGI_10027202	superfamily	243066	5	91	1.03E-10	53.7109	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#12914 - 	CGI_10027204	superfamily	243072	188	304	2.85E-28	107.855	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12914 - 	CGI_10027204	superfamily	243072	80	238	3.35E-28	107.855	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12914 - 	CGI_10027204	superfamily	243073	403	444	3.54E-11	58.2759	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#12914 - 	CGI_10027204	superfamily	243072	31	53	0.00670043	34.452	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#12915 - 	CGI_10027205	superfamily	247724	204	290	0.00539716	36.3343	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12915 - 	CGI_10027205	superfamily	247755	41	75	0.00706298	36.0687	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#12916 - 	CGI_10027206	superfamily	247724	27	189	7.12E-48	156.847	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12917 - 	CGI_10027207	superfamily	242323	81	320	2.90E-68	215.661	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#12917 - 	CGI_10027207	superfamily	242849	23	80	5.64E-11	57.5989	cl02041	Cyt-b5 superfamily	N	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#12920 - 	CGI_10027210	superfamily	178061	2	281	1.10E-163	458.858	cl18094	PLN02442 superfamily	 - 	 - 	S-formylglutathione hydrolase
Q#12922 - 	CGI_10027212	superfamily	243092	35	195	2.10E-23	100.872	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12922 - 	CGI_10027212	superfamily	243092	125	393	1.16E-12	67.7452	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12925 - 	CGI_10027215	superfamily	246680	12	90	0.00545084	34.0996	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#12932 - 	CGI_10027222	superfamily	247684	12	446	0	585.975	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#12935 - 	CGI_10027225	superfamily	243084	573	675	8.50E-53	177.941	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#12936 - 	CGI_10027226	superfamily	241568	601	660	1.58E-05	43.6056	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12936 - 	CGI_10027226	superfamily	241568	415	472	5.47E-05	42.0648	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12936 - 	CGI_10027226	superfamily	241568	476	531	0.000779627	38.598	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12936 - 	CGI_10027226	superfamily	241568	665	720	0.000892298	38.2128	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12937 - 	CGI_10027227	superfamily	248317	134	593	8.02E-104	325.49	cl17763	GDA1_CD39 superfamily	 - 	 - 	GDA1/CD39 (nucleoside phosphatase) family; GDA1/CD39 (nucleoside phosphatase) family.  
Q#12938 - 	CGI_10027228	superfamily	243092	16	328	3.65E-24	99.3316	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#12939 - 	CGI_10027229	superfamily	221381	213	494	1.25E-93	292.373	cl13455	DUF3508 superfamily	 - 	 - 	Domain of unknown function (DUF3508); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 280 amino acids in length. This domain has two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704.
Q#12940 - 	CGI_10027230	superfamily	247683	16	68	3.43E-22	89.5641	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#12940 - 	CGI_10027230	superfamily	246669	417	457	4.34E-12	63.9611	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12941 - 	CGI_10027231	superfamily	246669	2	163	8.48E-53	180.291	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#12942 - 	CGI_10027232	superfamily	244307	107	501	1.99E-178	523.044	cl06123	DHR2_DOCK superfamily	 - 	 - 	"Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins; DOCK proteins comprise a family of atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. They are also called the CZH (CED-5, Dock180, and MBC-zizimin homology) family, after the first family members identified. Dock180 was first isolated as a binding partner for the adaptor protein Crk. The Caenorhabditis elegans protein, Ced-5, is essential for cell migration and phagocytosis, while the Drosophila ortholog, Myoblast city (MBC), is necessary for myoblast fusion and dorsal closure. DOCKs are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1 (or Dock180), 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1, and DHR-2 (also called CZH2 or Docker). This alignment model represents the DHR-2 domain of DOCK proteins, which contains the catalytic GEF activity for Rac and/or Cdc42."
Q#12942 - 	CGI_10027232	superfamily	247999	800	845	0.000135403	40.6582	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#12943 - 	CGI_10027233	superfamily	248241	42	503	0	569.968	cl17687	5_nucleotid superfamily	 - 	 - 	"5' nucleotidase family; This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5."
Q#12944 - 	CGI_10027234	superfamily	243095	96	301	1.46E-66	218.099	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#12945 - 	CGI_10027235	superfamily	221838	224	429	1.10E-56	193.257	cl15150	Apc4 superfamily	 - 	 - 	"Anaphase-promoting complex, cyclosome, subunit 4; Apc4 is one of the larger of the subunits of the anaphase-promoting complex or cyclosome. This family represents the long domain downstream of the WD40 repeat/s that are present on the Apc4 subunits. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. Results in C.elegans show that the primary essential role of the spindle assembly checkpoint is not in the chromosome segregation process itself but rather in delaying anaphase onset until all chromosomes are properly attached to the spindle. the APC/C is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism."
Q#12945 - 	CGI_10027235	superfamily	205130	6	52	5.40E-14	67.7027	cl14918	Apc4_WD40 superfamily	 - 	 - 	"Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,"
Q#12946 - 	CGI_10027236	superfamily	222551	65	188	1.69E-06	43.9753	cl16625	DUF4285 superfamily	 - 	 - 	Domain of unknown function (DUF4285); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 157 and 206 amino acids in length.
Q#12950 - 	CGI_10027240	superfamily	243263	21	410	1.13E-71	234.61	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#12951 - 	CGI_10027241	superfamily	242166	78	174	2.67E-34	118.109	cl00881	SQR_QFR_TM superfamily	 - 	 - 	"Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQRs may reduce either high or low potential quinones while QFRs oxidize only low potential quinols. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit(s) containing the electron donor/acceptor (quinol or quinone). The reversible reduction of quinone is an essential feature of respiration, allowing the transfer of electrons between respiratory complexes. SQRs and QFRs can be classified into five types (A-E) according to the number of their hydrophobic subunits and heme groups. This classification is consistent with the characteristics and phylogeny of the catalytic and iron-sulfur subunits. Type E proteins, e.g. non-classical archael SQRs, contain atypical transmembrane subunits and are not included in this hierarchy. The heme and quinone binding sites reside in the transmembrane subunits. Although succinate oxidation and fumarate reduction are carried out by separate enzymes in most organisms, some bifunctional enzymes that exhibit both SQR and QFR activities exist."
Q#12952 - 	CGI_10027242	superfamily	149071	266	344	1.52E-11	61.9501	cl06710	DUF1647 superfamily	N	 - 	Protein of unknown function (DUF1647); The sequences making up this family are all derived from hypothetical proteins expressed by C. elegans. The region in question is approximately 160 amino acids long. The GO annotation for this protein indicates the protein to be involved in nematode larval development and to have a positive regulation on growth rate.
Q#12957 - 	CGI_10027247	superfamily	247744	1333	1509	3.01E-61	208.155	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#12957 - 	CGI_10027247	superfamily	203750	268	393	3.95E-29	115.87	cl18248	Sad1_UNC superfamily	 - 	 - 	"Sad1 / UNC-like C-terminal; The C. elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development. The S. pombe Sad1 protein localises at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2. The SUN domain of Sun2 has been demonstrated to be in the periplasm."
Q#12958 - 	CGI_10027248	superfamily	244843	2	36	3.22E-05	41.8329	cl08040	Ggt superfamily	NC	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#12961 - 	CGI_10027251	superfamily	244843	61	194	6.97E-29	111.939	cl08040	Ggt superfamily	N	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#12961 - 	CGI_10027251	superfamily	244843	2	74	0.000525808	38.7513	cl08040	Ggt superfamily	NC	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#12962 - 	CGI_10027252	superfamily	191217	1	67	4.64E-30	103.063	cl07859	zf-DNL superfamily	 - 	 - 	DNL zinc finger; The domain is named after a short C-terminal motif of D(N/H)L. This domain is a novel zinc-finger protein essential for protein import into mitochondria.
Q#12963 - 	CGI_10027253	superfamily	216212	280	802	0	675.162	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#12964 - 	CGI_10027254	superfamily	216212	397	923	0	734.097	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#12967 - 	CGI_10027257	superfamily	241568	144	169	0.00724393	32.82	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#12967 - 	CGI_10027257	superfamily	241619	13	73	0.00998409	32.5541	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#12970 - 	CGI_10027260	superfamily	247724	1	169	9.62E-101	291.415	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12971 - 	CGI_10027261	superfamily	243078	6	114	6.62E-36	134.647	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#12972 - 	CGI_10027262	superfamily	247724	27	196	6.10E-120	342.11	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#12973 - 	CGI_10027263	superfamily	243034	53	137	7.90E-06	45.0636	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#12973 - 	CGI_10027263	superfamily	243034	375	437	0.00125068	38.13	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#12974 - 	CGI_10027264	superfamily	247771	22	210	1.26E-79	249.093	cl17217	malate_synt superfamily	C	 - 	"Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle."
Q#12975 - 	CGI_10027265	superfamily	245009	18	134	2.42E-28	101.976	cl09109	NTF2_like superfamily	 - 	 - 	"Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example,  nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and  binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea and eukaryotes."
Q#12981 - 	CGI_10016599	superfamily	241600	300	510	4.66E-78	245.998	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12981 - 	CGI_10016599	superfamily	241600	74	250	2.70E-68	220.575	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#12983 - 	CGI_10016601	superfamily	241609	30	110	2.26E-20	81.6555	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#12983 - 	CGI_10016601	superfamily	241609	115	188	1.21E-16	71.2674	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#12987 - 	CGI_10016606	superfamily	241691	236	356	9.64E-05	41.3436	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#12988 - 	CGI_10016607	superfamily	241640	11	59	1.15E-23	90.0282	cl00149	Tryp_SPc superfamily	N	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#12989 - 	CGI_10016608	superfamily	245206	40	295	3.14E-146	415.455	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#12990 - 	CGI_10016609	superfamily	216421	104	384	4.46E-47	164.133	cl03153	Lamp superfamily	 - 	 - 	Lysosome-associated membrane glycoprotein (Lamp); Lysosome-associated membrane glycoprotein (Lamp).  
Q#12993 - 	CGI_10016612	superfamily	217615	60	232	1.09E-65	209.146	cl04158	Allantoicase superfamily	 - 	 - 	"Allantoicase repeat; This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)-ureidoglycolate + urea."
Q#12993 - 	CGI_10016612	superfamily	217615	255	413	4.91E-51	170.626	cl04158	Allantoicase superfamily	 - 	 - 	"Allantoicase repeat; This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)-ureidoglycolate + urea."
Q#12997 - 	CGI_10009619	superfamily	241752	80	168	5.88E-28	102.783	cl00283	ADP_ribosyl superfamily	C	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#12998 - 	CGI_10009620	superfamily	241752	102	214	1.18E-41	143.999	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#12999 - 	CGI_10009621	superfamily	241752	815	929	4.36E-38	139.762	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#12999 - 	CGI_10009621	superfamily	207713	640	709	4.48E-06	45.7937	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#13000 - 	CGI_10009622	superfamily	243106	63	131	1.35E-19	80.8984	cl02608	BAH superfamily	C	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#13002 - 	CGI_10009624	superfamily	246723	113	753	0	750.672	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#13003 - 	CGI_10009625	superfamily	241584	57	135	0.00149655	35.4775	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#13004 - 	CGI_10006516	superfamily	248318	203	236	1.11E-13	66.3053	cl17764	FYVE superfamily	C	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#13004 - 	CGI_10006516	superfamily	151903	496	537	1.70E-11	59.7756	cl12988	Rbsn superfamily	 - 	 - 	Rabenosyn Rab binding domain; Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking.
Q#13005 - 	CGI_10006517	superfamily	210108	3	42	1.44E-11	53.0796	cl15447	Ribosomal_L29e superfamily	 - 	 - 	Ribosomal L29e protein family; Ribosomal L29e protein family.  
Q#13007 - 	CGI_10006519	superfamily	216363	125	218	1.18E-12	61.3322	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#13008 - 	CGI_10006699	superfamily	245201	362	631	2.26E-117	364.451	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13008 - 	CGI_10006699	superfamily	243146	970	1012	2.32E-07	49.197	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13008 - 	CGI_10006699	superfamily	243146	789	834	4.56E-06	45.2419	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13008 - 	CGI_10006699	superfamily	243146	934	980	0.000208726	40.2343	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13008 - 	CGI_10006699	superfamily	243146	878	919	0.000362317	39.567	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13009 - 	CGI_10006700	superfamily	247776	8	119	7.29E-45	143.45	cl17222	Transthyretin_like superfamily	 - 	 - 	"Transthyretin_like.  This domain is present in the transthyretin-like protein (TLP) family which includes transthyretin (TTR) and a transthyretin-related protein called 5-hydroxyisourate hydrolase (HIUase).  TTR and HIUase are homotetrameric proteins with each subunit consisting of eight beta-strands arranged in two sheets and a short alpha-helix. The central channel of the tetramer contains two independent binding sites, each located between a pair of subunits. TTR transports thyroid hormones and retinol in the blood serum of vertebrates while HIUase catalyzes the second step in a three-step ureide pathway. TTRs are highly conserved and found only in vertebrates while the HIUases are found in a wide range of bacterial, plant, fungal, slime mold and vertebrate organisms."
Q#13010 - 	CGI_10006701	superfamily	241571	466	530	3.07E-08	52.7998	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#13010 - 	CGI_10006701	superfamily	246918	373	424	1.65E-15	73.0047	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13011 - 	CGI_10006702	superfamily	242006	87	280	4.14E-76	241.635	cl00653	Endonuclease_V superfamily	 - 	 - 	"Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases.  EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor.  EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown."
Q#13011 - 	CGI_10006702	superfamily	245010	405	487	0.0014762	37.2123	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#13012 - 	CGI_10006703	superfamily	216554	62	241	3.62E-33	122.203	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#13013 - 	CGI_10006704	superfamily	241578	550	700	4.12E-14	72.5986	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13013 - 	CGI_10006704	superfamily	241578	182	310	6.47E-05	44.1281	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13014 - 	CGI_10001377	superfamily	247856	84	136	8.45E-06	40.9941	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13018 - 	CGI_10009304	superfamily	241563	59	94	0.00127193	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13019 - 	CGI_10009305	superfamily	241563	61	96	0.00402266	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13020 - 	CGI_10009306	superfamily	247684	26	250	6.76E-56	189.411	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#13022 - 	CGI_10009308	superfamily	245226	24	127	6.35E-12	60.3921	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#13024 - 	CGI_10009310	superfamily	245606	37	203	2.08E-94	281.289	cl11410	TPP_enzyme_PYR superfamily	 - 	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#13024 - 	CGI_10009310	superfamily	217227	226	346	4.01E-31	115.001	cl08363	Transketolase_C superfamily	 - 	 - 	"Transketolase, C-terminal domain; The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site."
Q#13025 - 	CGI_10020348	superfamily	245601	5	89	1.34E-31	112.03	cl11399	HP superfamily	C	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#13026 - 	CGI_10020349	superfamily	192445	45	154	1.62E-21	87.4675	cl10818	Med4 superfamily	C	 - 	"Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter."
Q#13027 - 	CGI_10020350	superfamily	242885	41	202	5.63E-80	239.036	cl02106	IF4E superfamily	 - 	 - 	Eukaryotic initiation factor 4E; Eukaryotic initiation factor 4E.  
Q#13029 - 	CGI_10020352	superfamily	245213	259	293	3.32E-06	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13029 - 	CGI_10020352	superfamily	245213	182	217	1.61E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13030 - 	CGI_10020353	superfamily	213152	1231	1260	2.40E-05	43.2878	cl17045	TM_EGFR-like superfamily	C	 - 	"Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases; PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. They are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. They are activated by ligand-induced dimerization, resulting in the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Collectively, they can recognize a variety of ligands including EGF, TGFalpha, and neuregulins, among others. All four subfamily members can form homo- or heterodimers. HER3 contains an impaired kinase domain and depends on its heterodimerization partner for activation. EGFR subfamily members are involved in signaling pathways leading to a broad range of cellular responses including cell proliferation, differentiation, migration, growth inhibition, and apoptosis. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of EGFR family RTKs have been associated with increased breast cancer risk."
Q#13030 - 	CGI_10020353	superfamily	219525	393	440	1.15E-07	50.4953	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	234	281	6.05E-06	45.4877	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	451	496	2.79E-05	43.5618	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	718	764	3.59E-05	43.1766	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	826	874	4.68E-05	42.7914	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	882	928	0.000122663	41.6358	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	777	819	0.000160393	41.2506	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	662	710	0.000187254	40.8654	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	935	978	0.000520367	39.7098	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	504	554	0.0010685	38.5542	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	1156	1187	0.00148313	38.169	cl06646	GCC2_GCC3 superfamily	C	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	347	385	0.00188905	37.7838	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	294	333	0.00237024	37.7838	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13030 - 	CGI_10020353	superfamily	219525	563	607	0.00421841	37.0134	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#13031 - 	CGI_10020354	superfamily	241644	393	526	8.83E-25	103.051	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#13031 - 	CGI_10020354	superfamily	241644	543	691	1.62E-24	102.28	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#13031 - 	CGI_10020354	superfamily	241644	708	860	8.17E-18	83.0205	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#13031 - 	CGI_10020354	superfamily	244994	1658	1741	1.03E-15	75.3502	cl08520	Cdc6_C superfamily	 - 	 - 	"Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding; This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases the specificity of the ORC-origins interaction. Further studies suggest that hydrolysis of Cdc6-bound ATP promotes the association of the replication licensing factor Cdt1 with origins through an interaction with Orc6 and this in turn promotes the loading of MCM2-7 helicase onto chromatin. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication.  S-Cdk (S-phase cyclin and cyclin-dependent kinase complex) prevents rereplication by causing the Cdc6 protein to dissociate from ORC and prevents the Cdc6 and MCM proteins from reassembling at any origin. By phosphorylating Cdc6, S-Cdk also triggers Cdc6's ubiquitination.  The Cdc6 protein is composed of three domains, an N-terminal AAA+ domain with Walker A and B, and Sensor-1 and -2 motifs. The central region contains a conserved nucleotide binding/ATPase domain and is a member of the ATPase superfamily. The C-terminal domain (Cdc6_C) is a conserved winged-helix domain that possibly mediates protein-protein interactions or direct DNA interactions. Cdc6 is conserved in eukaryotes, and related genes are found in Archaea. The winged helix fold structure of Cdc6_C is similar to the structures of other eukaryotic replication initiators without apparent sequence similarity."
Q#13031 - 	CGI_10020354	superfamily	247743	1397	1560	4.91E-08	53.3039	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13031 - 	CGI_10020354	superfamily	243106	941	1063	1.60E-10	60.8532	cl02608	BAH superfamily	 - 	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#13032 - 	CGI_10020355	superfamily	217519	7	177	4.28E-87	260.94	cl04030	PRP38 superfamily	 - 	 - 	PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation.
Q#13033 - 	CGI_10020356	superfamily	217519	1	101	5.97E-47	155.01	cl04030	PRP38 superfamily	N	 - 	PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation.
Q#13034 - 	CGI_10020357	superfamily	241644	183	216	0.000743509	37.5669	cl00154	UBCc superfamily	C	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#13038 - 	CGI_10020361	superfamily	246680	608	689	1.85E-16	75.5885	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#13040 - 	CGI_10020363	superfamily	243141	26	181	3.76E-16	75.0454	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#13041 - 	CGI_10020364	superfamily	247057	315	379	1.67E-33	120.068	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#13041 - 	CGI_10020364	superfamily	247999	201	246	2.59E-10	55.9596	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#13042 - 	CGI_10020365	superfamily	245847	108	158	0.00817129	33.63	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13043 - 	CGI_10020366	superfamily	241574	599	805	5.31E-87	281.011	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#13043 - 	CGI_10020366	superfamily	241574	864	1054	2.88E-31	123.85	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#13045 - 	CGI_10020368	superfamily	151064	66	113	6.33E-23	88.1591	cl11145	DUF2453 superfamily	C	 - 	Protein of unknown function (DUF2453); Some members of this family are purported to contain GAF domains but this could not be confirmed. The function is not known. It is likely to be a transmembrane protein.
Q#13046 - 	CGI_10020369	superfamily	241578	267	403	4.40E-26	103.628	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13046 - 	CGI_10020369	superfamily	219821	184	253	7.53E-11	58.9218	cl07136	VWA_N superfamily	N	 - 	"VWA N-terminal; This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits."
Q#13047 - 	CGI_10020370	superfamily	247802	55	244	4.21E-139	408.978	cl17248	RIO superfamily	 - 	 - 	"RIO kinase family, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They function as non-ribosomal factors necessary for late 18S rRNA processing. RIO1 is also required for proper cell cycle progression and chromosome maintenance. The biological substrates for RIO kinases are still unknown."
Q#13047 - 	CGI_10020370	superfamily	218308	415	711	7.93E-63	216.409	cl09342	Peroxin-3 superfamily	 - 	 - 	Peroxin-3; Peroxin-3 is a peroxisomal protein. It is thought to be involve in membrane vesicle assembly prior to the translocation of matrix proteins.
Q#13048 - 	CGI_10020371	superfamily	243092	638	861	6.48E-27	113.584	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13048 - 	CGI_10020371	superfamily	243092	1262	1634	1.09E-24	106.65	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13048 - 	CGI_10020371	superfamily	243092	424	740	1.62E-23	103.184	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13048 - 	CGI_10020371	superfamily	243092	1502	1831	1.37E-16	81.6124	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13048 - 	CGI_10020371	superfamily	243092	788	1017	1.11E-12	69.286	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13048 - 	CGI_10020371	superfamily	191163	21	194	3.10E-11	63.9827	cl04888	DUF667 superfamily	 - 	 - 	"Protein of unknown function (DUF667); This family of proteins are highly conserved in eukaryotes. Some proteins in the family are annotated as transcription factors. However, there is currently no support for this in the literature."
Q#13048 - 	CGI_10020371	superfamily	243092	1189	1300	5.41E-11	64.2784	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13052 - 	CGI_10020375	superfamily	241631	11	170	1.31E-62	201.682	cl00136	Sec7 superfamily	 - 	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#13052 - 	CGI_10020375	superfamily	247725	208	320	4.11E-62	198.304	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13053 - 	CGI_10020376	superfamily	241782	135	499	5.49E-97	301.044	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#13054 - 	CGI_10020377	superfamily	247725	7	120	4.74E-65	209.91	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13054 - 	CGI_10020377	superfamily	243095	120	325	9.17E-61	201.518	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#13055 - 	CGI_10020378	superfamily	245201	9	294	1.46E-178	501.938	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13056 - 	CGI_10020379	superfamily	238191	110	209	1.15E-08	55.0308	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#13056 - 	CGI_10020379	superfamily	215859	304	346	0.000174801	41.0479	cl18347	Peptidase_S9 superfamily	N	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#13058 - 	CGI_10020381	superfamily	241753	96	506	0	831.701	cl00285	Aconitase superfamily	 - 	 - 	"Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Aconitase catalytic domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle.  Cis-aconitate is formed as an intermediate product during the course of the reaction. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. Aconitase, in its active form, contains a 4Fe-4S  iron-sulfur cluster; three cysteine residues have been shown to be ligands of the 4Fe-4S cluster. This is the Aconitase core domain, including structural domains 1, 2 and 3, which binds the Fe-S cluster. The aconitase family also contains the following proteins: - Iron-responsive  element binding protein (IRE-BP), a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in  the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of  transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the  alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid."
Q#13058 - 	CGI_10020381	superfamily	241693	588	736	6.32E-99	305.162	cl00215	Aconitase_swivel superfamily	 - 	 - 	"Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive  element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid."
Q#13059 - 	CGI_10020382	superfamily	247905	587	709	8.46E-27	108.864	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13059 - 	CGI_10020382	superfamily	247805	266	411	6.28E-17	80.4592	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#13060 - 	CGI_10020383	superfamily	203679	2	62	3.26E-09	47.9959	cl06533	Med9 superfamily	N	 - 	"RNA polymerase II transcription mediator complex subunit 9; This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter."
Q#13061 - 	CGI_10020384	superfamily	241733	1	58	1.46E-16	69.9844	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#13063 - 	CGI_10020386	superfamily	227527	8	230	2.41E-44	155.124	cl15315	LUC7 superfamily	 - 	 - 	"U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]"
Q#13064 - 	CGI_10020387	superfamily	245210	88	470	2.70E-155	489.377	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#13064 - 	CGI_10020387	superfamily	247637	1642	1930	5.73E-99	323.367	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#13064 - 	CGI_10020387	superfamily	245206	1947	2184	2.12E-72	252.755	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#13064 - 	CGI_10020387	superfamily	244888	578	892	1.07E-90	300.867	cl08282	Acyl_transf_1 superfamily	 - 	 - 	Acyl transferase domain; Acyl transferase domain.  
Q#13064 - 	CGI_10020387	superfamily	245206	1386	1600	2.45E-20	95.5936	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#13064 - 	CGI_10020387	superfamily	214837	940	1088	1.75E-14	74.185	cl11739	PKS_DH superfamily	 - 	 - 	Dehydratase domain in polyketide synthase (PKS) enzymes; Dehydratase domain in polyketide synthase (PKS) enzymes.  
Q#13065 - 	CGI_10020388	superfamily	241754	28	759	1.37E-158	483.306	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#13066 - 	CGI_10020389	superfamily	245208	39	468	0	651.014	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#13067 - 	CGI_10020390	superfamily	220679	4	142	5.79E-20	82.7601	cl18567	Methyltransf_16 superfamily	 - 	 - 	Putative methyltransferase; Putative methyltransferase.  
Q#13068 - 	CGI_10020391	superfamily	247805	50	242	9.26E-87	279.755	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#13068 - 	CGI_10020391	superfamily	247905	252	381	9.52E-35	130.821	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13068 - 	CGI_10020391	superfamily	246723	494	1135	2.58E-84	288.581	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#13069 - 	CGI_10020392	superfamily	243161	3	68	3.31E-07	44.6926	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#13070 - 	CGI_10020393	superfamily	247684	2	38	3.81E-16	75.1215	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#13071 - 	CGI_10020394	superfamily	218118	709	774	1.06E-11	61.8613	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#13072 - 	CGI_10020395	superfamily	248022	97	381	1.09E-29	118.534	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#13073 - 	CGI_10020396	superfamily	247792	145	184	0.00113828	35.114	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13074 - 	CGI_10020397	superfamily	247725	17	116	7.62E-08	48.6989	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13074 - 	CGI_10020397	superfamily	247725	130	223	3.81E-07	46.6519	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13077 - 	CGI_10004552	superfamily	203134	7	67	3.75E-30	110.079	cl04866	CHORD superfamily	 - 	 - 	"CHORD; CHORD represents a Zn binding domain. Silencing of the C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development."
Q#13077 - 	CGI_10004552	superfamily	241659	227	314	2.35E-29	108.538	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#13077 - 	CGI_10004552	superfamily	203134	150	214	2.87E-29	107.768	cl04866	CHORD superfamily	 - 	 - 	"CHORD; CHORD represents a Zn binding domain. Silencing of the C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development."
Q#13080 - 	CGI_10007398	superfamily	243077	1	29	4.03E-07	47.5401	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#13080 - 	CGI_10007398	superfamily	241832	86	143	3.24E-11	60.8509	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#13081 - 	CGI_10007399	superfamily	247805	201	404	7.03E-68	220.819	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#13081 - 	CGI_10007399	superfamily	247905	414	550	3.14E-32	120.806	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13083 - 	CGI_10007401	superfamily	243092	75	233	5.15E-19	85.4644	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13085 - 	CGI_10007403	superfamily	245599	274	435	2.16E-30	115.401	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#13087 - 	CGI_10007405	superfamily	241752	124	238	5.92E-41	138.221	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#13089 - 	CGI_10004647	superfamily	245205	22	144	3.34E-32	119.687	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#13089 - 	CGI_10004647	superfamily	245205	167	287	2.01E-18	81.3112	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#13090 - 	CGI_10001876	superfamily	204080	214	411	2.07E-43	152.426	cl18252	BAAT_C superfamily	 - 	 - 	BAAT / Acyl-CoA thioester hydrolase C terminal; This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT).
Q#13090 - 	CGI_10001876	superfamily	218259	15	150	2.10E-37	133.163	cl04742	Bile_Hydr_Trans superfamily	 - 	 - 	"Acyl-CoA thioester hydrolase/BAAT N-terminal region; This family consists of the amino termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT). This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism. For example, in peroxisomes, the hydrolase acts on bile-CoA esters."
Q#13092 - 	CGI_10001878	superfamily	218259	15	150	3.13E-36	128.155	cl04742	Bile_Hydr_Trans superfamily	 - 	 - 	"Acyl-CoA thioester hydrolase/BAAT N-terminal region; This family consists of the amino termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT). This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism. For example, in peroxisomes, the hydrolase acts on bile-CoA esters."
Q#13092 - 	CGI_10001878	superfamily	204080	214	313	1.22E-09	56.1265	cl18252	BAAT_C superfamily	C	 - 	BAAT / Acyl-CoA thioester hydrolase C terminal; This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT).
Q#13099 - 	CGI_10005842	superfamily	248360	13	157	7.21E-43	143.185	cl17806	DER1 superfamily	C	 - 	"Der1-like family; The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localised to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.)."
Q#13105 - 	CGI_10022058	superfamily	241972	49	288	5.86E-93	278.656	cl00600	Ribosomal_L7Ae superfamily	 - 	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#13106 - 	CGI_10022059	superfamily	203401	19	129	7.88E-28	100.453	cl05607	Med22 superfamily	 - 	 - 	"Surfeit locus protein 5 subunit 22 of Mediator complex; This family consists of several eukaryotic Surfeit locus protein 5 (SURF5) sequences. The human Surfeit locus has been mapped on chromosome 9q34.1. The locus includes six tightly clustered housekeeping genes (Surf1-6), and the gene organisation is similar in human, mouse and chicken Surfeit locus. The Med22 subunit of Mediator complex is part of the essential core head region."
Q#13107 - 	CGI_10022060	superfamily	247792	349	389	4.44E-05	40.892	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13109 - 	CGI_10022062	superfamily	245201	34	296	2.84E-44	159.201	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13110 - 	CGI_10022063	superfamily	241750	25	140	1.90E-17	82.2459	cl00281	metallo-dependent_hydrolases superfamily	NC	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#13113 - 	CGI_10022066	superfamily	241609	57	133	1.28E-22	85.8927	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#13113 - 	CGI_10022066	superfamily	241609	7	52	1.51E-13	61.6251	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#13114 - 	CGI_10022067	superfamily	241584	413	476	0.000939373	38.2463	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#13115 - 	CGI_10022068	superfamily	222048	544	662	0.00562108	37.6474	cl16238	ATG2_CAD superfamily	 - 	 - 	"Autophagy-related protein 2 CAD motif; The Atg2 protein, an integral membrane protein, is required for a range of functions including the regulation of autophagy in conjunction with the Atg1-Atg13 complex. Atg2 binds Atg9. The precise function of this region, with its characteristic highly conserved CAD sequence motif, is not known."
Q#13116 - 	CGI_10022069	superfamily	241584	578	641	0.000203273	40.5575	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#13117 - 	CGI_10022070	superfamily	204985	19	107	1.29E-13	67.9671	cl14987	Chorein_N superfamily	C	 - 	"N-terminal region of Chorein, a TM vesicle-mediated sorter; Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport."
Q#13118 - 	CGI_10022071	superfamily	241782	91	490	4.51E-115	345.728	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#13119 - 	CGI_10022072	superfamily	183292	47	456	0	534.786	cl18135	PRK11728 superfamily	 - 	 - 	hydroxyglutarate oxidase; Provisional
Q#13120 - 	CGI_10022073	superfamily	243109	539	706	9.52E-108	327.3	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#13120 - 	CGI_10022073	superfamily	241584	452	541	9.94E-11	59.4323	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#13120 - 	CGI_10022073	superfamily	128778	283	386	1.13E-17	80.3866	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#13120 - 	CGI_10022073	superfamily	241563	157	189	0.00240523	36.5463	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13121 - 	CGI_10022074	superfamily	218223	242	511	2.63E-110	340.115	cl04698	Radial_spoke superfamily	N	 - 	"Radial spokehead-like protein; This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene."
Q#13121 - 	CGI_10022074	superfamily	218223	14	181	1.09E-56	198.362	cl04698	Radial_spoke superfamily	C	 - 	"Radial spokehead-like protein; This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene."
Q#13122 - 	CGI_10022075	superfamily	241647	251	281	1.16E-08	52.145	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#13125 - 	CGI_10022078	superfamily	247684	6	429	5.21E-88	280.318	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#13126 - 	CGI_10022079	superfamily	245206	16	301	4.59E-101	318.177	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#13127 - 	CGI_10022080	superfamily	248438	7	108	8.29E-09	53.4001	cl17884	COG1214 superfamily	C	 - 	"Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]"
Q#13128 - 	CGI_10022081	superfamily	247727	43	136	4.10E-15	68.6106	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#13129 - 	CGI_10022082	superfamily	243035	120	223	2.54E-14	66.1041	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13130 - 	CGI_10022083	superfamily	241583	110	266	1.37E-77	242.495	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#13130 - 	CGI_10022083	superfamily	243048	311	493	2.14E-17	80.048	cl02471	HX superfamily	 - 	 - 	Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat.
Q#13131 - 	CGI_10022084	superfamily	243072	653	758	4.64E-09	57.0082	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13131 - 	CGI_10022084	superfamily	247038	487	568	0.000836869	40.5224	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13131 - 	CGI_10022084	superfamily	243697	2	88	1.57E-46	166.039	cl04295	CG-1 superfamily	N	 - 	CG-1 domain; CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein. CG-1 domains are associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin -binding domain and ankyrins (ANK) motifs.
Q#13131 - 	CGI_10022084	superfamily	221856	1461	1625	4.64E-29	117.372	cl15165	Cnd1_N superfamily	 - 	 - 	"non-SMC mitotic condensation complex subunit 1, N-term; The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis. This is the conserved N-terminus of the subunit 1."
Q#13133 - 	CGI_10022086	superfamily	241624	13	265	7.51E-65	206.023	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#13135 - 	CGI_10022088	superfamily	242385	1065	1370	0	608.676	cl01244	arom_aa_hydroxylase superfamily	 - 	 - 	"Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers."
Q#13136 - 	CGI_10022089	superfamily	241874	7	547	0	613.032	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#13137 - 	CGI_10022090	superfamily	241874	40	579	0	583.372	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#13138 - 	CGI_10022091	superfamily	248097	25	154	2.26E-35	121.218	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#13139 - 	CGI_10022092	superfamily	248097	53	176	1.16E-29	107.736	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#13140 - 	CGI_10022093	superfamily	241754	80	834	0	1227.06	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#13140 - 	CGI_10022093	superfamily	111612	32	74	1.41E-14	70.973	cl03686	Myosin_N superfamily	 - 	 - 	Myosin N-terminal SH3-like domain; This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown.
Q#13140 - 	CGI_10022093	superfamily	225871	1838	1956	0.0065799	38.6066	cl18728	COG3334 superfamily	C	 - 	Uncharacterized conserved protein [Function unknown]
Q#13142 - 	CGI_10022095	superfamily	247723	184	254	2.78E-35	124.997	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13142 - 	CGI_10022095	superfamily	247723	290	363	4.17E-26	100.006	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13142 - 	CGI_10022095	superfamily	247723	21	66	1.00E-20	85.4505	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13143 - 	CGI_10022096	superfamily	247723	26	105	5.46E-36	122.478	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13143 - 	CGI_10022096	superfamily	247723	118	161	1.02E-24	93.1793	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13144 - 	CGI_10022097	superfamily	241632	161	238	0.00494133	37.2321	cl00137	SERPIN superfamily	NC	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#13145 - 	CGI_10022098	superfamily	243072	10	112	3.89E-26	98.995	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13146 - 	CGI_10022099	superfamily	247794	6	315	4.99E-170	477.657	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#13147 - 	CGI_10022100	superfamily	247794	1	238	5.15E-130	372.883	cl17240	FDH_GDH_like superfamily	N	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#13149 - 	CGI_10022102	superfamily	245303	29	385	4.85E-132	388.841	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#13151 - 	CGI_10022104	superfamily	241599	11	66	3.43E-10	54.1717	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#13152 - 	CGI_10022105	superfamily	215647	463	537	3.92E-13	68.404	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#13152 - 	CGI_10022105	superfamily	215647	401	468	1.26E-12	66.8632	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#13152 - 	CGI_10022105	superfamily	243086	340	386	9.99E-10	55.459	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#13153 - 	CGI_10022106	superfamily	243026	4	130	5.15E-09	52.0731	cl02417	Myelin_PLP superfamily	N	 - 	Myelin proteolipid protein (PLP or lipophilin); Myelin proteolipid protein (PLP or lipophilin).  
Q#13159 - 	CGI_10006254	superfamily	217293	38	233	1.24E-37	136.609	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#13159 - 	CGI_10006254	superfamily	202474	240	319	8.74E-10	57.2785	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#13161 - 	CGI_10006256	superfamily	196138	123	176	4.23E-19	78.4687	cl11065	TAF8 superfamily	 - 	 - 	"TATA Binding Protein (TBP) Associated Factor 8; The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promoter recognition, or a role in the essential catalytic activity of the complex. The mouse ortholog of TAF8 is called taube nuss protein (TBN), and is required for early embryonic development. TBN mutant mice exhibit disturbances in the balance between cell death and cell survival in the early embryo. TAF8 plays a role in the differentiation of preadipocyte fibroblasts to adipocytes; it is also required for the integration of TAF10 into the TAF complex. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID.  TAF8 is also a component of a small TAF complex (SMAT), which contains TAF8, TAF10 and SUPT7L. Several TAFs interact via histone-fold motifs. The histone fold (HFD) is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. TAF8 contains an H4 related histone fold motif, and interacts with several subunits of TFIID, including TBP and the histone-fold protein TAF10. Currently, five HF-containing TAF pairs have been described or suggested to exist in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10."
Q#13161 - 	CGI_10006256	superfamily	248099	10	84	7.32E-21	83.913	cl17545	Bromo_TP superfamily	 - 	 - 	Bromodomain associated; This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold.
Q#13167 - 	CGI_10006262	superfamily	243269	1	401	3.88E-97	300.339	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#13168 - 	CGI_10006263	superfamily	245201	213	542	1.16E-58	204.64	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13170 - 	CGI_10002629	superfamily	243072	384	509	4.59E-40	145.219	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13170 - 	CGI_10002629	superfamily	243072	714	839	5.76E-40	145.219	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13170 - 	CGI_10002629	superfamily	243072	780	905	1.46E-38	140.982	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13170 - 	CGI_10002629	superfamily	243072	846	971	3.72E-38	139.826	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13170 - 	CGI_10002629	superfamily	243072	582	707	4.89E-36	134.048	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13170 - 	CGI_10002629	superfamily	243072	450	575	1.86E-31	120.951	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13170 - 	CGI_10002629	superfamily	243072	279	410	1.22E-29	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13171 - 	CGI_10012455	superfamily	245814	14	89	4.59E-07	45.8302	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13171 - 	CGI_10012455	superfamily	245814	160	235	0.000113723	39.2612	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13174 - 	CGI_10012458	superfamily	241640	1133	1368	3.62E-64	220.611	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#13174 - 	CGI_10012458	superfamily	243040	466	549	4.67E-14	71.3838	cl02447	CRD_FZ superfamily	C	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13174 - 	CGI_10012458	superfamily	243040	825	906	4.61E-13	68.6874	cl02447	CRD_FZ superfamily	C	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13174 - 	CGI_10012458	superfamily	243040	96	200	2.46E-12	66.3762	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13174 - 	CGI_10012458	superfamily	243040	698	804	1.23E-11	64.4502	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13174 - 	CGI_10012458	superfamily	243040	200	281	1.17E-10	61.3686	cl02447	CRD_FZ superfamily	C	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13174 - 	CGI_10012458	superfamily	243040	590	676	7.18E-10	59.0574	cl02447	CRD_FZ superfamily	C	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13174 - 	CGI_10012458	superfamily	243040	345	443	1.53E-09	57.9018	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13174 - 	CGI_10012458	superfamily	241613	1815	1846	2.63E-08	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13174 - 	CGI_10012458	superfamily	241613	959	995	2.16E-07	49.8978	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13174 - 	CGI_10012458	superfamily	241613	2051	2080	2.22E-06	47.2014	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13174 - 	CGI_10012458	superfamily	241613	998	1032	5.25E-06	46.0458	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13174 - 	CGI_10012458	superfamily	241613	1373	1401	0.000187453	41.4234	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13174 - 	CGI_10012458	superfamily	241613	1778	1813	0.00179327	38.3418	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13174 - 	CGI_10012458	superfamily	243051	1858	1990	1.29E-20	92.0284	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#13174 - 	CGI_10012458	superfamily	243051	1411	1563	1.38E-13	70.8425	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#13174 - 	CGI_10012458	superfamily	243051	1611	1774	1.55E-08	55.4345	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#13174 - 	CGI_10012458	superfamily	243040	3	62	0.000135577	42.4939	cl02447	CRD_FZ superfamily	N	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#13177 - 	CGI_10012461	superfamily	245595	356	480	9.98E-50	177.943	cl11393	Peptidase_M14_like superfamily	N	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#13177 - 	CGI_10012461	superfamily	245595	275	357	2.61E-30	121.704	cl11393	Peptidase_M14_like superfamily	C	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#13182 - 	CGI_10012466	superfamily	216574	162	299	9.10E-38	136.569	cl14794	FAD_binding_4 superfamily	 - 	 - 	"FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan."
Q#13184 - 	CGI_10012468	superfamily	246748	26	461	0	648.736	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#13185 - 	CGI_10012469	superfamily	241811	49	141	1.07E-19	79.0391	cl00355	Ribosomal_S14 superfamily	 - 	 - 	Ribosomal protein S14p/S29e; This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
Q#13187 - 	CGI_10012471	superfamily	243035	2	62	0.000163786	37.9646	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13187 - 	CGI_10012471	superfamily	241619	74	145	0.000284337	36.4061	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#13188 - 	CGI_10012472	superfamily	241559	86	183	8.60E-08	47.3055	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#13189 - 	CGI_10012473	superfamily	217210	719	1161	1.32E-94	315.371	cl10595	Ald_Xan_dh_C2 superfamily	 - 	 - 	Molybdopterin-binding domain of aldehyde dehydrogenase; Molybdopterin-binding domain of aldehyde dehydrogenase.  
Q#13189 - 	CGI_10012473	superfamily	243326	602	708	8.13E-26	104.522	cl03161	Ald_Xan_dh_C superfamily	 - 	 - 	"Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain.  "
Q#13189 - 	CGI_10012473	superfamily	201981	170	244	8.99E-17	77.5208	cl08334	Fer2_2 superfamily	 - 	 - 	[2Fe-2S] binding domain; [2Fe-2S] binding domain.  
Q#13189 - 	CGI_10012473	superfamily	244932	467	552	2.62E-09	56.3557	cl08390	CO_deh_flav_C superfamily	 - 	 - 	CO dehydrogenase flavoprotein C-terminal domain; CO dehydrogenase flavoprotein C-terminal domain.  
Q#13189 - 	CGI_10012473	superfamily	241649	104	160	0.00419972	37.1102	cl00159	fer2 superfamily	 - 	 - 	"2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin."
Q#13190 - 	CGI_10012474	superfamily	247724	9	239	8.89E-157	446.167	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13190 - 	CGI_10012474	superfamily	243184	335	438	1.04E-59	192.794	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#13190 - 	CGI_10012474	superfamily	243185	242	332	1.53E-57	186.604	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#13191 - 	CGI_10012475	superfamily	241894	16	74	3.63E-13	58.9562	cl00481	SecE superfamily	N	 - 	"SecE/Sec61-gamma subunits of protein translocation complex; SecE is part of the SecYEG complex in bacteria which translocates proteins from the cytoplasm. In eukaryotes the complex, made from Sec61-gamma and Sec61-alpha translocates protein from the cytoplasm to the ER. Archaea have a similar complex."
Q#13192 - 	CGI_10012476	superfamily	243056	116	419	1.86E-39	145.912	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#13194 - 	CGI_10012478	superfamily	243075	45	117	2.74E-19	81.9807	cl02536	SAND superfamily	 - 	 - 	"SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain."
Q#13195 - 	CGI_10012479	superfamily	247038	99	187	5.06E-13	63.6277	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13196 - 	CGI_10011917	superfamily	245201	587	835	3.95E-163	490.114	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13197 - 	CGI_10011918	superfamily	247860	67	492	0	772.002	cl17306	HgmA superfamily	 - 	 - 	"homogentisate 1,2-dioxygenase; Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers."
Q#13199 - 	CGI_10011920	superfamily	243109	426	543	2.59E-12	64.9905	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#13199 - 	CGI_10011920	superfamily	243109	43	161	8.38E-09	54.5901	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#13199 - 	CGI_10011920	superfamily	243109	273	344	9.02E-07	48.4443	cl02614	SPRY superfamily	N	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#13199 - 	CGI_10011920	superfamily	243109	596	725	6.48E-05	43.0515	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#13201 - 	CGI_10011922	superfamily	217473	99	323	2.34E-26	109.377	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#13202 - 	CGI_10011923	superfamily	248097	186	309	1.51E-29	110.047	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#13205 - 	CGI_10011926	superfamily	245835	97	160	0.0030757	38.0031	cl12013	BAR superfamily	NC	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#13205 - 	CGI_10011926	superfamily	241563	28	58	0.00405222	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13206 - 	CGI_10011927	superfamily	241563	18	50	0.000657748	37.7019	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13208 - 	CGI_10011930	superfamily	218109	236	267	1.03E-07	49.2462	cl12292	Gly_transf_sug superfamily	N	 - 	"Glycosyltransferase sugar-binding region containing DXD motif; The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases."
Q#13209 - 	CGI_10011931	superfamily	215647	96	308	1.31E-45	157.385	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#13209 - 	CGI_10011931	superfamily	243029	3	55	1.03E-06	45.4193	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#13210 - 	CGI_10011932	superfamily	215647	118	358	1.89E-53	180.882	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#13210 - 	CGI_10011932	superfamily	243029	36	108	5.05E-11	58.68	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#13214 - 	CGI_10004900	superfamily	241817	29	74	2.08E-19	78.3882	cl00365	F1-ATPase_gamma superfamily	C	 - 	"mitochondrial ATP synthase gamma subunit; The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain of F-ATPases is composed of alpha, beta, gamma, delta, and epsilon (not present in bacteria) subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain."
Q#13215 - 	CGI_10004901	superfamily	241817	10	208	6.51E-70	217.06	cl00365	F1-ATPase_gamma superfamily	N	 - 	"mitochondrial ATP synthase gamma subunit; The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain of F-ATPases is composed of alpha, beta, gamma, delta, and epsilon (not present in bacteria) subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain."
Q#13221 - 	CGI_10013649	superfamily	198867	46	146	7.85E-43	148.075	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#13221 - 	CGI_10013649	superfamily	243146	334	380	3.01E-15	70.2799	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13221 - 	CGI_10013649	superfamily	243146	228	273	3.30E-13	64.605	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13221 - 	CGI_10013649	superfamily	243146	289	333	1.34E-12	62.5759	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13221 - 	CGI_10013649	superfamily	243146	422	466	5.40E-11	58.0566	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13221 - 	CGI_10013649	superfamily	243146	195	239	4.88E-09	52.5607	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13221 - 	CGI_10013649	superfamily	243146	369	418	9.55E-08	48.8118	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13221 - 	CGI_10013649	superfamily	243066	5	41	9.95E-05	40.7521	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#13222 - 	CGI_10013650	superfamily	243034	2040	2172	4.96E-19	85.5095	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1272	1369	6.34E-14	70.8719	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1833	1934	3.15E-13	68.5608	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1657	1758	5.34E-13	68.1756	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1763	1864	1.96E-11	63.5532	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1377	1508	2.00E-10	60.4716	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1982	2070	3.57E-10	59.7012	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1480	1576	4.68E-09	56.2344	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1204	1301	7.91E-08	52.7676	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13222 - 	CGI_10013650	superfamily	243034	1581	1688	3.08E-07	50.8416	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13224 - 	CGI_10013652	superfamily	118132	12	57	0.00987064	35.2001	cl09814	MamL-1 superfamily	 - 	 - 	"MamL-1 domain; The MamL-1 domain is a polypeptide of up to 70 residues, numbers 15-67 of which adopt an elongated kinked helix that wraps around ANK and CSL forming one of the complexes in the build-up of the Notch transcriptional complex for recruiting general transcription factors."
Q#13226 - 	CGI_10013654	superfamily	222150	263	288	4.10E-05	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13227 - 	CGI_10013655	superfamily	206088	18	49	5.72E-09	48.4863	cl16476	zf-CCHC_3 superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#13228 - 	CGI_10013656	superfamily	245213	399	433	4.75E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13228 - 	CGI_10013656	superfamily	245213	287	321	0.000175562	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13228 - 	CGI_10013656	superfamily	245213	479	511	0.0068564	34.9198	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13228 - 	CGI_10013656	superfamily	219501	19	86	4.41E-12	62.3478	cl06622	MNNL superfamily	 - 	 - 	N terminus of Notch ligand; This entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins.
Q#13229 - 	CGI_10013657	superfamily	241686	539	601	1.05E-16	77.2609	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#13229 - 	CGI_10013657	superfamily	241686	339	402	1.48E-15	73.7941	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#13229 - 	CGI_10013657	superfamily	241686	170	232	1.85E-15	73.7941	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#13229 - 	CGI_10013657	superfamily	241686	248	308	5.96E-15	72.2533	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#13229 - 	CGI_10013657	superfamily	241686	419	479	6.52E-13	66.0901	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#13229 - 	CGI_10013657	superfamily	241686	614	677	8.03E-13	66.0901	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#13229 - 	CGI_10013657	superfamily	241686	73	151	4.65E-08	52.2229	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#13229 - 	CGI_10013657	superfamily	248469	1246	1372	0.0020597	38.8903	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#13229 - 	CGI_10013657	superfamily	215733	838	1084	1.33E-60	208.958	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#13230 - 	CGI_10013658	superfamily	148061	61	240	2.71E-77	234.642	cl18026	FRG1 superfamily	 - 	 - 	"FRG1-like family; The human FRG1 gene maps to human chromosome 4q35 and has been identified as a candidate for facioscapulohumeral muscular dystrophy. Currently, the function of FRG1 is unknown."
Q#13233 - 	CGI_10013661	superfamily	241573	64	240	1.29E-45	163.272	cl00051	CysPc superfamily	C	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#13234 - 	CGI_10013662	superfamily	241573	67	243	1.29E-47	169.82	cl00051	CysPc superfamily	C	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#13236 - 	CGI_10013664	superfamily	246925	197	305	0.00132457	39.6462	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#13238 - 	CGI_10013666	superfamily	243034	266	347	0.000287262	39.6708	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13238 - 	CGI_10013666	superfamily	243158	335	370	1.54E-08	51.4056	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#13238 - 	CGI_10013666	superfamily	243158	373	407	0.000990117	37.5384	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#13239 - 	CGI_10013667	superfamily	247743	26	178	1.49E-07	49.0667	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13239 - 	CGI_10013667	superfamily	203973	249	338	1.46E-20	84.4804	cl16006	Rep_fac_C superfamily	 - 	 - 	"Replication factor C C-terminal domain; This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A."
Q#13240 - 	CGI_10013668	superfamily	247068	457	553	5.17E-28	110.096	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13240 - 	CGI_10013668	superfamily	247068	243	340	2.64E-25	102.392	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13240 - 	CGI_10013668	superfamily	247068	562	657	8.27E-23	95.0729	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13240 - 	CGI_10013668	superfamily	247068	356	449	1.93E-15	73.8869	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13240 - 	CGI_10013668	superfamily	247068	133	235	9.05E-13	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13240 - 	CGI_10013668	superfamily	247068	679	756	9.85E-13	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13240 - 	CGI_10013668	superfamily	247068	24	124	7.32E-07	48.4638	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13243 - 	CGI_10013671	superfamily	248012	564	695	1.26E-24	100.426	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#13243 - 	CGI_10013671	superfamily	214507	450	503	6.44E-05	41.2616	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#13245 - 	CGI_10005050	superfamily	224772	2	41	0.000368133	36.1565	cl15312	KptA superfamily	N	 - 	"RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]"
Q#13246 - 	CGI_10005051	superfamily	247725	633	748	6.83E-62	204.42	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13246 - 	CGI_10005051	superfamily	243053	242	478	1.13E-58	199.786	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#13249 - 	CGI_10005054	superfamily	217293	318	502	6.10E-08	52.2499	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#13250 - 	CGI_10005055	superfamily	241810	85	140	1.87E-07	46.739	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#13252 - 	CGI_10005057	superfamily	245814	692	768	2.10E-09	55.5224	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13254 - 	CGI_10000710	superfamily	241888	1	182	1.66E-93	275.799	cl00473	BI-1-like superfamily	N	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#13255 - 	CGI_10000711	superfamily	218440	18	210	0.00409386	38.3641	cl14936	AF-4 superfamily	NC	 - 	"AF-4 proto-oncoprotein; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila."
Q#13255 - 	CGI_10000711	superfamily	208802	216	275	0.00722572	37.0255	cl07974	DRE_TIM_metallolyase superfamily	NC	 - 	"DRE-TIM metallolyase superfamily; The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC.  These members all share a conserved  triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices.  The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel.  In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM"."
Q#13258 - 	CGI_10000633	superfamily	241645	6	92	1.82E-40	130.43	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#13259 - 	CGI_10000959	superfamily	241600	40	258	1.85E-86	259.095	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#13260 - 	CGI_10001106	superfamily	241811	5	55	4.45E-26	92.8257	cl00355	Ribosomal_S14 superfamily	 - 	 - 	Ribosomal protein S14p/S29e; This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
Q#13261 - 	CGI_10001107	superfamily	241739	158	413	2.62E-162	468.613	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#13261 - 	CGI_10001107	superfamily	241738	419	641	3.02E-77	246.826	cl00266	HGTP_anticodon superfamily	 - 	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#13261 - 	CGI_10001107	superfamily	241805	63	112	1.42E-17	77.6608	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#13261 - 	CGI_10001107	superfamily	241805	17	38	0.000193971	39.9112	cl00349	S15_NS1_EPRS_RNA-bind superfamily	N	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#13261 - 	CGI_10001107	superfamily	241805	137	164	0.000788549	38.0622	cl00349	S15_NS1_EPRS_RNA-bind superfamily	C	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#13262 - 	CGI_10001720	superfamily	241623	123	365	1.01E-137	397.46	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#13262 - 	CGI_10001720	superfamily	202180	408	439	1.68E-08	50.54	cl03505	FATC superfamily	 - 	 - 	"FATC domain; The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability."
Q#13264 - 	CGI_10001816	superfamily	247684	24	87	3.19E-15	69.9987	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#13265 - 	CGI_10001817	superfamily	110440	310	335	0.000487165	37.3873	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#13270 - 	CGI_10003138	superfamily	221744	25	236	2.74E-14	72.0835	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#13270 - 	CGI_10003138	superfamily	247057	589	655	0.00524917	35.5896	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#13271 - 	CGI_10003139	superfamily	245202	13	88	1.28E-29	107.67	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#13273 - 	CGI_10003141	superfamily	243689	35	97	2.07E-08	52.2457	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#13273 - 	CGI_10003141	superfamily	219817	106	225	1.71E-06	47.2277	cl07129	Xpo1 superfamily	 - 	 - 	"Exportin 1-like protein; The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus."
Q#13275 - 	CGI_10003143	superfamily	245210	13	260	6.89E-110	329.994	cl09938	cond_enzymes superfamily	N	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#13275 - 	CGI_10003143	superfamily	242376	295	387	2.62E-23	93.0586	cl01225	SCP2 superfamily	 - 	 - 	"SCP-2 sterol transfer family; This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145."
Q#13276 - 	CGI_10002148	superfamily	241600	115	265	1.37E-48	162.025	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#13276 - 	CGI_10002148	superfamily	241619	38	84	0.00016845	38.7173	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#13277 - 	CGI_10002149	superfamily	241600	126	338	3.11E-83	253.702	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#13277 - 	CGI_10002149	superfamily	241619	34	80	9.01E-05	39.8729	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#13281 - 	CGI_10002034	superfamily	241832	127	230	1.17E-54	173.126	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#13281 - 	CGI_10002034	superfamily	241832	32	86	3.35E-11	57.7316	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#13282 - 	CGI_10007588	superfamily	217293	81	228	1.57E-20	88.4587	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#13282 - 	CGI_10007588	superfamily	202474	235	332	6.20E-13	66.5233	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#13283 - 	CGI_10007590	superfamily	241748	314	525	1.30E-25	105.721	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#13283 - 	CGI_10007590	superfamily	216431	117	253	2.62E-06	46.1221	cl08317	Creatinase_N superfamily	 - 	 - 	Creatinase/Prolidase N-terminal domain; This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.
Q#13286 - 	CGI_10007593	superfamily	241868	132	298	8.41E-74	227.388	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#13287 - 	CGI_10007594	superfamily	220647	33	151	4.39E-11	56.5672	cl18565	L_HGMIC_fpl superfamily	C	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#13289 - 	CGI_10007596	superfamily	220647	8	177	2.66E-20	83.9163	cl18565	L_HGMIC_fpl superfamily	 - 	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#13295 - 	CGI_10018345	superfamily	247856	51	111	3.91E-14	70.3263	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13297 - 	CGI_10018347	superfamily	247723	129	206	1.11E-43	144.69	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13298 - 	CGI_10018348	superfamily	238191	25	238	5.95E-58	192.932	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#13299 - 	CGI_10018349	superfamily	238191	21	256	9.33E-14	70.824	cl18907	Esterase_lipase superfamily	N	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#13300 - 	CGI_10018350	superfamily	238191	3	80	9.80E-07	45.0156	cl18907	Esterase_lipase superfamily	N	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#13302 - 	CGI_10018352	superfamily	238191	31	415	3.94E-81	261.113	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#13303 - 	CGI_10018353	superfamily	247743	303	449	1.50E-07	51.8168	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13303 - 	CGI_10018353	superfamily	243092	1069	1283	0.00233764	40.396	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13305 - 	CGI_10018355	superfamily	248097	37	156	3.22E-31	110.433	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#13306 - 	CGI_10018356	superfamily	248097	5	69	1.26E-08	46.8746	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#13307 - 	CGI_10018357	superfamily	241613	37	72	0.000297508	38.3418	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13307 - 	CGI_10018357	superfamily	214531	316	344	0.000572198	37.5813	cl18310	LY superfamily	C	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#13309 - 	CGI_10018359	superfamily	247727	122	228	0.000110031	39.3355	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#13310 - 	CGI_10018360	superfamily	202224	46	154	3.15E-19	81.1879	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#13311 - 	CGI_10018361	superfamily	222437	612	763	3.34E-78	253.406	cl16458	Rab3-GTPase_cat superfamily	 - 	 - 	"Rab3 GTPase-activating protein catalytic subunit; This family is the probable catalytic subunit of the GTPase activating protein that has specificity for Rab3 subfamily (RAB3A, RAB3B, RAB3C and RAB3D). It is likely to convert active Rab3-GTP to the inactive form Rab3-GDP. Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones. The Rab3 GTPase-activating complex is a heterodimer composed of RAB3GAP and RAB3-GAP150. This complex interacts with DMXL2."
Q#13312 - 	CGI_10018362	superfamily	247038	834	899	6.48E-09	56.3089	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13312 - 	CGI_10018362	superfamily	247038	322	375	9.79E-08	52.8421	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13312 - 	CGI_10018362	superfamily	247038	56	124	4.73E-07	50.9161	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13312 - 	CGI_10018362	superfamily	247038	649	741	3.57E-06	48.2197	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13312 - 	CGI_10018362	superfamily	247038	996	1079	7.84E-06	47.0641	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13312 - 	CGI_10018362	superfamily	220608	1177	1294	3.75E-34	130.889	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#13312 - 	CGI_10018362	superfamily	220608	1963	2093	1.31E-13	71.183	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#13312 - 	CGI_10018362	superfamily	247038	916	993	3.71E-11	62.8452	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13312 - 	CGI_10018362	superfamily	247038	147	223	0.000296535	42.0444	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13312 - 	CGI_10018362	superfamily	247038	747	821	0.000925326	40.5036	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13313 - 	CGI_10018363	superfamily	243035	32	156	2.79E-15	68.0301	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13314 - 	CGI_10018364	superfamily	243035	145	269	1.22E-15	70.3413	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13314 - 	CGI_10018364	superfamily	243035	29	126	4.55E-10	55.3185	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13315 - 	CGI_10018365	superfamily	247038	218	301	4.09E-10	58.2349	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13315 - 	CGI_10018365	superfamily	247038	948	998	3.37E-06	46.2937	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#13316 - 	CGI_10018366	superfamily	242856	79	152	6.90E-38	127.111	cl02050	Ribosomal_S25 superfamily	N	 - 	S25 ribosomal protein; S25 ribosomal protein.  
Q#13317 - 	CGI_10018367	superfamily	241607	380	410	2.81E-06	44.183	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#13317 - 	CGI_10018367	superfamily	241607	313	353	7.78E-05	39.9458	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#13317 - 	CGI_10018367	superfamily	242318	91	212	1.43E-20	88.4106	cl01126	EI24 superfamily	N	 - 	"Etoposide-induced protein 2.4 (EI24); This family contains a number of eukaryotic etoposide-induced 2.4 (EI24) proteins approximately 350 residues long as well as bacterial CysZ proteins (formerly known as DUF540). In cells treated with the cytotoxic drug etoposide, EI24 is induced by p53. It has been suggested to play an important role in negative cell growth control."
Q#13319 - 	CGI_10018369	superfamily	243035	144	224	1.38E-06	44.533	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13320 - 	CGI_10003317	superfamily	243179	39	117	4.78E-07	45.4165	cl02781	tetraspanin_LEL superfamily	C	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#13321 - 	CGI_10003318	superfamily	248469	407	522	4.56E-13	68.1655	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#13321 - 	CGI_10003318	superfamily	248469	154	242	3.46E-11	62.3875	cl17915	HAD_like superfamily	N	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#13321 - 	CGI_10003318	superfamily	218493	1000	1138	1.50E-43	156.363	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#13321 - 	CGI_10003318	superfamily	248054	618	648	0.00194061	37.8368	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#13322 - 	CGI_10003319	superfamily	247740	71	393	1.67E-165	470.828	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#13325 - 	CGI_10003322	superfamily	216653	146	261	1.18E-09	56.0663	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#13326 - 	CGI_10002975	superfamily	244859	2	190	3.57E-12	62.9493	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#13331 - 	CGI_10027269	superfamily	247792	332	375	2.51E-10	55.5296	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13333 - 	CGI_10027271	superfamily	241600	64	274	1.39E-85	257.554	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#13335 - 	CGI_10027273	superfamily	213147	46	173	2.57E-57	196.367	cl17040	ADDz superfamily	 - 	 - 	"ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain; The ADDz zinc finger domain is present in the chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2 type transcription factor protein. The Dnmt3 family includes two active DNA methyltransferases, Dnmt3a and -3b, and one regulatory factor Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif."
Q#13335 - 	CGI_10027273	superfamily	247905	1412	1595	8.03E-17	79.9744	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13335 - 	CGI_10027273	superfamily	247805	998	1159	8.55E-14	71.2144	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#13338 - 	CGI_10027276	superfamily	247684	13	427	1.05E-87	279.933	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#13339 - 	CGI_10027277	superfamily	217661	20	142	2.05E-32	113.134	cl18422	Pam16 superfamily	 - 	 - 	"Pam16; The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM). In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane. Pam16 has a degenerate J domain. J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle. Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel. Pam18 stimulates the ATPase activity of mtHsp70."
Q#13340 - 	CGI_10027278	superfamily	246925	14	98	0.001289	38.8758	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#13341 - 	CGI_10027279	superfamily	192997	292	427	1.06E-28	113.445	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#13342 - 	CGI_10027280	superfamily	243072	47	182	1.94E-24	98.6098	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13342 - 	CGI_10027280	superfamily	241596	280	330	8.34E-07	46.4383	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#13342 - 	CGI_10027280	superfamily	243123	348	389	2.07E-07	47.9381	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#13343 - 	CGI_10027281	superfamily	243093	19	99	3.05E-05	43.673	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#13344 - 	CGI_10027282	superfamily	247683	366	413	2.83E-16	75.1918	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#13344 - 	CGI_10027282	superfamily	247683	107	156	4.03E-16	74.8066	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#13344 - 	CGI_10027282	superfamily	247683	1071	1121	5.36E-08	51.3095	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#13344 - 	CGI_10027282	superfamily	247683	265	321	7.73E-12	62.5557	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#13345 - 	CGI_10027283	superfamily	222370	28	109	1.18E-28	104.912	cl16386	Longin superfamily	 - 	 - 	"Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain."
Q#13345 - 	CGI_10027283	superfamily	201526	124	180	2.49E-22	87.9788	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#13346 - 	CGI_10027284	superfamily	246597	55	129	1.06E-29	110.781	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#13346 - 	CGI_10027284	superfamily	246597	203	271	1.12E-26	102.306	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#13347 - 	CGI_10027285	superfamily	220736	407	543	2.38E-27	107.01	cl11068	PTEN_C2 superfamily	 - 	 - 	"C2 domain of PTEN tumour-suppressor protein; This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane."
Q#13347 - 	CGI_10027285	superfamily	241574	302	400	5.92E-09	54.3797	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#13351 - 	CGI_10027289	superfamily	245226	146	313	7.28E-18	80.0372	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#13353 - 	CGI_10027291	superfamily	245864	52	319	7.37E-37	137.41	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#13354 - 	CGI_10027292	superfamily	248264	55	153	4.20E-10	55.7062	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#13357 - 	CGI_10027295	superfamily	215869	115	480	7.61E-40	147.274	cl10564	SecY superfamily	 - 	 - 	SecY translocase; SecY translocase.  
Q#13357 - 	CGI_10027295	superfamily	204513	78	112	3.48E-07	47.0327	cl11188	Plug_translocon superfamily	 - 	 - 	Plug domain of Sec61p; The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74.
Q#13358 - 	CGI_10027296	superfamily	241640	215	453	5.57E-88	270.687	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#13359 - 	CGI_10027297	superfamily	241640	23	255	6.45E-88	263.368	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#13360 - 	CGI_10027298	superfamily	245323	2756	3037	9.15E-145	455.164	cl10511	Beach superfamily	 - 	 - 	"BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins."
Q#13360 - 	CGI_10027298	superfamily	247725	2595	2719	6.28E-34	130.108	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13360 - 	CGI_10027298	superfamily	248318	3572	3625	7.26E-22	93.2693	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#13360 - 	CGI_10027298	superfamily	243092	3106	3298	6.96E-20	92.7832	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13361 - 	CGI_10027299	superfamily	246680	551	633	0.000258885	40.0114	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#13362 - 	CGI_10027300	superfamily	243352	3	279	7.26E-109	319.154	cl03224	Porin3 superfamily	 - 	 - 	"Eukaryotic porin family that forms channels in the mitochondrial outer membrane; The porin family 3 contains two sub-families that play vital roles in the mitochondrial outer membrane, a translocase for unfolded pre-proteins (Tom40) and the voltage-dependent anion channel (VDAC) that regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane."
Q#13363 - 	CGI_10027301	superfamily	206528	197	270	1.64E-26	100.326	cl18290	PAP2_C superfamily	 - 	 - 	PAP2 superfamily C-terminal; This family is closely related to the C-terminal a region of PAP2.
Q#13367 - 	CGI_10027305	superfamily	243179	125	261	1.09E-18	78.9289	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#13369 - 	CGI_10027307	superfamily	243306	8	205	6.66E-94	275.597	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#13370 - 	CGI_10027308	superfamily	245835	10	252	4.94E-85	274.598	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#13370 - 	CGI_10027308	superfamily	243095	242	437	8.15E-84	269.712	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#13371 - 	CGI_10027309	superfamily	242916	28	179	1.60E-45	153.974	cl02166	RRS1 superfamily	 - 	 - 	Ribosome biogenesis regulatory protein (RRS1); This family consists of several eukaryotic ribosome biogenesis regulatory (RRS1) proteins. RRS1 is a nuclear protein that is essential for the maturation of 25 S rRNA and the 60 S ribosomal subunit assembly in Saccharomyces cerevisiae.
Q#13374 - 	CGI_10027312	superfamily	241675	173	408	8.96E-133	394.691	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#13374 - 	CGI_10027312	superfamily	146962	143	179	3.39E-05	43.1952	cl04602	DUF592 superfamily	N	 - 	Protein of unknown function (DUF592); This region is found in some SIR2 family proteins (pfam02146).
Q#13375 - 	CGI_10027313	superfamily	243077	14	68	9.26E-06	40.2213	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#13376 - 	CGI_10027315	superfamily	245814	36	93	6.48E-08	49.3275	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13376 - 	CGI_10027315	superfamily	245814	195	270	5.00E-06	43.9664	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13376 - 	CGI_10027315	superfamily	245814	109	165	5.42E-05	40.8532	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13377 - 	CGI_10027316	superfamily	245814	158	214	3.50E-06	43.1644	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13378 - 	CGI_10027317	superfamily	245814	8	62	7.18E-06	40.0828	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13380 - 	CGI_10027319	superfamily	241666	39	357	3.52E-74	234.837	cl00184	CAS_like superfamily	 - 	 - 	"Clavaminic acid synthetase (CAS) -like;  CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to succinate and CO2"
Q#13381 - 	CGI_10027320	superfamily	246680	1475	1542	5.42E-11	61.1974	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#13381 - 	CGI_10027320	superfamily	246680	1360	1437	2.53E-08	53.1082	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#13382 - 	CGI_10027321	superfamily	222170	51	114	0.00112917	35.6838	cl16285	Dehalogenase superfamily	N	 - 	Reductive dehalogenase subunit; This family is most frequently associated with a Fer4 iron-sulfur cluster towards the C-terminal region.
Q#13384 - 	CGI_10027323	superfamily	245601	1	63	2.59E-16	74.2808	cl11399	HP superfamily	C	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#13384 - 	CGI_10027323	superfamily	245601	238	294	0.00387503	36.1461	cl11399	HP superfamily	N	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#13387 - 	CGI_10027326	superfamily	243050	292	346	1.12E-22	89.4573	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13387 - 	CGI_10027326	superfamily	243050	78	136	6.94E-22	87.1071	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13387 - 	CGI_10027326	superfamily	243050	233	284	1.39E-21	86.3756	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13387 - 	CGI_10027326	superfamily	243050	182	225	6.58E-16	70.9299	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13387 - 	CGI_10027326	superfamily	243050	28	75	1.80E-13	64.163	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13388 - 	CGI_10027327	superfamily	195146	119	202	1.48E-35	125.125	cl05674	PET superfamily	 - 	 - 	"PET ((Prickle Espinas Testin) domain is involved in protein-protein interactions; PET domain is involved in protein-protein interactions and is usually found in conjunction with LIM domain, which is also a protein-protein interaction domain. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. The PET domain has been found at the N-terminal of four known groups of proteins: prickle, testin, LIMPETin/LIM-9 and overexpressed breast tumor protein (OEBT). Prickle has been implicated in regulation of cell movement through its association with the Dishevelled (Dsh) protein in the planar cell polarity (PCP) pathway. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell contact areas, and at focal adhesion plaques. It interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin, and is involved in cell motility and adhesion events. Knockout mice experiments reveal tumor repressor function of Testin.  LIMPETin/LIM-9 contains an N-terminal PET domain and 6 LIM domains at the C-terminal.  In Schistosoma mansoni, where LIMPETin was first identified, it is down regulated in sexually mature adult females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator.  In C. elegans, LIM-9 may play a role in regulating the assembly and maintenance of the muscle A-band by forming a protein complex with SCPL-1 and UNC-89 and other proteins. OEBT displays a PET domain with two LIM domains, and is predicted to be localized in the nucleus with a possible role in cancer differentiation."
Q#13388 - 	CGI_10027327	superfamily	243050	212	269	1.22E-23	91.6915	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13389 - 	CGI_10027328	superfamily	241832	366	414	2.63E-05	42.2954	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#13390 - 	CGI_10027329	superfamily	222150	560	582	0.000209901	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13390 - 	CGI_10027329	superfamily	222150	587	609	0.000572371	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13390 - 	CGI_10027329	superfamily	222150	94	116	0.000762343	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13390 - 	CGI_10027329	superfamily	222150	67	89	0.00180981	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13390 - 	CGI_10027329	superfamily	222150	670	694	0.00272428	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13392 - 	CGI_10027331	superfamily	204716	28	178	0.00121258	37.9903	cl18257	Git3 superfamily	C	 - 	"G protein-coupled glucose receptor regulating Gpa2; Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This is the conserved N-terminus of these proteins, and the C-terminal conserved region is now in family Git3_C."
Q#13392 - 	CGI_10027331	superfamily	207642	178	240	0.00336288	35.1594	cl02558	GED superfamily	 - 	 - 	Dynamin GTPase effector domain; Dynamin GTPase effector domain.  
Q#13394 - 	CGI_10027333	superfamily	109875	25	95	1.28E-11	57.1004	cl17923	T4_deiodinase superfamily	C	 - 	"Iodothyronine deiodinase; Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3)."
Q#13395 - 	CGI_10027334	superfamily	109875	1	67	1.38E-20	81.368	cl17923	T4_deiodinase superfamily	N	 - 	"Iodothyronine deiodinase; Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3)."
Q#13399 - 	CGI_10027338	superfamily	245864	4	160	3.04E-41	147.04	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#13400 - 	CGI_10003601	superfamily	149481	11	211	1.18E-28	116.355	cl07163	CLCA_N superfamily	 - 	 - 	Calcium-activated chloride channel; The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells and has four or five putative transmembrane regions. Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors. The domain described here is found at the N-terminus of CLCAs.
Q#13400 - 	CGI_10003601	superfamily	149481	210	416	2.34E-27	112.503	cl07163	CLCA_N superfamily	N	 - 	Calcium-activated chloride channel; The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells and has four or five putative transmembrane regions. Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors. The domain described here is found at the N-terminus of CLCAs.
Q#13400 - 	CGI_10003601	superfamily	150094	606	675	1.62E-13	69.7109	cl09605	DUF1973 superfamily	N	 - 	Domain of unknown function (DUF1973); Members of his family of functionally uncharacterized domains are found in various eukaryotic calcium-dependent chloride channels.
Q#13401 - 	CGI_10003602	superfamily	242123	41	352	1.87E-167	472.663	cl00826	DS superfamily	 - 	 - 	"Deoxyhypusine synthase; Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalyzed by the enzyme deoxyhypusine synthase (DS) EC:1.1.1.249. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation."
Q#13402 - 	CGI_10003603	superfamily	221406	23	524	0	621.79	cl13500	DUF3550 superfamily	 - 	 - 	Protein of unknown function (DUF3550/UPF0682); This family of proteins is functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 249 to 606 amino acids in length.
Q#13404 - 	CGI_10003605	superfamily	245201	19	275	2.20E-172	487.651	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13404 - 	CGI_10003605	superfamily	246710	307	370	2.23E-06	45.5712	cl14783	DOMON_like superfamily	C	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#13404 - 	CGI_10003605	superfamily	241832	369	423	6.29E-25	97.91	cl00388	Thioredoxin_like superfamily	NC	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#13405 - 	CGI_10002168	superfamily	247723	179	247	1.00E-05	43.4477	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13405 - 	CGI_10002168	superfamily	222269	474	534	1.82E-05	45.007	cl18657	Cupin_8 superfamily	N	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#13406 - 	CGI_10002169	superfamily	243703	2	38	1.34E-13	59.1443	cl04309	RNAP_Rpb7_N_like superfamily	C	 - 	"RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex."
Q#13408 - 	CGI_10013968	superfamily	217473	96	319	3.68E-28	114.384	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#13411 - 	CGI_10013971	superfamily	241578	219	396	4.60E-47	163.54	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13411 - 	CGI_10013971	superfamily	207701	2	95	1.05E-16	76.9494	cl02699	VIT superfamily	N	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#13412 - 	CGI_10013972	superfamily	241599	194	256	1.99E-20	82.6764	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#13413 - 	CGI_10013973	superfamily	246683	24	347	2.06E-138	399.187	cl14648	Aldose_epim superfamily	 - 	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#13414 - 	CGI_10013974	superfamily	246683	25	349	6.66E-153	436.167	cl14648	Aldose_epim superfamily	 - 	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#13417 - 	CGI_10013977	superfamily	247984	187	401	5.68E-43	154.305	cl17430	FtsJ superfamily	 - 	 - 	"FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping."
Q#13417 - 	CGI_10013977	superfamily	243107	41	73	8.66E-11	58.6728	cl02611	G-patch superfamily	C	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#13417 - 	CGI_10013977	superfamily	241647	716	746	0.00361246	36.0395	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#13418 - 	CGI_10013978	superfamily	241624	435	709	9.84E-90	285.374	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#13418 - 	CGI_10013978	superfamily	149089	703	781	2.91E-14	69.6078	cl06733	PP2C_C superfamily	 - 	 - 	"Protein serine/threonine phosphatase 2C, C-terminal domain; Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain."
Q#13418 - 	CGI_10013978	superfamily	215882	139	271	1.17E-11	62.6834	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#13418 - 	CGI_10013978	superfamily	247725	233	325	1.05E-05	45.3106	cl17171	PH-like superfamily	NC	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13420 - 	CGI_10013980	superfamily	241728	9	164	6.11E-47	151.54	cl00253	Dtyr_deacylase superfamily	 - 	 - 	D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding
Q#13421 - 	CGI_10013981	superfamily	217473	145	322	1.75E-26	109.762	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#13422 - 	CGI_10013982	superfamily	243034	27	129	8.31E-11	57.7752	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13422 - 	CGI_10013982	superfamily	246597	144	332	2.83E-141	405.864	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#13423 - 	CGI_10013983	superfamily	217473	140	199	1.30E-05	45.0485	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#13425 - 	CGI_10013985	superfamily	219532	4	24	0.000395548	34.9826	cl06657	OB_NTP_bind superfamily	N	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#13426 - 	CGI_10013986	superfamily	241983	10	334	3.62E-44	154.823	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#13427 - 	CGI_10005149	superfamily	241555	8	169	2.26E-25	98.7826	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#13432 - 	CGI_10005154	superfamily	245827	172	583	9.23E-128	391.198	cl11986	TOP1Ac superfamily	 - 	 - 	"DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand."
Q#13432 - 	CGI_10005154	superfamily	242046	3	166	1.05E-49	172.418	cl00718	TOPRIM superfamily	 - 	 - 	"Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function."
Q#13433 - 	CGI_10005155	superfamily	241766	14	300	5.25E-126	364.467	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#13435 - 	CGI_10004542	superfamily	241599	3	54	5.08E-11	54.9421	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#13436 - 	CGI_10004543	superfamily	110440	251	278	0.00557805	33.9205	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#13438 - 	CGI_10004545	superfamily	244906	9	90	2.45E-19	79.1664	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#13439 - 	CGI_10004546	superfamily	248282	91	151	0.000136345	42.0009	cl17728	DUF11 superfamily	 - 	 - 	Domain of unknown function DUF11; A domain of unknown function found in multiple copies in several archaebacterial proteins.
Q#13441 - 	CGI_10004548	superfamily	147590	7	71	1.61E-19	76.5257	cl07862	ATP_synt_H superfamily	 - 	 - 	ATP synthase subunit H; ATP synthase subunit H is an extremely hydrophobic of approximately 9 kDa. This subunit may be required for assembly of vacuolar ATPase.
Q#13442 - 	CGI_10004549	superfamily	248054	15	49	7.78E-05	40.9184	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#13444 - 	CGI_10004031	superfamily	245598	89	285	1.55E-73	235.251	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#13444 - 	CGI_10004031	superfamily	244899	395	451	0.000226704	39.7806	cl08302	S-100 superfamily	N	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#13444 - 	CGI_10004031	superfamily	247856	427	479	0.000632126	38.2977	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13445 - 	CGI_10004032	superfamily	247912	53	406	6.18E-28	113.75	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#13447 - 	CGI_10019109	superfamily	243072	7	124	3.45E-29	104.773	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13448 - 	CGI_10019110	superfamily	247792	477	517	6.49E-06	43.5884	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13449 - 	CGI_10019111	superfamily	241677	39	161	1.25E-73	220.686	cl00197	cyclophilin superfamily	C	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#13452 - 	CGI_10019114	superfamily	247723	122	207	1.33E-59	186.061	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13452 - 	CGI_10019114	superfamily	247723	22	111	3.21E-58	182.995	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13456 - 	CGI_10019118	superfamily	241619	4	53	0.000462518	37.1765	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#13458 - 	CGI_10019120	superfamily	241619	1	53	5.22E-05	36.2937	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#13464 - 	CGI_10019126	superfamily	202746	190	418	2.68E-82	255.682	cl08402	Hexokinase_2 superfamily	 - 	 - 	Hexokinase; Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains.
Q#13465 - 	CGI_10019127	superfamily	241559	24	126	2.00E-26	100.248	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#13466 - 	CGI_10019128	superfamily	241559	22	124	5.21E-33	119.508	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#13469 - 	CGI_10019131	superfamily	241559	13	166	5.86E-30	110.263	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#13470 - 	CGI_10019132	superfamily	243092	1756	2043	1.80E-69	238.389	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13470 - 	CGI_10019132	superfamily	243092	2007	2337	4.30E-44	164.815	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13470 - 	CGI_10019132	superfamily	218721	509	665	1.76E-22	101.039	cl05344	TROVE superfamily	N	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#13470 - 	CGI_10019132	superfamily	218721	317	412	4.63E-17	84.0897	cl05344	TROVE superfamily	C	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#13470 - 	CGI_10019132	superfamily	205451	977	1057	1.18E-08	54.8919	cl16203	DUF4062 superfamily	 - 	 - 	"Domain of unknown function (DUF4062); This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif."
Q#13470 - 	CGI_10019132	superfamily	247743	1212	1337	0.000132761	43.3424	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13473 - 	CGI_10019135	superfamily	248054	38	83	0.000144492	39.7628	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#13474 - 	CGI_10019136	superfamily	243158	284	318	2.84E-05	41.3904	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#13474 - 	CGI_10019136	superfamily	243158	210	243	0.000121636	39.4644	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#13474 - 	CGI_10019136	superfamily	243158	166	197	0.000446733	37.9236	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#13474 - 	CGI_10019136	superfamily	236274	69	144	0.00230708	37.7055	cl18891	PRK08485 superfamily	N	 - 	DNA polymerase III subunit delta'; Validated
Q#13474 - 	CGI_10019136	superfamily	243158	370	400	0.00886682	34.0716	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#13475 - 	CGI_10019137	superfamily	222150	1092	1117	0.00147585	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13475 - 	CGI_10019137	superfamily	222150	474	499	0.00181044	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13477 - 	CGI_10019139	superfamily	241636	190	376	6.15E-76	239.027	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#13479 - 	CGI_10019141	superfamily	247727	159	293	1.28E-12	65.3903	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#13479 - 	CGI_10019141	superfamily	241636	109	136	0.000376229	39.4932	cl00145	TBOX superfamily	C	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#13480 - 	CGI_10019142	superfamily	247727	83	259	1.07E-18	81.5687	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#13482 - 	CGI_10019144	superfamily	242091	155	276	1.38E-22	93.5477	cl00786	MgtE superfamily	 - 	 - 	Divalent cation transporter; This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. Related regions are found also in archaebacterial and eukaryotic proteins. All the archaebacterial and eukaryotic examples have two copies of the region. This suggests that the eubacterial examples may act as dimers. Members of this family probably transport Mg2+ or other divalent cations into the cell. The alignment contains two highly conserved aspartates that may be involved in cation binding (Bateman A unpubl.)
Q#13482 - 	CGI_10019144	superfamily	242091	333	517	4.86E-08	51.9901	cl00786	MgtE superfamily	 - 	 - 	Divalent cation transporter; This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. Related regions are found also in archaebacterial and eukaryotic proteins. All the archaebacterial and eukaryotic examples have two copies of the region. This suggests that the eubacterial examples may act as dimers. Members of this family probably transport Mg2+ or other divalent cations into the cell. The alignment contains two highly conserved aspartates that may be involved in cation binding (Bateman A unpubl.)
Q#13484 - 	CGI_10019146	superfamily	243066	394	490	8.79E-29	112.014	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#13484 - 	CGI_10019146	superfamily	243146	724	779	1.26E-08	52.6638	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13484 - 	CGI_10019146	superfamily	243146	834	884	1.85E-06	46.5006	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13484 - 	CGI_10019146	superfamily	198867	497	588	3.41E-06	46.3827	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#13484 - 	CGI_10019146	superfamily	243146	685	725	2.29E-05	43.2057	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13484 - 	CGI_10019146	superfamily	243146	894	926	0.00370905	36.4855	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13485 - 	CGI_10019147	superfamily	242035	6	157	3.23E-37	126.603	cl00698	CGI-121 superfamily	 - 	 - 	"Kinase binding protein CGI-121; CGI-121 has been shown to bind to the p53-related protein kinase (PRPK). PRPK is a novel protein kinase which binds to and induces phosphorylation of the tumour suppressor protein p53. CGI-121 is part of a conserved protein complex, KEOPS. The KEOPS complex is involved in telomere uncapping and telomere elongation. Interestingly this family also include archaeal homologues, formerly in the DUF509 family. A structure for these proteins has been solved by structural genomics."
Q#13486 - 	CGI_10019148	superfamily	214507	348	399	3.24E-08	49.736	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#13487 - 	CGI_10019149	superfamily	242885	51	214	9.02E-57	180.101	cl02106	IF4E superfamily	 - 	 - 	Eukaryotic initiation factor 4E; Eukaryotic initiation factor 4E.  
Q#13488 - 	CGI_10016102	superfamily	217613	177	290	1.13E-55	178.137	cl04154	Cullin_binding superfamily	 - 	 - 	"Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices."
Q#13489 - 	CGI_10016103	superfamily	247743	378	517	2.88E-06	46.1344	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13490 - 	CGI_10016104	superfamily	247824	104	295	7.61E-12	63.7827	cl17270	APH_ChoK_like superfamily	N	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#13492 - 	CGI_10016106	superfamily	216334	97	202	0.00240058	37.7456	cl12245	Glypican superfamily	N	 - 	Glypican; Glypican.  
Q#13493 - 	CGI_10016107	superfamily	247824	53	226	1.89E-07	48.5549	cl17270	APH_ChoK_like superfamily	 - 	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#13494 - 	CGI_10016108	superfamily	216334	20	449	5.02E-162	479.569	cl12245	Glypican superfamily	C	 - 	Glypican; Glypican.  
Q#13495 - 	CGI_10016109	superfamily	246669	623	818	6.02E-81	266.88	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#13495 - 	CGI_10016109	superfamily	244307	1690	2102	0	571.977	cl06123	DHR2_DOCK superfamily	 - 	 - 	"Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins; DOCK proteins comprise a family of atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. They are also called the CZH (CED-5, Dock180, and MBC-zizimin homology) family, after the first family members identified. Dock180 was first isolated as a binding partner for the adaptor protein Crk. The Caenorhabditis elegans protein, Ced-5, is essential for cell migration and phagocytosis, while the Drosophila ortholog, Myoblast city (MBC), is necessary for myoblast fusion and dorsal closure. DOCKs are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1 (or Dock180), 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1, and DHR-2 (also called CZH2 or Docker). This alignment model represents the DHR-2 domain of DOCK proteins, which contains the catalytic GEF activity for Rac and/or Cdc42."
Q#13495 - 	CGI_10016109	superfamily	247725	150	257	4.75E-41	150.141	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13495 - 	CGI_10016109	superfamily	221285	36	131	9.27E-21	90.4882	cl13339	DUF3398 superfamily	 - 	 - 	Domain of unknown function (DUF3398); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 100 amino acids in length.
Q#13496 - 	CGI_10016110	superfamily	248109	75	155	0.00459174	34.1741	cl17555	NLPC_P60 superfamily	C	 - 	NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
Q#13497 - 	CGI_10016111	superfamily	245814	157	236	1.43E-08	50.1803	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13497 - 	CGI_10016111	superfamily	241607	104	136	0.000175257	38.0198	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#13497 - 	CGI_10016111	superfamily	243049	26	84	0.000115692	38.9859	cl02472	IGFBP superfamily	C	 - 	Insulin-like growth factor binding protein; Insulin-like growth factor binding protein.  
Q#13498 - 	CGI_10016112	superfamily	241563	68	109	1.00E-05	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13499 - 	CGI_10016113	superfamily	241563	31	72	2.80E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13500 - 	CGI_10016114	superfamily	241563	83	124	1.41E-05	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13500 - 	CGI_10016114	superfamily	241563	43	73	0.00617166	35.1476	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13501 - 	CGI_10016115	superfamily	222150	70	97	0.000773286	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13501 - 	CGI_10016115	superfamily	222150	41	67	0.00213782	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13502 - 	CGI_10016116	superfamily	222150	279	306	0.000270919	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13502 - 	CGI_10016116	superfamily	222150	250	276	0.000691127	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13503 - 	CGI_10016117	superfamily	222150	277	304	0.00083981	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13503 - 	CGI_10016117	superfamily	222150	248	274	0.00120595	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13505 - 	CGI_10016119	superfamily	220647	7	169	2.54E-26	100.48	cl18565	L_HGMIC_fpl superfamily	 - 	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#13506 - 	CGI_10016120	superfamily	190261	128	190	5.86E-22	89.9154	cl03504	RFX_DNA_binding superfamily	 - 	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#13507 - 	CGI_10016121	superfamily	242902	1144	1312	4.18E-45	162.105	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#13507 - 	CGI_10016121	superfamily	243056	817	1012	8.53E-16	77.7845	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#13508 - 	CGI_10016122	superfamily	217598	1	71	6.50E-28	103.318	cl04130	KCNQ_channel superfamily	N	 - 	KCNQ voltage-gated potassium channel; This family matches to the C-terminal tail of KCNQ type potassium channels.
Q#13509 - 	CGI_10016123	superfamily	243072	93	222	5.19E-28	111.321	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13509 - 	CGI_10016123	superfamily	243072	172	315	3.09E-24	100.151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13509 - 	CGI_10016123	superfamily	243072	302	415	1.36E-19	86.6686	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13509 - 	CGI_10016123	superfamily	243072	428	548	1.02E-14	72.4162	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13511 - 	CGI_10005242	superfamily	247725	148	275	2.96E-75	232.957	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13511 - 	CGI_10005242	superfamily	241631	2	121	2.35E-43	151.221	cl00136	Sec7 superfamily	N	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#13512 - 	CGI_10012581	superfamily	241799	2	49	7.45E-13	59.1128	cl00339	SugarP_isomerase superfamily	N	 - 	"SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway."
Q#13513 - 	CGI_10012582	superfamily	245201	10	141	1.38E-82	249.415	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13515 - 	CGI_10012584	superfamily	248458	175	348	3.95E-07	50.0049	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13516 - 	CGI_10012585	superfamily	248458	20	302	2.55E-08	53.8569	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13518 - 	CGI_10012587	superfamily	248458	61	312	0.00460321	37.2933	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13519 - 	CGI_10012588	superfamily	248458	169	548	3.91E-27	112.022	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13520 - 	CGI_10012589	superfamily	247723	15	103	1.93E-66	202.483	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13521 - 	CGI_10012590	superfamily	220626	130	387	6.35E-32	121.959	cl18564	GpcrRhopsn4 superfamily	 - 	 - 	"Rhodopsin-like GPCR transmembrane domain; This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans. GPCRs are integral membrane receptors whose intracellular actions are mediated by signalling pathways involving G proteins and downstream secondary messengers."
Q#13525 - 	CGI_10012595	superfamily	248458	183	292	0.000738262	40.7601	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13525 - 	CGI_10012595	superfamily	241607	393	433	1.33E-10	57.6994	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#13528 - 	CGI_10012598	superfamily	241609	141	214	5.78E-27	102.456	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#13528 - 	CGI_10012598	superfamily	241609	221	291	1.83E-26	100.915	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#13528 - 	CGI_10012598	superfamily	243093	4	65	2.88E-08	50.6066	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#13530 - 	CGI_10012600	superfamily	241672	7	340	2.33E-98	296.448	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#13531 - 	CGI_10007464	superfamily	241574	354	582	5.59E-93	293.723	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#13531 - 	CGI_10007464	superfamily	241574	639	824	3.38E-13	68.7665	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#13533 - 	CGI_10007466	superfamily	190881	374	413	0.00265632	35.5471	cl18167	Sulf_transp superfamily	 - 	 - 	Sulphur transport; This is an integral membrane protein. It is predicted to have a function in the transport of sulphur-containing molecules. It contains several conserved glycines and an invariant cysteine that is probably an important functional residue.
Q#13535 - 	CGI_10007468	superfamily	241574	398	573	1.02E-56	197.038	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#13535 - 	CGI_10007468	superfamily	241574	642	798	1.26E-12	67.6109	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#13535 - 	CGI_10007468	superfamily	245847	49	183	3.57E-09	55.9715	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13539 - 	CGI_10007473	superfamily	204376	86	143	1.11E-06	44.0561	cl10817	DUF2260 superfamily	C	 - 	"Uncharacterized conserved protein (DUF2260); This domain, found in various hypothetical bacterial proteins, has no known function."
Q#13540 - 	CGI_10007474	superfamily	241782	173	532	1.27E-105	324.156	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#13540 - 	CGI_10007474	superfamily	241782	1	69	1.00E-13	72.4357	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#13541 - 	CGI_10006391	superfamily	247683	25	80	7.21E-13	60.8441	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#13542 - 	CGI_10006392	superfamily	247792	7	54	0.000184548	39.7364	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13542 - 	CGI_10006392	superfamily	241563	152	183	0.000770489	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13545 - 	CGI_10005402	superfamily	241563	68	109	0.000100903	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13546 - 	CGI_10005403	superfamily	215647	88	245	3.16E-34	127.34	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#13546 - 	CGI_10005403	superfamily	243029	13	80	1.69E-08	50.8121	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#13547 - 	CGI_10005404	superfamily	215647	125	354	4.24E-53	178.186	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#13547 - 	CGI_10005404	superfamily	243029	36	102	5.52E-19	80.2512	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#13550 - 	CGI_10028517	superfamily	243097	61	345	2.83E-97	298.141	cl02572	PIPKc superfamily	 - 	 - 	"Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs."
Q#13551 - 	CGI_10028518	superfamily	243097	65	149	1.35E-18	81.5697	cl02572	PIPKc superfamily	C	 - 	"Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs."
Q#13557 - 	CGI_10028525	superfamily	243161	7	80	2.58E-07	43.5778	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#13559 - 	CGI_10028528	superfamily	215647	97	342	1.38E-57	200.913	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#13559 - 	CGI_10028528	superfamily	217252	1476	1538	1.21E-19	87.2351	cl08372	Pyr_redox_dim superfamily	 - 	 - 	"Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases."
Q#13559 - 	CGI_10028528	superfamily	215691	1303	1381	1.78E-16	77.241	cl15766	Pyr_redox superfamily	 - 	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#13559 - 	CGI_10028528	superfamily	248054	1133	1310	5.04E-07	50.7639	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#13559 - 	CGI_10028528	superfamily	243146	458	507	1.90E-05	44.2023	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13559 - 	CGI_10028528	superfamily	243146	561	614	0.000197988	41.1207	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13559 - 	CGI_10028528	superfamily	243146	606	646	0.000272777	40.7226	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13559 - 	CGI_10028528	superfamily	243146	664	710	0.00219458	38.0391	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13560 - 	CGI_10028529	superfamily	245201	311	508	8.34E-41	152.305	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13560 - 	CGI_10028529	superfamily	246680	13	98	2.26E-14	70.9045	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#13561 - 	CGI_10028530	superfamily	242903	217	352	2.85E-55	186.847	cl02148	APC10-like superfamily	 - 	 - 	"APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An  APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here."
Q#13561 - 	CGI_10028530	superfamily	241594	531	831	9.24E-57	197.143	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#13563 - 	CGI_10028532	superfamily	204522	482	536	2.28E-15	70.5861	cl11212	PNPOx_C superfamily	 - 	 - 	"Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Pyridoxine 5'-phosphate oxidase (PNPOx) catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate (PLP), a cofactor used by many enzymes involved in amino acid metabolism. The enzyme oxidises either the 4'-hydroxyl group of pyridoxine 5'-phosphate (PNP) or the 4'-primary amine of pyridoxamine 5'-phosphate (PMP) to an aldehyde. PNPOx is a homodimeric enzyme with one flavin mononucleotide (FMN) molecule non-covalently bound to each subunit. This domain represents one of the two dimerisation regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In Myxococcus xanthus pdxH, S6 runs from residues 178-192, S7 from 200-206 and S8 from 211-215. the extended loop, of residues 167-177 may well be involved in the pocket formed between the two dimers that positions the FMN molecule."
Q#13563 - 	CGI_10028532	superfamily	241815	72	95	7.09E-10	58.1687	cl00361	Transcrip_reg superfamily	C	 - 	"Transcriptional regulator; This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region."
Q#13563 - 	CGI_10028532	superfamily	241827	141	195	1.03E-09	55.7082	cl00381	PNPOx_like superfamily	C	 - 	"Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; The PNPOx-like superfamily is composed of pyridoxine 5'-phosphate (PNP) oxidases and other flavin mononucleotide (FMN) binding proteins, which catalyze FMN-mediated redox reactions."
Q#13563 - 	CGI_10028532	superfamily	241827	397	427	2.03E-06	45.693	cl00381	PNPOx_like superfamily	N	 - 	"Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; The PNPOx-like superfamily is composed of pyridoxine 5'-phosphate (PNP) oxidases and other flavin mononucleotide (FMN) binding proteins, which catalyze FMN-mediated redox reactions."
Q#13564 - 	CGI_10028533	superfamily	241599	144	203	5.35E-13	64.1868	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#13565 - 	CGI_10028534	superfamily	223224	759	1301	0	648.535	cl18700	HyuB superfamily	 - 	 - 	"N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]"
Q#13565 - 	CGI_10028534	superfamily	216816	257	558	6.85E-97	312.686	cl18380	Hydantoinase_A superfamily	 - 	 - 	Hydantoinase/oxoprolinase; This family includes the enzymes hydantoinase and oxoprolinase EC:3.5.2.9. Both reactions involve the hydrolysis of 5-membered rings via hydrolysis of their internal imide bonds.
Q#13565 - 	CGI_10028534	superfamily	218571	33	238	2.19E-57	197.477	cl05110	Hydant_A_N superfamily	 - 	 - 	Hydantoinase/oxoprolinase N-terminal region; This family is found at the N-terminus of the pfam01968 family.
Q#13566 - 	CGI_10028535	superfamily	247792	21	46	0.00993585	33.9584	cl17238	RING superfamily	N	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13566 - 	CGI_10028535	superfamily	241645	321	395	0.00150335	36.8524	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#13567 - 	CGI_10028536	superfamily	247724	44	130	7.44E-22	86.741	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13569 - 	CGI_10028538	superfamily	216434	19	212	1.09E-59	205.389	cl08318	PPDK_N superfamily	N	 - 	"Pyruvate phosphate dikinase, PEP/pyruvate binding domain; This enzyme catalyzes the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP)."
Q#13569 - 	CGI_10028538	superfamily	248254	605	681	1.38E-11	62.0144	cl17700	PEP-utilizers superfamily	C	 - 	"PEP-utilising enzyme, mobile domain; This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it."
Q#13570 - 	CGI_10028539	superfamily	241680	54	246	0.00856987	36.8926	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#13572 - 	CGI_10028541	superfamily	248192	35	362	2.16E-74	239.864	cl17638	PLN02808 superfamily	 - 	 - 	alpha-galactosidase
Q#13573 - 	CGI_10028542	superfamily	243362	1239	1434	5.10E-33	127.156	cl03262	DnaJ_C superfamily	 - 	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#13573 - 	CGI_10028542	superfamily	243077	1134	1188	1.90E-23	96.4605	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#13573 - 	CGI_10028542	superfamily	241663	878	1128	1.56E-63	220	cl00181	Endostatin-like superfamily	 - 	 - 	"Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; endostatin XVIII is monomeric and contains a heparin-binding epitope and zinc binding sites while endostatin XV is trimeric and contains neither of these sites; the generation of endostatin or endostatin-like collagen XV/XVIII fragments is catalyzed by proteolytic enzymes within the protease-sensitive hinge region of the C-terminal domain; endostatin inhibits endothelial cell migration in vitro and appears to be highly effective in murine in vivo studies"
Q#13574 - 	CGI_10028543	superfamily	247792	14	64	1.08E-06	46.67	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13574 - 	CGI_10028543	superfamily	241563	99	130	0.000341958	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13575 - 	CGI_10028544	superfamily	247792	14	62	1.02E-09	55.1444	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13575 - 	CGI_10028544	superfamily	241563	102	135	0.00148073	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13576 - 	CGI_10028545	superfamily	207662	107	190	1.07E-54	179.724	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#13576 - 	CGI_10028545	superfamily	245599	211	454	3.73E-99	300.961	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#13578 - 	CGI_10028547	superfamily	207662	130	199	1.07E-43	150.644	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#13578 - 	CGI_10028547	superfamily	245599	291	513	7.78E-90	278.236	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#13579 - 	CGI_10028548	superfamily	248313	104	188	0.000553463	37.981	cl17759	EamA superfamily	N	 - 	EamA-like transporter family; This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.
Q#13581 - 	CGI_10028550	superfamily	241752	133	484	4.72E-158	455.576	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#13581 - 	CGI_10028550	superfamily	242589	7	108	1.55E-43	150.17	cl01581	WGR superfamily	 - 	 - 	"WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain."
Q#13587 - 	CGI_10028556	superfamily	248458	27	202	1.78E-29	118.57	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13587 - 	CGI_10028556	superfamily	248458	447	540	0.000295197	41.9157	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13587 - 	CGI_10028556	superfamily	248458	269	338	0.00530101	38.0637	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13589 - 	CGI_10028558	superfamily	243077	26	79	5.41E-23	88.3713	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#13595 - 	CGI_10028564	superfamily	247057	36	74	0.00505098	31.5381	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#13597 - 	CGI_10028566	superfamily	247856	65	120	8.28E-10	51.0093	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13598 - 	CGI_10028568	superfamily	152928	30	111	2.25E-32	112.875	cl13875	DUF3695 superfamily	 - 	 - 	Protein of unknown function (DUF3695); This family of proteins is found in eukaryotes. Proteins in this family are typically between 157 and 192 amino acids in length. There is a single completely conserved residue D that may be functionally important.
Q#13602 - 	CGI_10028572	superfamily	246925	11	115	0.000477096	38.1054	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#13602 - 	CGI_10028572	superfamily	214507	134	158	0.00642333	32.402	cl15307	LRRCT superfamily	C	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#13603 - 	CGI_10028573	superfamily	214545	465	600	2.02E-20	88.916	cl10551	CULLIN superfamily	 - 	 - 	Cullin; Cullin.  
Q#13603 - 	CGI_10028573	superfamily	198939	710	770	2.45E-20	86.1528	cl08488	APC2 superfamily	 - 	 - 	"Anaphase promoting complex (APC) subunit 2; The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyze the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein."
Q#13604 - 	CGI_10028574	superfamily	247743	446	532	0.000431576	41.3627	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13604 - 	CGI_10028574	superfamily	117164	1636	1695	3.09E-16	76.5173	cl07270	DUF1771 superfamily	 - 	 - 	Domain of unknown function (DUF1771); This domain is always found adjacent to pfam01713.
Q#13604 - 	CGI_10028574	superfamily	243111	1706	1778	1.87E-15	74.6419	cl02619	Smr superfamily	 - 	 - 	"Smr domain; This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2. This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no significant double strand cleavage or exonuclease activity. The full-length human NEDD4-binding protein 2 also has the polynucleotide kinase activity."
Q#13604 - 	CGI_10028574	superfamily	241998	1072	1179	0.00290897	40.7364	cl00640	DHQS superfamily	C	 - 	"3-dehydroquinate synthase (EC 4.6.1.3); 3-Dehydroquinate synthase is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyzes the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides."
Q#13604 - 	CGI_10028574	superfamily	243130	1186	1224	0.00307317	37.8299	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#13605 - 	CGI_10028575	superfamily	247805	347	486	1.54E-25	104.342	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#13605 - 	CGI_10028575	superfamily	247905	511	668	4.12E-10	58.7885	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13605 - 	CGI_10028575	superfamily	243778	723	813	3.71E-37	135.815	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#13605 - 	CGI_10028575	superfamily	219532	847	947	7.96E-32	121.267	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#13606 - 	CGI_10028576	superfamily	245201	65	180	0.000121942	42.609	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#13607 - 	CGI_10028577	superfamily	241559	1287	1374	5.33E-07	50.7723	cl00030	CH superfamily	N	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#13607 - 	CGI_10028577	superfamily	241559	1436	1485	1.76E-13	69.622	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#13608 - 	CGI_10028578	superfamily	245847	680	833	2.44E-34	129.394	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13608 - 	CGI_10028578	superfamily	243119	859	910	2.92E-07	48.9692	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#13609 - 	CGI_10028579	superfamily	241600	8	76	4.28E-16	68.843	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#13613 - 	CGI_10028583	superfamily	243035	317	443	9.47E-24	95.3793	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13613 - 	CGI_10028583	superfamily	243035	191	288	2.29E-19	83.4381	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13613 - 	CGI_10028583	superfamily	243035	19	155	7.02E-24	96.2197	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13616 - 	CGI_10003868	superfamily	248289	14	50	0.000286368	34.414	cl17735	VWC superfamily	C	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#13617 - 	CGI_10003869	superfamily	199005	13	49	2.79E-07	47.2267	cl10889	Cir_N superfamily	 - 	 - 	"N-terminal domain of CBF1 interacting co-repressor CIR; This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex."
Q#13618 - 	CGI_10003870	superfamily	222436	59	253	8.78E-40	140.868	cl16454	DUF4203 superfamily	 - 	 - 	Domain of unknown function (DUF4203); This is the N-terminal region of 7tm proteins. The function is not known.
Q#13623 - 	CGI_10017851	superfamily	248097	11	58	3.05E-06	39.941	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#13625 - 	CGI_10017853	superfamily	245847	31	176	0.00435542	35.556	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13626 - 	CGI_10017854	superfamily	241763	165	390	4.39E-106	315.479	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#13626 - 	CGI_10017854	superfamily	117343	1	77	1.54E-37	132.958	cl07399	CathepsinC_exc superfamily	N	 - 	"Cathepsin C exclusion domain; Cathepsin C (dipeptidyl peptidase I) is the physiological activator of a group of serine proteases. This domain corresponds to the exclusion domain whose structure excludes the approach of a polypeptide apart from its termini. It forms an enclosed beta barrel structure composed from 8 anti-parallel beta strands. Based on a structural comparison and interaction data, it is suggested that the exclusion domain originates from a metallo-protease inhibitor."
Q#13626 - 	CGI_10017854	superfamily	203856	106	142	0.00486481	34.4889	cl06937	Propeptide_C1 superfamily	 - 	 - 	Peptidase family C1 propeptide; This motif is found at the N terminal of some members of the Peptidase_C1 family (pfam00112) and is involved in activation of this peptidase.
Q#13627 - 	CGI_10017855	superfamily	243038	128	214	2.15E-13	65.0545	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#13627 - 	CGI_10017855	superfamily	247725	7	111	2.35E-15	71.245	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#13629 - 	CGI_10017857	superfamily	207701	43	150	5.64E-32	117.781	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#13629 - 	CGI_10017857	superfamily	241578	233	312	6.54E-10	56.8397	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13629 - 	CGI_10017857	superfamily	244875	342	410	0.00820938	36.6108	cl08255	Na_K-ATPase superfamily	N	 - 	Sodium / potassium ATPase beta chain; Sodium / potassium ATPase beta chain.  
Q#13630 - 	CGI_10017858	superfamily	244837	86	341	5.83E-66	222.179	cl07971	Glyco_hydro_3 superfamily	 - 	 - 	Glycosyl hydrolase family 3 N terminal domain; Glycosyl hydrolase family 3 N terminal domain.  
Q#13630 - 	CGI_10017858	superfamily	222669	652	719	2.30E-08	52.0108	cl17048	Fn3-like superfamily	 - 	 - 	Fibronectin type III-like domain; This domain has a fibronectin type III-like structure. It is often found in association with pfam00933 and pfam01915. Its function is unknown.
Q#13631 - 	CGI_10017859	superfamily	243353	656	699	1.78E-10	57.4392	cl03225	GRIP superfamily	 - 	 - 	"GRIP domain; The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures in."
Q#13632 - 	CGI_10017860	superfamily	203864	721	750	1.35E-05	43.1839	cl06967	NUC153 superfamily	 - 	 - 	NUC153 domain; This small domain is found in a a novel nucleolar family.
Q#13633 - 	CGI_10017861	superfamily	241596	19	78	7.27E-10	56.0683	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#13633 - 	CGI_10017861	superfamily	243045	99	166	8.96E-10	56.4875	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#13633 - 	CGI_10017861	superfamily	243045	240	301	4.34E-07	48.3983	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#13633 - 	CGI_10017861	superfamily	204647	463	492	0.00921523	34.5851	cl12942	HIF-1 superfamily	 - 	 - 	"Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex."
Q#13634 - 	CGI_10017862	superfamily	247675	41	323	4.63E-123	358.731	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#13635 - 	CGI_10017863	superfamily	217408	566	1084	1.87E-64	228.964	cl15645	Nucleoporin_C superfamily	 - 	 - 	"Non-repetitive/WGA-negative nucleoporin C-terminal; This is the C-termainl half of a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and proteins. Two nucleoporin classes are known: one is characterized by the FG repeat pfam03093; the other is represented by this family, and lacks any repeats. RNA undergoing nuclear export first encounters the basket of the nuclear pore and many nucleoporins are accessible on the basket side of the pore."
Q#13640 - 	CGI_10017868	superfamily	241870	14	168	1.32E-53	182.677	cl00451	MoCF_BD superfamily	 - 	 - 	"MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin."
Q#13641 - 	CGI_10017869	superfamily	241870	167	518	1.45E-125	375.293	cl00451	MoCF_BD superfamily	 - 	 - 	"MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin."
Q#13641 - 	CGI_10017869	superfamily	217567	42	131	5.63E-20	86.8476	cl04083	MoeA_N superfamily	C	 - 	MoeA N-terminal region (domain I and II); This family contains two structural domains. One of these contains the conserved DGXA motif. This region is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this region is uncertain.
Q#13643 - 	CGI_10017871	superfamily	243263	64	524	3.63E-86	278.522	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#13645 - 	CGI_10017873	superfamily	241584	3355	3431	0.00525466	38.6315	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#13645 - 	CGI_10017873	superfamily	241619	1638	1673	0.0022071	39.4877	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#13646 - 	CGI_10017874	superfamily	201590	512	664	2.30E-10	60.3042	cl03090	HH_signal superfamily	N	 - 	"Hedgehog amino-terminal signalling domain; For the carboxyl Hint module, see pfam01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation."
Q#13646 - 	CGI_10017874	superfamily	201590	812	893	0.00336945	38.3478	cl03090	HH_signal superfamily	N	 - 	"Hedgehog amino-terminal signalling domain; For the carboxyl Hint module, see pfam01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation."
Q#13647 - 	CGI_10017875	superfamily	245213	42	78	4.19E-12	61.1134	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13647 - 	CGI_10017875	superfamily	245213	10	40	0.000281304	38.7718	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13647 - 	CGI_10017875	superfamily	220376	128	252	1.33E-10	58.5739	cl10729	DUF2040 superfamily	 - 	 - 	"Coiled-coil domain-containing protein 55 (DUF2040); This entry is a conserved domain of approximately 130 residues of proteins conserved from fungi to humans. The proteins do contain a coiled-coil domain, but the function is unknown."
Q#13648 - 	CGI_10000789	superfamily	248291	109	172	2.41E-13	62.3109	cl17737	Skp1_POZ superfamily	N	 - 	"Skp1 family, tetramerisation domain; Skp1 family, tetramerisation domain.  "
Q#13650 - 	CGI_10005796	superfamily	241754	474	816	1.94E-67	233.281	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#13653 - 	CGI_10005799	superfamily	241563	84	122	6.43E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13656 - 	CGI_10000747	superfamily	241760	9	57	2.58E-21	88.1727	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#13656 - 	CGI_10000747	superfamily	241760	65	113	2.58E-21	88.1727	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#13657 - 	CGI_10003823	superfamily	243035	287	404	2.34E-11	60.3261	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13657 - 	CGI_10003823	superfamily	243035	126	197	2.08E-09	54.5481	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13657 - 	CGI_10003823	superfamily	244363	51	112	0.00151894	37.794	cl06336	Commd superfamily	NC	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#13659 - 	CGI_10003826	superfamily	243161	44	81	0.00242271	33.1774	cl02739	THAP superfamily	NC	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#13661 - 	CGI_10004998	superfamily	115363	278	321	5.44E-05	40.433	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#13661 - 	CGI_10004998	superfamily	241578	37	152	0.00534483	36.2784	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13662 - 	CGI_10004999	superfamily	222258	28	75	7.97E-05	42.17	cl18656	AAA_30 superfamily	NC	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#13663 - 	CGI_10005000	superfamily	115363	273	292	4.49E-05	40.433	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#13665 - 	CGI_10005002	superfamily	115363	153	215	2.91E-10	55.841	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#13665 - 	CGI_10005002	superfamily	115363	228	271	6.47E-08	49.2926	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#13665 - 	CGI_10005002	superfamily	207713	330	400	1.17E-05	42.7122	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#13666 - 	CGI_10002314	superfamily	245206	37	310	4.74E-83	254.895	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#13667 - 	CGI_10002315	superfamily	243066	11	98	3.27E-16	69.5041	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#13669 - 	CGI_10002317	superfamily	247856	82	132	0.00798282	32.1345	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13670 - 	CGI_10002318	superfamily	241874	15	95	3.67E-41	142.588	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#13671 - 	CGI_10012437	superfamily	115363	661	745	0.00149343	37.7366	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#13671 - 	CGI_10012437	superfamily	241578	522	598	0.00186129	38.9748	cl00057	vWFA superfamily	NC	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13673 - 	CGI_10012439	superfamily	216363	4	77	2.39E-15	65.5694	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#13676 - 	CGI_10012442	superfamily	241563	68	109	5.37E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13676 - 	CGI_10012442	superfamily	241563	28	59	0.0020477	36.3032	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13677 - 	CGI_10012443	superfamily	241578	211	393	1.42E-64	211.869	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13677 - 	CGI_10012443	superfamily	219821	59	196	2.80E-22	92.8194	cl07136	VWA_N superfamily	 - 	 - 	"VWA N-terminal; This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits."
Q#13677 - 	CGI_10012443	superfamily	217211	425	518	1.15E-15	72.7021	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#13678 - 	CGI_10012444	superfamily	247750	1	237	1.70E-105	314.976	cl17196	E1_enzyme_family superfamily	 - 	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#13678 - 	CGI_10012444	superfamily	247750	326	368	5.42E-14	70.3741	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#13679 - 	CGI_10012445	superfamily	217473	130	338	1.97E-25	106.295	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#13680 - 	CGI_10012446	superfamily	241563	187	228	3.87E-09	53.6372	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13681 - 	CGI_10012447	superfamily	241571	603	708	3.94E-12	64.3558	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#13681 - 	CGI_10012447	superfamily	243061	182	287	3.53E-30	116.287	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#13681 - 	CGI_10012447	superfamily	243061	18	118	7.39E-30	115.132	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#13681 - 	CGI_10012447	superfamily	243061	309	393	1.27E-19	85.8566	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#13681 - 	CGI_10012447	superfamily	243061	402	497	3.59E-17	78.923	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#13681 - 	CGI_10012447	superfamily	243061	505	600	2.17E-11	61.7138	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#13681 - 	CGI_10012447	superfamily	243068	716	857	3.61E-09	57.17	cl02523	Zona_pellucida superfamily	NC	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#13681 - 	CGI_10012447	superfamily	243061	123	175	2.92E-08	52.7294	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#13686 - 	CGI_10012452	superfamily	247750	4	254	1.15E-118	359.296	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#13686 - 	CGI_10012452	superfamily	247750	322	479	4.73E-74	243.351	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#13686 - 	CGI_10012452	superfamily	202124	227	289	8.33E-12	61.024	cl08340	UBACT superfamily	 - 	 - 	Repeat in ubiquitin-activating (UBA) protein; Repeat in ubiquitin-activating (UBA) protein.  
Q#13687 - 	CGI_10012453	superfamily	243092	305	431	0.00402984	38.0848	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13687 - 	CGI_10012453	superfamily	110440	484	508	0.00629603	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#13688 - 	CGI_10012454	superfamily	245106	1	84	5.46E-45	143.168	cl09615	UBA_e1_C superfamily	N	 - 	Ubiquitin-activating enzyme e1 C-terminal domain; This presumed domain found at the C-terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterized.
Q#13689 - 	CGI_10008437	superfamily	243141	3	115	4.13E-24	93.535	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#13690 - 	CGI_10008438	superfamily	248097	140	263	5.11E-15	68.831	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#13691 - 	CGI_10008439	superfamily	243034	1245	1375	7.52E-07	49.3008	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13691 - 	CGI_10008439	superfamily	247743	219	290	0.00303943	38.6663	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13691 - 	CGI_10008439	superfamily	247743	779	824	0.000497966	41.0312	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13692 - 	CGI_10008440	superfamily	247743	118	274	4.09E-09	55.6688	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13693 - 	CGI_10008441	superfamily	243072	2	122	7.73E-33	117.099	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13695 - 	CGI_10008443	superfamily	245210	39	421	0	513.565	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#13696 - 	CGI_10008444	superfamily	241554	53	130	7.56E-11	56.1998	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#13698 - 	CGI_10008446	superfamily	221499	18	72	9.53E-23	90.7437	cl13671	CAF1C_H4-bd superfamily	 - 	 - 	Histone-binding protein RBBP4 or subunit C of CAF1 complex; The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an alpha helix which sits just upstream of the WD40 seven-bladed beta-propeller in the human RbAp46 protein. RbAp46 folds into the beta-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six.
Q#13698 - 	CGI_10008446	superfamily	243092	106	279	8.21E-18	81.6124	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13698 - 	CGI_10008446	superfamily	243092	203	379	3.69E-06	46.9444	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13699 - 	CGI_10008447	superfamily	247856	271	336	9.82E-22	90.3566	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13699 - 	CGI_10008447	superfamily	247856	14	80	1.34E-11	61.4667	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13700 - 	CGI_10008448	superfamily	244906	1531	1584	3.03E-18	81.8027	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#13700 - 	CGI_10008448	superfamily	192987	731	836	0.0026048	38.3223	cl13724	TMF_TATA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family."
Q#13701 - 	CGI_10008449	superfamily	241750	8	50	0.000258973	36.8836	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#13706 - 	CGI_10018055	superfamily	243161	3	104	5.65E-16	72.853	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#13708 - 	CGI_10018057	superfamily	247755	441	654	3.92E-135	406.54	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#13708 - 	CGI_10018057	superfamily	216049	148	396	6.85E-43	158.218	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#13708 - 	CGI_10018057	superfamily	216049	743	921	1.19E-24	105.061	cl18356	ABC_membrane superfamily	C	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#13710 - 	CGI_10018059	superfamily	241636	62	254	4.52E-105	312.214	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#13712 - 	CGI_10018061	superfamily	220533	53	670	0	541.545	cl12375	Dpy19 superfamily	 - 	 - 	"Q-cell neuroblast polarisation; Dyp-19, formerly known as DUF2211, is a transmembrane domain family that is required to orient the neuroblast cells, QR and QL accurately on the anterior-posterior axis: QL and QR are born in the same anterior-posterior position, but polarise and migrate left-right asymmetrically, QL migrating towards the posterior and QR migrating towards the anterior. It is also required, with unc-40, to express mab-5 correctly in the Q cell descendants. The Dpy-19 protein derives from the C. elegans DUMPY mutant."
Q#13713 - 	CGI_10018062	superfamily	241554	63	90	0.0008769	35.0542	cl00019	Macro superfamily	NC	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#13714 - 	CGI_10018063	superfamily	248458	327	474	1.28E-10	62.3313	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13714 - 	CGI_10018063	superfamily	248458	40	218	1.35E-10	62.3313	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13715 - 	CGI_10018064	superfamily	244881	17	300	0	523.369	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#13716 - 	CGI_10018065	superfamily	209898	31	53	0.00596541	32.3754	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#13717 - 	CGI_10018067	superfamily	245835	110	321	0.00753248	37.7206	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#13719 - 	CGI_10018069	superfamily	221612	62	224	1.02E-20	92.122	cl13889	DUF3715 superfamily	 - 	 - 	"Protein of unknown function (DUF3715); This domain family is found in eukaryotes, and is approximately 170 amino acids in length."
Q#13719 - 	CGI_10018069	superfamily	222449	1418	1486	0.00585	38.646	cl16468	Shisa superfamily	N	 - 	Wnt and FGF inhibitory regulator; Shisa is a transcription factor-type molecule that physically interacts with immature forms of the Wnt receptor Frizzled and the FGF receptor within the endoplasmic reticulum to inhibit their post-translational maturation and trafficking to the cell surface.
Q#13721 - 	CGI_10018071	superfamily	243072	125	201	1.56E-07	47.3782	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13721 - 	CGI_10018071	superfamily	241699	16	100	1.89E-28	103.81	cl00221	ACBP superfamily	 - 	 - 	Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Q#13722 - 	CGI_10018072	superfamily	244897	26	210	1.65E-23	96.0158	cl08298	PTZ00007 superfamily	C	 - 	(NAP-L) nucleosome assembly protein -L; Provisional
Q#13723 - 	CGI_10018073	superfamily	243050	23	76	1.44E-25	94.0281	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13723 - 	CGI_10018073	superfamily	243050	93	139	1.69E-19	77.9095	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13724 - 	CGI_10018074	superfamily	247724	10	175	1.81E-129	364.928	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13727 - 	CGI_10018077	superfamily	243084	1413	1524	1.58E-48	170.908	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#13727 - 	CGI_10018077	superfamily	243084	1535	1645	1.03E-44	159.737	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#13727 - 	CGI_10018077	superfamily	246955	591	1056	1.54E-171	531.506	cl15417	DUF3591 superfamily	 - 	 - 	"Protein of unknown function (DUF3591); This domain is found in eukaryotes and is typically between 445 to 462 amino acids in length. Most members are annotated as being transcription initiation factor TFIID subunit 1, and this region is the conserved central portion of these proteins."
Q#13727 - 	CGI_10018077	superfamily	246955	1084	1320	2.22E-10	64.6951	cl15417	DUF3591 superfamily	N	 - 	"Protein of unknown function (DUF3591); This domain is found in eukaryotes and is typically between 445 to 462 amino acids in length. Most members are annotated as being transcription initiation factor TFIID subunit 1, and this region is the conserved central portion of these proteins."
Q#13727 - 	CGI_10018077	superfamily	150052	18	45	2.06E-05	44.6816	cl07760	TBP-binding superfamily	C	 - 	"TATA box-binding protein binding; Members of this family adopt a structure consisting of three alpha helices and a beta-hairpin. They bind to TATA box-binding protein (TBP), inhibiting TBP interaction with the TATA element, thereby resulting in shutting down of gene transcription."
Q#13728 - 	CGI_10018078	superfamily	216939	3	69	3.41E-09	50.3541	cl03492	PC4 superfamily	 - 	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#13729 - 	CGI_10018079	superfamily	244880	2	163	1.14E-29	108.017	cl08263	TBP_TLF superfamily	 - 	 - 	"TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many equivalent positions, suggesting similar structure. However, TLFs contain distinct, conserved amino acids at several positions that distinguish them from TBP."
Q#13732 - 	CGI_10018083	superfamily	241555	3	216	1.48E-66	210.598	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#13733 - 	CGI_10018084	superfamily	243066	50	69	0.000307535	34.5889	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#13734 - 	CGI_10018085	superfamily	243066	48	141	3.03E-26	103.466	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#13734 - 	CGI_10018085	superfamily	198867	150	247	6.72E-26	102.42	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#13734 - 	CGI_10018085	superfamily	243146	389	442	0.000217426	39.739	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13734 - 	CGI_10018085	superfamily	243146	444	480	0.00922016	34.6524	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#13738 - 	CGI_10018089	superfamily	247724	14	174	6.27E-118	334.976	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13740 - 	CGI_10018091	superfamily	192535	43	166	0.00122864	38.3458	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#13741 - 	CGI_10022675	superfamily	247907	2499	2650	1.43E-27	112.897	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#13741 - 	CGI_10022675	superfamily	247907	2929	3066	1.72E-24	103.652	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#13741 - 	CGI_10022675	superfamily	247907	2311	2473	4.20E-24	102.496	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#13741 - 	CGI_10022675	superfamily	247907	2745	2882	3.88E-20	90.9404	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#13741 - 	CGI_10022675	superfamily	247907	2120	2278	1.02E-16	80.9252	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#13741 - 	CGI_10022675	superfamily	238012	956	1003	1.26E-15	75.0834	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	858	905	8.99E-14	69.6906	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	1052	1093	6.41E-12	64.2978	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	811	849	8.46E-12	63.9126	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	1401	1450	1.74E-11	63.1422	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	647	692	2.86E-11	62.3718	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	1506	1543	2.94E-09	56.5938	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	907	955	3.57E-09	56.2086	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	1007	1050	1.48E-07	51.5862	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	1451	1502	2.55E-05	45.0378	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	352	395	3.35E-05	44.6526	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	1098	1155	7.18E-05	43.497	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	243034	3142	3210	0.000102923	43.5228	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13741 - 	CGI_10022675	superfamily	238012	759	808	0.000235327	41.9562	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	238012	697	758	0.000443957	41.1858	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#13741 - 	CGI_10022675	superfamily	243198	27	264	6.81E-72	243.959	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#13741 - 	CGI_10022675	superfamily	243080	470	597	3.47E-29	116.592	cl02548	Laminin_B superfamily	 - 	 - 	Laminin B (Domain IV); Laminin B (Domain IV).  
Q#13741 - 	CGI_10022675	superfamily	243080	1220	1345	9.61E-21	91.9388	cl02548	Laminin_B superfamily	 - 	 - 	Laminin B (Domain IV); Laminin B (Domain IV).  
Q#13741 - 	CGI_10022675	superfamily	243092	3306	3485	7.18E-14	73.9084	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13741 - 	CGI_10022675	superfamily	203372	1994	2124	2.66E-06	49.0088	cl05515	Laminin_II superfamily	 - 	 - 	"Laminin Domain II; It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure."
Q#13742 - 	CGI_10022676	superfamily	243034	654	749	1.31E-11	62.3976	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13742 - 	CGI_10022676	superfamily	242008	555	618	0.00660602	37.9876	cl00656	Cas1_I-II-III superfamily	N	 - 	"CRISPR/Cas system-associated protein Cas1; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain"
Q#13743 - 	CGI_10022677	superfamily	243092	20	104	1.49E-13	66.2044	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13744 - 	CGI_10022678	superfamily	201844	209	237	3.31E-15	70.017	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#13745 - 	CGI_10022679	superfamily	201844	44	74	1.66E-14	66.5502	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#13745 - 	CGI_10022679	superfamily	201844	92	121	9.92E-13	61.5426	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#13745 - 	CGI_10022679	superfamily	201844	6	33	3.92E-12	60.0018	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#13745 - 	CGI_10022679	superfamily	201844	152	179	1.75E-11	58.0758	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#13745 - 	CGI_10022679	superfamily	219850	188	236	4.91E-05	43.3747	cl07173	SNF2_assoc superfamily	N	 - 	Bacterial SNF2 helicase associated; This domain is found in bacterial proteins of the SWF/SNF/SWI helicase family to the N-terminus of the SNF2 family N-terminal domain (pfam00176) and together with the Helicase conserved C-terminal domain (pfam00271). The function of the domain is not clear.
Q#13746 - 	CGI_10022680	superfamily	247727	84	191	0.000217388	39.3355	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#13750 - 	CGI_10022684	superfamily	189857	7	108	1.29E-28	102.713	cl07832	Caveolin superfamily	N	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#13751 - 	CGI_10022685	superfamily	189857	1	121	1.02E-40	134.3	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#13752 - 	CGI_10022686	superfamily	247746	32	142	0.00268964	36.8526	cl17192	ATP-synt_B superfamily	 - 	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#13753 - 	CGI_10022687	superfamily	245106	43	168	5.25E-72	215.586	cl09615	UBA_e1_C superfamily	 - 	 - 	Ubiquitin-activating enzyme e1 C-terminal domain; This presumed domain found at the C-terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterized.
Q#13754 - 	CGI_10022688	superfamily	247068	353	442	1.36E-14	71.1905	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13754 - 	CGI_10022688	superfamily	247068	40	129	6.17E-13	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13754 - 	CGI_10022688	superfamily	247068	246	339	2.88E-11	61.5605	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13754 - 	CGI_10022688	superfamily	247068	567	656	1.18E-08	53.8566	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13754 - 	CGI_10022688	superfamily	247068	141	233	1.36E-08	53.4714	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13754 - 	CGI_10022688	superfamily	247068	464	548	3.62E-08	52.3158	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13754 - 	CGI_10022688	superfamily	247068	836	901	3.15E-07	49.2342	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13754 - 	CGI_10022688	superfamily	247068	666	757	1.31E-06	47.3082	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#13757 - 	CGI_10022691	superfamily	203031	32	86	1.23E-05	40.004	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#13758 - 	CGI_10022692	superfamily	241691	198	254	0.00114266	37.4916	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#13759 - 	CGI_10022693	superfamily	218847	23	170	1.98E-38	131.854	cl18479	CDO_I superfamily	 - 	 - 	Cysteine dioxygenase type I; Cysteine dioxygenase type I (EC:1.13.11.20) converts cysteine to cysteinesulphinic acid and is the rate-limiting step in sulphate production.
Q#13760 - 	CGI_10022694	superfamily	246669	533	651	9.03E-72	232.19	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#13760 - 	CGI_10022694	superfamily	246669	379	493	1.82E-53	180.915	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#13760 - 	CGI_10022694	superfamily	246669	221	340	2.53E-51	175.157	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#13761 - 	CGI_10022695	superfamily	247723	148	199	1.04E-20	86.6876	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13762 - 	CGI_10022696	superfamily	204577	87	198	5.30E-25	97.3756	cl12569	DUF2838 superfamily	 - 	 - 	Protein of unknown function (DUF2838); This bacterial family of proteins has no known function.
Q#13763 - 	CGI_10022697	superfamily	247905	904	1036	1.49E-22	95.3824	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13763 - 	CGI_10022697	superfamily	247805	501	690	1.90E-12	66.2068	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#13764 - 	CGI_10022698	superfamily	217311	33	399	1.86E-126	383.225	cl18402	DUF229 superfamily	N	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#13767 - 	CGI_10022701	superfamily	244363	26	188	3.50E-75	226.041	cl06336	Commd superfamily	 - 	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#13769 - 	CGI_10022703	superfamily	245213	3264	3300	2.93E-10	59.5726	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1447	1484	2.99E-10	59.5726	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2069	2105	1.04E-09	58.0318	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1681	1718	1.51E-09	57.6466	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2532	2568	1.66E-09	57.2614	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	905	942	2.22E-09	56.8762	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	3186	3222	3.30E-09	56.491	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2763	2798	3.93E-09	56.491	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	3109	3146	4.01E-09	56.1058	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	944	980	4.59E-09	56.1058	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2953	2990	6.53E-09	55.7206	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1876	1913	9.04E-09	55.3354	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1720	1757	1.22E-08	54.9502	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2108	2143	1.67E-08	54.565	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1524	1560	2.38E-08	54.1798	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1331	1367	2.47E-08	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1759	1797	2.50E-08	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2380	2416	3.97E-08	53.4094	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2839	2874	4.46E-08	53.4094	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	3032	3068	4.54E-08	53.0242	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2915	2950	6.54E-08	52.639	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2456	2492	9.79E-08	52.2538	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	3224	3260	1.10E-07	52.2538	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2571	2606	1.25E-07	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2029	2066	1.29E-07	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1915	1950	1.51E-07	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2647	2682	2.22E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	3148	3183	2.32E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1371	1405	2.37E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1100	1137	2.86E-07	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2494	2530	3.25E-07	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	3070	3106	4.05E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1953	1989	4.49E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1991	2026	4.69E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	866	903	6.53E-07	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2685	2721	6.81E-07	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	982	1020	7.02E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2877	2913	7.48E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1060	1097	8.32E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1799	1836	8.60E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	3302	3338	9.11E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1142	1174	1.32E-06	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1177	1213	1.78E-06	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2609	2644	2.46E-06	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1022	1057	3.27E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1407	1445	3.36E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2723	2760	7.16E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1563	1600	7.51E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2992	3030	1.08E-05	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1293	1328	1.16E-05	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1255	1291	1.28E-05	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1838	1873	1.42E-05	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1603	1641	1.55E-05	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1486	1521	1.64E-05	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2146	2181	1.84E-05	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2418	2454	1.98E-05	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2340	2377	3.36E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2223	2260	0.000124925	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2801	2836	0.000127195	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1643	1679	0.000135876	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	1221	1252	0.00179573	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	840	864	0.00221218	39.5422	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	245213	2306	2338	0.00561166	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13769 - 	CGI_10022703	superfamily	243060	3580	3649	4.61E-09	57.3888	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#13769 - 	CGI_10022703	superfamily	243060	3837	3936	3.84E-06	48.5292	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#13769 - 	CGI_10022703	superfamily	243060	3459	3538	1.96E-05	46.218	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#13769 - 	CGI_10022703	superfamily	243060	117	215	2.39E-05	46.218	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#13769 - 	CGI_10022703	superfamily	243060	3714	3777	4.88E-05	45.0624	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#13773 - 	CGI_10022707	superfamily	247723	483	539	3.05E-08	51.4992	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13774 - 	CGI_10022708	superfamily	243035	84	191	1.23E-21	86.1345	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13775 - 	CGI_10022709	superfamily	243035	107	204	2.61E-20	82.6677	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13776 - 	CGI_10022710	superfamily	241691	16	170	2.42E-06	44.697	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#13780 - 	CGI_10004339	superfamily	248338	158	271	0.00311496	37.5809	cl17784	Peptidase_C48 superfamily	NC	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#13781 - 	CGI_10004340	superfamily	243263	37	218	4.45E-36	137.539	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#13781 - 	CGI_10004340	superfamily	243263	3	43	2.22E-08	54.3362	cl02990	ASC superfamily	C	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#13784 - 	CGI_10004489	superfamily	216339	170	406	5.32E-149	425.646	cl08308	Tub superfamily	 - 	 - 	Tub family; Tub family.  
Q#13790 - 	CGI_10006088	superfamily	241622	235	315	1.96E-22	92.2446	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#13790 - 	CGI_10006088	superfamily	241622	362	415	1.68E-09	55.3384	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#13790 - 	CGI_10006088	superfamily	244397	569	616	0.00207632	37.2693	cl06515	DUF1525 superfamily	NC	 - 	Protein of unknown function (DUF1525); Protein of unknown function (DUF1525).  
Q#13791 - 	CGI_10006089	superfamily	247058	1	185	7.09E-59	186.997	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#13800 - 	CGI_10005287	superfamily	247724	3	137	1.64E-22	89.9019	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13802 - 	CGI_10005289	superfamily	217900	5	106	2.33E-33	127.698	cl04403	APG9 superfamily	N	 - 	"Autophagy protein Apg9; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways."
Q#13805 - 	CGI_10015178	superfamily	241563	11	43	1.41E-07	48.2444	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13806 - 	CGI_10015179	superfamily	219431	138	188	2.24E-05	42.8032	cl06504	zf-CW superfamily	 - 	 - 	"CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found."
Q#13807 - 	CGI_10015180	superfamily	247856	97	159	3.17E-16	74.8917	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13807 - 	CGI_10015180	superfamily	247856	216	278	1.83E-15	72.5805	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13807 - 	CGI_10015180	superfamily	247856	23	83	2.15E-15	72.1953	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13807 - 	CGI_10015180	superfamily	247856	290	349	4.32E-13	65.6469	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13807 - 	CGI_10015180	superfamily	247057	784	831	4.61E-05	42.2265	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#13808 - 	CGI_10015181	superfamily	243069	192	278	0.00202081	37.7324	cl02525	Band_7 superfamily	NC	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#13809 - 	CGI_10015182	superfamily	220608	39	151	1.17E-25	104.31	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#13810 - 	CGI_10015183	superfamily	220608	31	151	8.20E-24	98.9174	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#13811 - 	CGI_10015184	superfamily	222150	1531	1556	0.000171956	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13811 - 	CGI_10015184	superfamily	222150	233	257	0.000237433	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13812 - 	CGI_10015185	superfamily	241874	26	578	0	551.4	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#13814 - 	CGI_10015187	superfamily	245847	22	170	2.24E-37	134.787	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13814 - 	CGI_10015187	superfamily	245847	212	349	2.26E-27	107.438	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13814 - 	CGI_10015187	superfamily	245847	399	535	0.000485771	39.0228	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13816 - 	CGI_10015189	superfamily	147024	89	264	1.27E-62	204.585	cl04658	OGFr_N superfamily	 - 	 - 	"Opioid growth factor receptor (OGFr) conserved region; Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The Opioid growth factor receptor is an integral membrane protein associated with the nucleus. The conserved region is situated at the N-terminus of the member proteins with a series of imperfect repeats lying immediately to its C-terminus."
Q#13817 - 	CGI_10015190	superfamily	247755	446	684	1.42E-138	408.851	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#13817 - 	CGI_10015190	superfamily	216049	129	399	3.30E-33	128.943	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#13818 - 	CGI_10015191	superfamily	198738	317	405	1.50E-39	137.399	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#13818 - 	CGI_10015191	superfamily	247057	116	194	6.03E-20	83.5657	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#13819 - 	CGI_10015192	superfamily	198738	314	402	1.26E-43	148.57	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#13819 - 	CGI_10015192	superfamily	247057	163	241	5.43E-25	97.0477	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#13822 - 	CGI_10015195	superfamily	245208	3	630	0	677.51	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#13823 - 	CGI_10015196	superfamily	243082	421	523	8.47E-06	45.7414	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#13824 - 	CGI_10005534	superfamily	246616	2	192	3.61E-18	81.1993	cl14105	MetH superfamily	 - 	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#13825 - 	CGI_10005535	superfamily	245864	54	388	1.93E-53	185.174	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#13826 - 	CGI_10005536	superfamily	243135	249	524	6.38E-103	316.144	cl02666	KU superfamily	 - 	 - 	"Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by non-homologous end-joining. The bacterial Ku homologs does not contain the conserved N-terminal extension that is present in the eukaryotic Ku protein."
Q#13826 - 	CGI_10005536	superfamily	241578	28	244	6.34E-63	208.756	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13826 - 	CGI_10005536	superfamily	207684	570	605	0.000756736	37.7436	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#13828 - 	CGI_10005538	superfamily	241889	89	234	8.54E-57	183.986	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#13830 - 	CGI_10005540	superfamily	241777	349	498	1.91E-37	138.892	cl00316	Cation_efflux superfamily	N	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#13830 - 	CGI_10005540	superfamily	241777	166	292	7.25E-29	114.239	cl00316	Cation_efflux superfamily	C	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#13831 - 	CGI_10005541	superfamily	241862	438	563	2.26E-23	99.3528	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#13838 - 	CGI_10014948	superfamily	192535	71	189	3.24E-07	50.6722	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#13841 - 	CGI_10014951	superfamily	147626	77	106	0.000433474	36.8495	cl05227	DUF1519 superfamily	N	 - 	Protein of unknown function (DUF1519); This family consists of several putative homing endonuclease proteins of around 245 residues in length which appear to be found exclusively in Naegleria species. The function of this family is unclear.
Q#13842 - 	CGI_10014952	superfamily	222150	753	777	0.000511814	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#13843 - 	CGI_10014953	superfamily	247792	9	59	4.24E-08	50.1368	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13845 - 	CGI_10014955	superfamily	247792	866	916	2.32E-08	52.448	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13845 - 	CGI_10014955	superfamily	243056	143	303	9.05E-48	171.721	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#13846 - 	CGI_10014956	superfamily	241647	6	36	4.35E-09	48.6782	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#13846 - 	CGI_10014956	superfamily	244886	45	153	4.67E-59	181.377	cl08278	Rotamase_2 superfamily	 - 	 - 	PPIC-type PPIASE domain; PPIC-type PPIASE domain.  
Q#13847 - 	CGI_10014957	superfamily	243034	1127	1242	5.42E-16	75.8795	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13847 - 	CGI_10014957	superfamily	243034	1066	1155	7.52E-08	51.9972	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13847 - 	CGI_10014957	superfamily	243034	934	1049	2.28E-07	50.4564	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13847 - 	CGI_10014957	superfamily	243034	1212	1282	2.97E-07	50.0712	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13848 - 	CGI_10014958	superfamily	241795	445	575	3.24E-56	189.729	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#13848 - 	CGI_10014958	superfamily	241795	310	442	5.70E-56	188.958	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#13848 - 	CGI_10014958	superfamily	241795	161	295	1.11E-46	163.535	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#13848 - 	CGI_10014958	superfamily	241832	11	112	5.49E-39	140.934	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#13848 - 	CGI_10014958	superfamily	220249	787	854	3.41E-19	83.4236	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#13849 - 	CGI_10014959	superfamily	220249	54	121	1.80E-17	71.8676	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#13850 - 	CGI_10014960	superfamily	245230	2	305	5.69E-63	214.099	cl10017	Tubulin_FtsZ superfamily	C	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#13850 - 	CGI_10014960	superfamily	245230	258	356	2.14E-09	58.0931	cl10017	Tubulin_FtsZ superfamily	N	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#13851 - 	CGI_10014961	superfamily	247743	1317	1402	0.00759381	38.6663	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13851 - 	CGI_10014961	superfamily	193256	2299	2562	2.73E-64	223.671	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#13851 - 	CGI_10014961	superfamily	193251	1926	2199	4.90E-50	182.443	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#13851 - 	CGI_10014961	superfamily	193257	2942	3157	8.69E-45	165.544	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#13851 - 	CGI_10014961	superfamily	193253	2574	2922	1.61E-39	153.654	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#13851 - 	CGI_10014961	superfamily	247743	1593	1736	3.13E-06	48.8308	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#13855 - 	CGI_10005607	superfamily	198825	62	134	4.46E-30	105.959	cl03763	CaMBD superfamily	 - 	 - 	"Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other."
Q#13855 - 	CGI_10005607	superfamily	219619	4	44	1.28E-08	47.9728	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#13858 - 	CGI_10011151	superfamily	241792	3	141	7.33E-82	240.534	cl00332	Ribosomal_S11 superfamily	 - 	 - 	Ribosomal protein S11; Ribosomal protein S11.  
Q#13859 - 	CGI_10011152	superfamily	241974	525	617	3.36E-19	83.8302	cl00604	STAS superfamily	 - 	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#13859 - 	CGI_10011152	superfamily	216188	194	488	2.42E-54	188.196	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#13859 - 	CGI_10011152	superfamily	205965	78	158	4.85E-36	130.61	cl18285	Sulfate_tra_GLY superfamily	 - 	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#13860 - 	CGI_10011153	superfamily	248020	23	353	1.12E-35	139.907	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#13861 - 	CGI_10011154	superfamily	248020	23	353	1.68E-37	140.678	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#13862 - 	CGI_10011155	superfamily	246925	29	171	8.30E-12	65.4545	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#13863 - 	CGI_10011156	superfamily	246925	19	158	0.000108946	40.0314	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#13864 - 	CGI_10011157	superfamily	241554	2	164	2.01E-26	103.504	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#13865 - 	CGI_10011158	superfamily	241613	34	67	4.56E-09	53.7498	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13865 - 	CGI_10011158	superfamily	241613	233	267	9.66E-09	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13865 - 	CGI_10011158	superfamily	241613	74	107	1.31E-08	52.209	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13865 - 	CGI_10011158	superfamily	241613	151	181	2.18E-07	48.7422	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13865 - 	CGI_10011158	superfamily	241613	199	229	3.35E-06	45.2754	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#13865 - 	CGI_10011158	superfamily	245213	353	384	0.00106566	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13865 - 	CGI_10011158	superfamily	214531	472	511	2.29E-10	57.6116	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#13865 - 	CGI_10011158	superfamily	214531	513	554	2.08E-09	54.9153	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#13865 - 	CGI_10011158	superfamily	214531	560	601	3.77E-09	54.1449	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#13865 - 	CGI_10011158	superfamily	214531	425	460	0.000751318	38.3517	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#13865 - 	CGI_10011158	superfamily	215683	622	662	0.00542738	35.9939	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#13866 - 	CGI_10011159	superfamily	247692	68	432	3.85E-158	460.423	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#13867 - 	CGI_10011160	superfamily	247724	132	351	3.31E-142	412.655	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13867 - 	CGI_10011160	superfamily	243184	446	553	7.05E-57	187.494	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#13867 - 	CGI_10011160	superfamily	243185	359	440	1.20E-36	130.748	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#13868 - 	CGI_10011161	superfamily	227527	8	224	1.96E-35	132.012	cl15315	LUC7 superfamily	 - 	 - 	"U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]"
Q#13869 - 	CGI_10011162	superfamily	114045	836	902	6.91E-05	45.0126	cl15903	Herpes_LMP1 superfamily	NC	 - 	"Herpesvirus latent membrane protein 1 (LMP1); This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1 of EBV is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N-terminus and a long cytoplasmic carboxy tail of 200 amino acids. EBV latent membrane protein 1 (LMP1) is essential for EBV-mediated transformation and has been associated with several cases of malignancies. EBV-like viruses in Cynomolgus monkeys (Macaca fascicularis) have been associated with high lymphoma rates in immunosuppressed monkeys"
Q#13869 - 	CGI_10011162	superfamily	114045	720	817	0.000691354	41.931	cl15903	Herpes_LMP1 superfamily	N	 - 	"Herpesvirus latent membrane protein 1 (LMP1); This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1 of EBV is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N-terminus and a long cytoplasmic carboxy tail of 200 amino acids. EBV latent membrane protein 1 (LMP1) is essential for EBV-mediated transformation and has been associated with several cases of malignancies. EBV-like viruses in Cynomolgus monkeys (Macaca fascicularis) have been associated with high lymphoma rates in immunosuppressed monkeys"
Q#13870 - 	CGI_10011163	superfamily	243092	96	211	9.66E-06	45.7888	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13872 - 	CGI_10011165	superfamily	241640	219	389	0.004801	36.0113	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#13874 - 	CGI_10011167	superfamily	241640	195	366	0.00268923	36.7817	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#13875 - 	CGI_10011168	superfamily	219740	194	351	1.42E-06	48.9546	cl06992	Peptidase_S64 superfamily	N	 - 	"Peptidase family S64; This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1. The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS:S1) and to have a typical trypsin-like catalytic triad."
Q#13876 - 	CGI_10000778	superfamily	243092	2	52	0.000601605	36.544	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13877 - 	CGI_10001266	superfamily	247684	9	100	4.84E-14	66.1467	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#13878 - 	CGI_10001267	superfamily	247684	34	253	1.57E-26	107.378	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#13879 - 	CGI_10018717	superfamily	243124	147	205	1.15E-12	62.0593	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#13880 - 	CGI_10018718	superfamily	241886	5	234	1.18E-64	205.871	cl00470	Aldo_ket_red superfamily	C	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#13886 - 	CGI_10018724	superfamily	245847	78	193	0.000697851	37.8672	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#13887 - 	CGI_10018725	superfamily	241610	1	52	4.01E-16	67.275	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#13888 - 	CGI_10018726	superfamily	247724	165	375	3.50E-15	73.3497	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13891 - 	CGI_10004715	superfamily	247792	275	315	1.09E-07	47.7596	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#13891 - 	CGI_10004715	superfamily	248312	25	143	2.25E-05	42.7344	cl17758	PMP22_Claudin superfamily	C	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#13892 - 	CGI_10004716	superfamily	248312	26	164	5.55E-05	40.4232	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#13893 - 	CGI_10004717	superfamily	207690	382	402	0.00580427	34.6009	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#13894 - 	CGI_10004718	superfamily	241628	250	429	1.47E-56	192.442	cl00130	PseudoU_synth superfamily	C	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#13894 - 	CGI_10004718	superfamily	241628	107	135	3.89E-09	56.4662	cl00130	PseudoU_synth superfamily	C	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#13895 - 	CGI_10004719	superfamily	241628	2	238	1.20E-55	185.123	cl00130	PseudoU_synth superfamily	N	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#13896 - 	CGI_10004720	superfamily	217473	516	677	3.30E-18	85.4945	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#13897 - 	CGI_10004721	superfamily	216981	145	268	4.07E-13	65.2466	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#13898 - 	CGI_10004722	superfamily	247724	5	123	5.52E-62	189.847	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#13900 - 	CGI_10003351	superfamily	241567	10	148	5.93E-31	114.235	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#13901 - 	CGI_10003352	superfamily	241567	378	512	1.07E-27	112.694	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#13901 - 	CGI_10003352	superfamily	241567	14	156	1.48E-26	109.227	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#13901 - 	CGI_10003352	superfamily	241567	663	753	3.27E-09	56.8399	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#13901 - 	CGI_10003352	superfamily	241567	242	355	1.96E-06	48.3655	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#13902 - 	CGI_10003353	superfamily	241787	31	85	1.92E-07	43.7374	cl00326	Ribosomal_L23 superfamily	C	 - 	Ribosomal protein L23; Ribosomal protein L23.  
Q#13903 - 	CGI_10003354	superfamily	245084	1	318	0	576.02	cl09506	catalase_like superfamily	N	 - 	"Catalase-like heme-binding proteins and protein domains; Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity."
Q#13904 - 	CGI_10003355	superfamily	245084	65	494	0	849.897	cl09506	catalase_like superfamily	 - 	 - 	"Catalase-like heme-binding proteins and protein domains; Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity."
Q#13907 - 	CGI_10015305	superfamily	247905	47	91	1.86E-05	41.0693	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13908 - 	CGI_10015306	superfamily	247905	2	38	2.51E-06	43.7397	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13912 - 	CGI_10015310	superfamily	241563	60	99	7.56E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13912 - 	CGI_10015310	superfamily	110440	521	547	0.00327917	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#13917 - 	CGI_10015315	superfamily	247905	102	146	0.000123067	39.9137	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13918 - 	CGI_10015316	superfamily	245818	242	389	2.55E-19	85.3015	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#13918 - 	CGI_10015316	superfamily	247723	51	129	5.27E-13	65.8742	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#13918 - 	CGI_10015316	superfamily	217750	480	536	0.000215548	40.255	cl04280	PAP_assoc superfamily	 - 	 - 	Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.
Q#13919 - 	CGI_10015317	superfamily	241599	240	289	3.32E-06	43.7713	cl00084	homeodomain superfamily	C	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#13920 - 	CGI_10015318	superfamily	245818	157	278	8.87E-16	71.8195	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#13922 - 	CGI_10015320	superfamily	238191	14	157	2.32E-22	97.788	cl18907	Esterase_lipase superfamily	NC	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#13925 - 	CGI_10015323	superfamily	227463	7	274	1.99E-27	109.399	cl12195	COG5134 superfamily	 - 	 - 	Uncharacterized conserved protein [Function unknown]
Q#13926 - 	CGI_10015324	superfamily	248014	709	893	3.97E-53	183.152	cl17460	Csf4_U superfamily	 - 	 - 	CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Q#13926 - 	CGI_10015324	superfamily	219153	246	432	4.44E-50	174.851	cl15854	DEAD_2 superfamily	 - 	 - 	"DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast."
Q#13926 - 	CGI_10015324	superfamily	248014	44	85	0.00506662	39.1863	cl17460	Csf4_U superfamily	C	 - 	CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Q#13927 - 	CGI_10015325	superfamily	243175	123	194	1.04E-20	83.4443	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#13927 - 	CGI_10015325	superfamily	241832	1	43	4.80E-05	39.9146	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#13928 - 	CGI_10015326	superfamily	207613	551	586	9.45E-10	55.0177	cl02491	VHP superfamily	 - 	 - 	Villin headpiece domain; Villin headpiece domain.  
Q#13933 - 	CGI_10015331	superfamily	247692	244	590	0	552.898	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#13933 - 	CGI_10015331	superfamily	247692	88	178	1.43E-23	102.295	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#13934 - 	CGI_10015332	superfamily	243092	58	346	3.60E-10	60.0412	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#13936 - 	CGI_10015334	superfamily	245213	62	85	0.00163161	34.7598	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13937 - 	CGI_10001870	superfamily	247866	320	471	0.00452365	37.8172	cl17312	PhyH superfamily	C	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#13940 - 	CGI_10001220	superfamily	243051	57	143	1.09E-17	75.1069	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#13941 - 	CGI_10003739	superfamily	216981	51	140	9.46E-05	40.2086	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#13942 - 	CGI_10003741	superfamily	227778	25	129	0.000208668	39.7915	cl17122	VPS24 superfamily	C	 - 	Conserved protein implicated in secretion [Cell motility and secretion]
Q#13943 - 	CGI_10003742	superfamily	243072	59	189	8.05E-31	114.788	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13943 - 	CGI_10003742	superfamily	243072	140	271	7.71E-23	92.8318	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#13943 - 	CGI_10003742	superfamily	243073	361	400	1.06E-14	67.8805	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#13944 - 	CGI_10003743	superfamily	243130	805	844	2.52E-06	45.5339	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#13944 - 	CGI_10003743	superfamily	245342	353	454	4.25E-06	45.8623	cl10594	ERCC4 superfamily	 - 	 - 	ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Q#13945 - 	CGI_10003744	superfamily	202224	1473	1573	3.55E-11	62.3132	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#13945 - 	CGI_10003744	superfamily	214721	1387	1439	0.000374724	40.3132	cl18313	JmjC superfamily	 - 	 - 	"A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press)."
Q#13950 - 	CGI_10023604	superfamily	207794	326	771	0	574.24	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#13950 - 	CGI_10023604	superfamily	243574	873	1031	1.13E-28	114.349	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#13950 - 	CGI_10023604	superfamily	243574	28	187	9.94E-21	91.2371	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#13950 - 	CGI_10023604	superfamily	207794	1167	1203	1.48E-12	70.0133	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#13950 - 	CGI_10023604	superfamily	245008	790	821	1.96E-07	49.8792	cl09101	E_set superfamily	C	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#13950 - 	CGI_10023604	superfamily	245008	1198	1247	0.000432752	39.864	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#13951 - 	CGI_10023605	superfamily	207794	319	620	3.91E-133	400.9	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#13951 - 	CGI_10023605	superfamily	243574	26	184	1.04E-26	107.03	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#13953 - 	CGI_10023607	superfamily	246918	469	527	1.05E-11	60.6783	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	497	549	3.29E-12	62.9895	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	614	660	2.10E-10	57.5967	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	383	435	9.46E-10	55.6707	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	326	378	1.00E-09	55.6707	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	269	321	1.22E-09	55.2855	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	155	207	8.91E-08	49.8927	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	98	136	7.74E-06	44.4999	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	212	264	2.14E-05	42.9591	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13954 - 	CGI_10023608	superfamily	246918	34	88	0.000113206	41.0331	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13955 - 	CGI_10023609	superfamily	246918	808	860	6.42E-15	71.4639	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13955 - 	CGI_10023609	superfamily	246918	922	974	1.99E-13	66.8415	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13955 - 	CGI_10023609	superfamily	246918	694	746	6.45E-13	65.6859	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13955 - 	CGI_10023609	superfamily	246918	580	618	4.61E-08	51.4335	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13955 - 	CGI_10023609	superfamily	246918	516	574	4.21E-07	48.7371	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13955 - 	CGI_10023609	superfamily	246918	637	689	1.57E-06	46.8111	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#13957 - 	CGI_10023611	superfamily	219936	108	218	4.42E-13	64.1941	cl18534	SPA superfamily	 - 	 - 	Stabilisation of polarity axis; Yeast AFI1 (ARF3-interaction protein 1) has been shown to interact with the outer plaque of the spindle pole body. In Aspergillus nidulans the protein member is necessary for stabilisation of the polarity axes during septation. and in S. cerevisiae it functions as a polarisation-specific docking factor.
Q#13958 - 	CGI_10023612	superfamily	242889	422	490	2.42E-09	55.7111	cl02111	PCI superfamily	C	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#13963 - 	CGI_10023617	superfamily	246709	34	123	0.00512693	34.9505	cl14782	RNase_H superfamily	C	 - 	"RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription."
Q#13965 - 	CGI_10023619	superfamily	241622	254	335	1.18E-20	86.0814	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#13967 - 	CGI_10023621	superfamily	248458	166	525	2.83E-16	79.2801	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#13968 - 	CGI_10023622	superfamily	241563	60	95	0.00257223	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#13970 - 	CGI_10023624	superfamily	128778	40	153	0.00104924	37.6295	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#13970 - 	CGI_10023624	superfamily	110440	424	446	0.00491836	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#13971 - 	CGI_10023625	superfamily	109916	1302	1449	2.38E-29	117.158	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	412	559	2.85E-28	114.076	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	1009	1151	2.39E-25	105.602	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	1599	1743	1.17E-23	100.594	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	720	850	1.05E-20	92.12	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	1457	1594	2.66E-15	75.9416	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	111	244	2.85E-15	75.9416	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	1161	1298	7.95E-14	71.7044	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	258	408	8.15E-13	68.6228	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	1895	2026	1.54E-12	67.8524	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	565	713	2.85E-12	67.082	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	858	971	1.07E-07	52.8296	cl03002	CIMR superfamily	C	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	1750	1887	2.45E-05	45.1256	cl03002	CIMR superfamily	 - 	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	2203	2243	0.000547022	41.2736	cl03002	CIMR superfamily	C	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13971 - 	CGI_10023625	superfamily	109916	12	102	0.00212965	39.3476	cl03002	CIMR superfamily	N	 - 	Cation-independent mannose-6-phosphate receptor repeat; The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Q#13972 - 	CGI_10023626	superfamily	245213	622	658	5.98E-10	56.1058	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13972 - 	CGI_10023626	superfamily	245213	546	582	3.65E-09	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13972 - 	CGI_10023626	superfamily	245213	585	620	3.55E-08	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13972 - 	CGI_10023626	superfamily	245814	336	406	8.07E-07	47.4839	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13972 - 	CGI_10023626	superfamily	245213	660	695	2.94E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13972 - 	CGI_10023626	superfamily	245814	235	308	5.11E-05	42.0911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13972 - 	CGI_10023626	superfamily	241578	17	185	6.34E-33	125.964	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#13972 - 	CGI_10023626	superfamily	245213	193	228	0.000153004	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#13972 - 	CGI_10023626	superfamily	245814	509	543	0.00739163	35.747	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#13973 - 	CGI_10023627	superfamily	247780	364	501	3.66E-59	196.988	cl17226	NAD_bind_amino_acid_DH superfamily	C	 - 	"NAD(P) binding domain of amino acid dehydrogenase-like proteins; Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel  domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts."
Q#13973 - 	CGI_10023627	superfamily	247739	62	248	6.01E-27	107.324	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#13973 - 	CGI_10023627	superfamily	202408	244	341	8.58E-44	152.269	cl08368	ELFV_dehydrog_N superfamily	N	 - 	"Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Glu/Leu/Phe/Val dehydrogenase, dimerisation domain.  "
Q#13977 - 	CGI_10023631	superfamily	195146	24	120	1.43E-61	203.355	cl05674	PET superfamily	 - 	 - 	"PET ((Prickle Espinas Testin) domain is involved in protein-protein interactions; PET domain is involved in protein-protein interactions and is usually found in conjunction with LIM domain, which is also a protein-protein interaction domain. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. The PET domain has been found at the N-terminal of four known groups of proteins: prickle, testin, LIMPETin/LIM-9 and overexpressed breast tumor protein (OEBT). Prickle has been implicated in regulation of cell movement through its association with the Dishevelled (Dsh) protein in the planar cell polarity (PCP) pathway. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell contact areas, and at focal adhesion plaques. It interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin, and is involved in cell motility and adhesion events. Knockout mice experiments reveal tumor repressor function of Testin.  LIMPETin/LIM-9 contains an N-terminal PET domain and 6 LIM domains at the C-terminal.  In Schistosoma mansoni, where LIMPETin was first identified, it is down regulated in sexually mature adult females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator.  In C. elegans, LIM-9 may play a role in regulating the assembly and maintenance of the muscle A-band by forming a protein complex with SCPL-1 and UNC-89 and other proteins. OEBT displays a PET domain with two LIM domains, and is predicted to be localized in the nucleus with a possible role in cancer differentiation."
Q#13977 - 	CGI_10023631	superfamily	195146	197	272	2.28E-43	152.893	cl05674	PET superfamily	N	 - 	"PET ((Prickle Espinas Testin) domain is involved in protein-protein interactions; PET domain is involved in protein-protein interactions and is usually found in conjunction with LIM domain, which is also a protein-protein interaction domain. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. The PET domain has been found at the N-terminal of four known groups of proteins: prickle, testin, LIMPETin/LIM-9 and overexpressed breast tumor protein (OEBT). Prickle has been implicated in regulation of cell movement through its association with the Dishevelled (Dsh) protein in the planar cell polarity (PCP) pathway. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell contact areas, and at focal adhesion plaques. It interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin, and is involved in cell motility and adhesion events. Knockout mice experiments reveal tumor repressor function of Testin.  LIMPETin/LIM-9 contains an N-terminal PET domain and 6 LIM domains at the C-terminal.  In Schistosoma mansoni, where LIMPETin was first identified, it is down regulated in sexually mature adult females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator.  In C. elegans, LIM-9 may play a role in regulating the assembly and maintenance of the muscle A-band by forming a protein complex with SCPL-1 and UNC-89 and other proteins. OEBT displays a PET domain with two LIM domains, and is predicted to be localized in the nucleus with a possible role in cancer differentiation."
Q#13977 - 	CGI_10023631	superfamily	243050	343	398	7.43E-34	124.847	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13977 - 	CGI_10023631	superfamily	243050	403	461	1.26E-33	124.088	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13977 - 	CGI_10023631	superfamily	243050	280	338	3.88E-28	108.499	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13977 - 	CGI_10023631	superfamily	243050	128	186	3.88E-28	108.499	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#13980 - 	CGI_10023634	superfamily	246723	22	342	1.20E-173	499.743	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#13980 - 	CGI_10023634	superfamily	204144	356	500	1.58E-42	148.936	cl08525	Leuk-A4-hydro_C superfamily	 - 	 - 	"Leukotriene A4 hydrolase, C-terminal; Members of this family adopt a structure consisting of two layers of parallel alpha-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. They are required for the formation of a deep cleft harbouring the catalytic Zn2+ site in Leukotriene A4 hydrolase."
Q#13982 - 	CGI_10023636	superfamily	215754	214	305	1.36E-21	86.9236	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#13982 - 	CGI_10023636	superfamily	215754	117	208	9.62E-20	81.916	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#13982 - 	CGI_10023636	superfamily	215754	1	115	3.22E-16	71.9008	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#13983 - 	CGI_10023637	superfamily	150854	32	278	2.56E-51	172.599	cl10929	MRP-S22 superfamily	 - 	 - 	"Mitochondrial 28S ribosomal protein S22; This is the conserved N-terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them."
Q#13984 - 	CGI_10023638	superfamily	247905	336	458	2.62E-25	102.701	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#13984 - 	CGI_10023638	superfamily	247805	52	194	7.84E-19	84.3112	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#13985 - 	CGI_10023639	superfamily	151040	666	899	2.25E-96	304.244	cl11116	DUF2451 superfamily	 - 	 - 	Protein of unknown function C-terminus (DUF2451); This protein is found in eukaryotes but its function is not known. The C-terminal part of some members is DUF2450.
Q#13987 - 	CGI_10023641	superfamily	243109	219	422	4.12E-93	280.72	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#13987 - 	CGI_10023641	superfamily	243109	34	199	2.66E-70	221.784	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#13988 - 	CGI_10023642	superfamily	247099	48	423	2.16E-142	418.742	cl15845	MntH superfamily	 - 	 - 	Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]
Q#13989 - 	CGI_10023643	superfamily	243035	21	105	2.36E-15	66.8745	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#13990 - 	CGI_10023644	superfamily	248020	72	404	1.61E-41	152.619	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#13991 - 	CGI_10023645	superfamily	241580	360	433	1.14E-08	52.9414	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#13994 - 	CGI_10023648	superfamily	241754	17	153	3.65E-39	149.555	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#13995 - 	CGI_10023649	superfamily	216739	442	476	0.000236848	39.7234	cl03383	PC_rep superfamily	 - 	 - 	Proteasome/cyclosome repeat; Proteasome/cyclosome repeat.  
Q#13995 - 	CGI_10023649	superfamily	216739	689	720	0.00433191	36.2566	cl03383	PC_rep superfamily	 - 	 - 	Proteasome/cyclosome repeat; Proteasome/cyclosome repeat.  
Q#13996 - 	CGI_10023650	superfamily	243034	958	1057	4.76E-10	58.1604	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13996 - 	CGI_10023650	superfamily	243034	661	736	1.79E-07	50.4564	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13996 - 	CGI_10023650	superfamily	243034	1027	1122	8.32E-07	48.5304	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13996 - 	CGI_10023650	superfamily	243034	695	790	0.00380463	36.9744	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#13999 - 	CGI_10026546	superfamily	245598	137	333	1.22E-71	230.629	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#13999 - 	CGI_10026546	superfamily	247856	430	500	0.00013069	40.2237	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#13999 - 	CGI_10026546	superfamily	247856	475	527	0.000687749	38.2977	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#14000 - 	CGI_10026547	superfamily	245598	84	207	4.87E-28	109.291	cl11396	Patatin_and_cPLA2 superfamily	C	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#14000 - 	CGI_10026547	superfamily	244899	253	300	4.82E-05	41.3214	cl08302	S-100 superfamily	N	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#14001 - 	CGI_10026548	superfamily	241620	27	65	6.41E-08	43.798	cl00113	CRIB superfamily	 - 	 - 	"PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules."
Q#14002 - 	CGI_10026549	superfamily	241620	25	67	1.65E-15	70.7619	cl00113	CRIB superfamily	 - 	 - 	"PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules."
Q#14002 - 	CGI_10026549	superfamily	245201	183	477	3.87E-150	433.176	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14007 - 	CGI_10026554	superfamily	241742	893	1039	1.98E-41	150.443	cl00271	PI3Ka superfamily	 - 	 - 	"Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture."
Q#14007 - 	CGI_10026554	superfamily	246669	708	875	3.66E-32	124.778	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#14007 - 	CGI_10026554	superfamily	207610	513	599	8.62E-16	75.4429	cl02484	PI3K_rbd superfamily	 - 	 - 	"PI3-kinase family, ras-binding domain; Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding pfam00788 domains (unpublished observation)."
Q#14007 - 	CGI_10026554	superfamily	241623	1069	1129	2.80E-11	65.2938	cl00119	PI3Kc_like superfamily	C	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#14009 - 	CGI_10026556	superfamily	243034	601	702	2.62E-07	50.4564	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#14009 - 	CGI_10026556	superfamily	243034	240	333	1.53E-05	45.0636	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#14010 - 	CGI_10026557	superfamily	216152	141	421	5.51E-94	302.696	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#14011 - 	CGI_10026558	superfamily	216152	130	348	6.22E-63	206.396	cl02988	Glyco_transf_10 superfamily	C	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#14013 - 	CGI_10026560	superfamily	243035	25	112	5.92E-17	73.8081	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14013 - 	CGI_10026560	superfamily	243035	146	221	8.63E-10	53.3926	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14014 - 	CGI_10026561	superfamily	243035	204	300	2.00E-17	75.7341	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14014 - 	CGI_10026561	superfamily	245205	42	123	4.43E-08	49.1585	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#14015 - 	CGI_10026562	superfamily	241599	188	246	4.14E-22	86.9136	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#14018 - 	CGI_10026565	superfamily	241599	128	173	3.05E-21	83.832	cl00084	homeodomain superfamily	N	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#14020 - 	CGI_10026567	superfamily	215733	207	446	1.05E-39	148.482	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#14020 - 	CGI_10026567	superfamily	222006	569	605	6.21E-07	48.7578	cl16182	Hydrolase_like2 superfamily	N	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#14020 - 	CGI_10026567	superfamily	221564	1	113	2.11E-06	47.5915	cl13797	P5-ATPase superfamily	 - 	 - 	"P5-type ATPase cation transporter; This domain family is found in eukaryotes, and is typically between 110 and 126 amino acids in length. The family is found in association with pfam00122, pfam00702. P-type ATPases comprise a large superfamily of proteins, present in both prokaryotes and eukaryotes, that transport inorganic cations and other substrates across cell membranes."
Q#14020 - 	CGI_10026567	superfamily	243244	147	195	3.13E-05	43.293	cl02930	Cation_ATPase_N superfamily	N	 - 	"Cation transporter/ATPase, N-terminus; Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport."
Q#14020 - 	CGI_10026567	superfamily	226572	795	838	9.59E-05	42.546	cl18761	COG4087 superfamily	NC	 - 	Soluble P-type ATPase [General function prediction only]
Q#14021 - 	CGI_10026568	superfamily	241874	40	620	0	590.305	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#14022 - 	CGI_10026569	superfamily	241564	1103	1171	4.50E-22	92.3287	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#14022 - 	CGI_10026569	superfamily	241564	729	796	2.54E-18	81.5431	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#14023 - 	CGI_10026570	superfamily	247792	110	151	3.29E-11	55.0784	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#14024 - 	CGI_10026571	superfamily	217293	11	171	1.10E-29	114.267	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#14024 - 	CGI_10026571	superfamily	202474	222	281	0.000449016	39.9445	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#14025 - 	CGI_10026572	superfamily	118686	105	212	1.12E-22	90.2385	cl10855	LOH1CR12 superfamily	 - 	 - 	Tumour suppressor protein; This is a region of 130 amino acids that is the most conserved region of hypothetical proteins involved in loss of heterozygosity and thus tumour suppression. The exact function is not known.
Q#14026 - 	CGI_10026573	superfamily	247875	88	274	3.92E-36	128.935	cl17321	2OG-FeII_Oxy_2 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; 2OG-Fe(II) oxygenase superfamily.  
Q#14029 - 	CGI_10026576	superfamily	221296	14	1682	0	1053.46	cl13353	DUF3414 superfamily	 - 	 - 	Protein of unknown function (DUF3414); This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 764 to 2011 amino acids in length. This protein has a conserved LLG sequence motif.
Q#14031 - 	CGI_10015197	superfamily	243189	66	148	4.31E-30	107.015	cl02793	Cyt_c_Oxidase_Va superfamily	N	 - 	"Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios."
Q#14034 - 	CGI_10015200	superfamily	248472	49	160	6.17E-32	111.972	cl17918	Ribosomal_P1_P2_L12p superfamily	 - 	 - 	"Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have two copies each of P1 and P2 (two heterodimers). Bacteria may have four or six copies (two or three homodimers), depending on the species. As in bacteria, the stalk is crucial for binding of initiation, elongation, and release factors in eukaryotes and archaea."
Q#14035 - 	CGI_10015201	superfamily	204614	1	127	5.77E-39	129.691	cl12769	Med21 superfamily	 - 	 - 	"Subunit 21 of Mediator complex; Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator."
Q#14036 - 	CGI_10015202	superfamily	206009	356	421	2.34E-35	131.136	cl16430	Clathrin_H_link superfamily	 - 	 - 	"Clathrin-H-link; This short domain is found on clathrins, and often appears on proteins directly downstream from the Clathrin-link domain pfam09268."
Q#14036 - 	CGI_10015202	superfamily	150065	331	354	1.40E-05	44.4544	cl07778	Clathrin-link superfamily	 - 	 - 	"Clathrin, heavy-chain linker; Members of this family adopt a structure consisting of alpha-alpha superhelix. They are predominantly found in clathrin, where they act as a heavy-chain linker domain."
Q#14036 - 	CGI_10015202	superfamily	216475	256	288	0.00211362	37.9117	cl03194	Clathrin_propel superfamily	 - 	 - 	"Clathrin propeller repeat; Clathrin is the scaffold protein of the basket-like coat that surrounds coated vesicles. The soluble assembly unit, a triskelion, contains three heavy chains and three light chains in an extended three-legged structure. Each leg contains one heavy and one light chain. The N-terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller."
Q#14036 - 	CGI_10015202	superfamily	216475	19	56	0.00648526	36.3709	cl03194	Clathrin_propel superfamily	 - 	 - 	"Clathrin propeller repeat; Clathrin is the scaffold protein of the basket-like coat that surrounds coated vesicles. The soluble assembly unit, a triskelion, contains three heavy chains and three light chains in an extended three-legged structure. Each leg contains one heavy and one light chain. The N-terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller."
Q#14036 - 	CGI_10015202	superfamily	216475	296	330	0.00702617	36.3709	cl03194	Clathrin_propel superfamily	 - 	 - 	"Clathrin propeller repeat; Clathrin is the scaffold protein of the basket-like coat that surrounds coated vesicles. The soluble assembly unit, a triskelion, contains three heavy chains and three light chains in an extended three-legged structure. Each leg contains one heavy and one light chain. The N-terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller."
Q#14037 - 	CGI_10015203	superfamily	246918	87	134	8.09E-08	47.9667	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14040 - 	CGI_10015206	superfamily	241886	1	236	1.53E-71	222.434	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#14041 - 	CGI_10015207	superfamily	241886	11	220	1.05E-71	222.434	cl00470	Aldo_ket_red superfamily	C	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#14042 - 	CGI_10015208	superfamily	241886	233	507	6.50E-86	269.429	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#14042 - 	CGI_10015208	superfamily	241886	1	232	1.54E-66	218.968	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#14043 - 	CGI_10015209	superfamily	241886	11	269	2.59E-88	267.118	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#14044 - 	CGI_10015210	superfamily	199575	1	116	1.06E-52	166.246	cl15439	BTG superfamily	 - 	 - 	BTG family; BTG family.  
Q#14045 - 	CGI_10015211	superfamily	218891	9	262	1.40E-22	97.0698	cl05564	Ins_P5_2-kin superfamily	C	 - 	"Inositol-pentakisphosphate 2-kinase; This is a family of inositol-pentakisphosphate 2-kinases (EC 2.7.1.158) (also known as inositol 1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5 2-kinase) and InsP5 2-kinase). This enzyme phosphorylates Ins(1,3,4,5,6)P5 to form Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, nonhomologous end-joining, endocytosis and ion channel regulation."
Q#14045 - 	CGI_10015211	superfamily	218891	418	502	1.37E-07	52.0015	cl05564	Ins_P5_2-kin superfamily	N	 - 	"Inositol-pentakisphosphate 2-kinase; This is a family of inositol-pentakisphosphate 2-kinases (EC 2.7.1.158) (also known as inositol 1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5 2-kinase) and InsP5 2-kinase). This enzyme phosphorylates Ins(1,3,4,5,6)P5 to form Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, nonhomologous end-joining, endocytosis and ion channel regulation."
Q#14046 - 	CGI_10015212	superfamily	241563	74	112	8.09E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14047 - 	CGI_10015213	superfamily	241563	65	100	0.00120971	35.726	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14047 - 	CGI_10015213	superfamily	242730	161	239	0.0024874	36.0851	cl01825	Phage_Mu_Gam superfamily	C	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#14049 - 	CGI_10015215	superfamily	110440	92	119	0.00281364	32.3797	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14050 - 	CGI_10015216	superfamily	241563	62	102	0.000251731	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14054 - 	CGI_10001871	superfamily	219275	12	344	2.11E-101	310.821	cl06188	ORC3_N superfamily	 - 	 - 	Origin recognition complex (ORC) subunit 3 N-terminus; This family represents the N-terminus (approximately 300 residues) of subunit 3 of the eukaryotic origin recognition complex (ORC). Origin recognition complex (ORC) is composed of six subunits that are essential for cell viability. They collectively bind to the autonomously replicating sequence (ARS) in a sequence-specific manner and lead to the chromatin loading of other replication factors that are essential for initiation of DNA replication.
Q#14055 - 	CGI_10001357	superfamily	247916	68	171	2.33E-07	49.3214	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#14055 - 	CGI_10001357	superfamily	242215	128	287	0.00571213	37.6485	cl00949	Acetyltransf_2 superfamily	N	 - 	"N-acetyltransferase; Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30kDa. It facilitates the transfer of an acetyl group from Acetyl Coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (M. tuberculosis, M. smegmatis etc) to man. It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat Tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid."
Q#14056 - 	CGI_10001651	superfamily	241554	3	104	3.97E-21	88.0963	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#14056 - 	CGI_10001651	superfamily	241554	161	292	2.25E-07	48.806	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#14059 - 	CGI_10002364	superfamily	247805	35	181	1.21E-08	51.5692	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#14061 - 	CGI_10027425	superfamily	221744	35	299	1.07E-22	95.1954	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#14063 - 	CGI_10027427	superfamily	221744	308	557	8.45E-07	49.7419	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#14071 - 	CGI_10027437	superfamily	247792	75	122	5.12E-08	47.8256	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#14072 - 	CGI_10027438	superfamily	222324	56	144	3.56E-14	64.3354	cl16352	zf-3CxxC superfamily	 - 	 - 	Zinc-binding domain; This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue.
Q#14073 - 	CGI_10027439	superfamily	117982	61	95	0.000142179	36.9981	cl09683	CFC superfamily	 - 	 - 	"Cripto_Frl-1_Cryptic (CFC); CFC domain is one half of the membrane protein Cripto, a protein overexpressed in many tumours and structurally similar to the C-terminal extracellular portions of Jagged 1 and Jagged 2. CFC is approx 40-residues long, compacted by three internal disulphide bridges, and binds Alk4 via a hydrophobic patch. CFC is structurally homologous to the VWFC-like domain."
Q#14075 - 	CGI_10027441	superfamily	216112	402	766	7.34E-71	243.743	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#14075 - 	CGI_10027441	superfamily	221913	1532	1741	2.75E-57	200.074	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#14075 - 	CGI_10027441	superfamily	221913	2634	2745	1.82E-27	113.404	cl18626	AAA_12 superfamily	N	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#14075 - 	CGI_10027441	superfamily	222258	1484	1521	4.44E-05	45.6368	cl18656	AAA_30 superfamily	NC	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#14075 - 	CGI_10027441	superfamily	216112	2608	2635	0.000382127	43.8243	cl02964	RNB superfamily	C	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#14076 - 	CGI_10027442	superfamily	216112	516	720	1.38E-58	207.919	cl02964	RNB superfamily	C	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#14078 - 	CGI_10027444	superfamily	216112	10	368	1.15E-76	253.373	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#14079 - 	CGI_10027445	superfamily	221913	276	483	4.21E-60	198.533	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#14079 - 	CGI_10027445	superfamily	222258	216	297	1.17E-07	50.6444	cl18656	AAA_30 superfamily	N	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#14079 - 	CGI_10027445	superfamily	222258	28	62	3.09E-05	43.7108	cl18656	AAA_30 superfamily	C	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#14080 - 	CGI_10027446	superfamily	222592	23	103	6.06E-35	118.038	cl16705	Ribosomal_L18_c superfamily	 - 	 - 	Ribosomal L18 C-terminal region; This domain is the C-terminal end of ribosomal L18/L5 proteins.
Q#14082 - 	CGI_10027448	superfamily	241571	203	315	2.17E-22	94.0162	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14082 - 	CGI_10027448	superfamily	241613	165	199	1.29E-13	66.4613	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#14082 - 	CGI_10027448	superfamily	241571	461	570	1.42E-13	68.2078	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14082 - 	CGI_10027448	superfamily	243035	39	162	3.63E-10	58.4001	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14082 - 	CGI_10027448	superfamily	241571	339	449	3.55E-07	49.3331	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14082 - 	CGI_10027448	superfamily	243092	607	687	3.17E-05	45.4036	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14083 - 	CGI_10027449	superfamily	241571	166	278	3.64E-21	92.4754	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14083 - 	CGI_10027449	superfamily	243035	2	125	9.91E-11	61.8669	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14083 - 	CGI_10027449	superfamily	241568	762	816	3.34E-10	59.0136	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14083 - 	CGI_10027449	superfamily	241613	128	162	4.78E-09	55.2906	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#14083 - 	CGI_10027449	superfamily	245213	2189	2225	3.62E-08	52.639	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14083 - 	CGI_10027449	superfamily	245213	2559	2594	5.42E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14083 - 	CGI_10027449	superfamily	245213	2478	2516	3.28E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14083 - 	CGI_10027449	superfamily	245213	2518	2555	1.97E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14083 - 	CGI_10027449	superfamily	245213	2677	2706	6.76E-05	43.009	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14083 - 	CGI_10027449	superfamily	241568	986	1041	9.64E-05	42.8352	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14083 - 	CGI_10027449	superfamily	241568	1286	1341	0.000116124	42.8352	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14083 - 	CGI_10027449	superfamily	245213	2442	2476	0.000344723	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14083 - 	CGI_10027449	superfamily	245213	2072	2107	0.000470545	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14083 - 	CGI_10027449	superfamily	241568	820	863	0.00521634	37.8276	cl00043	CCP superfamily	C	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14083 - 	CGI_10027449	superfamily	241568	1120	1163	0.00915174	37.0572	cl00043	CCP superfamily	C	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14083 - 	CGI_10027449	superfamily	222049	2343	2427	7.43E-06	46.5631	cl16239	Mucin2_WxxW superfamily	 - 	 - 	"Mucin-2 protein WxxW repeating region; This family is repeating region found on mucins 2 and 5. The function is not known, but the repeat can be present in up to 32 copies, as in a member from Branchiostoma floridae. The region carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues."
Q#14083 - 	CGI_10027449	superfamily	111397	1550	1628	1.77E-05	45.4099	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#14083 - 	CGI_10027449	superfamily	241571	302	412	1.79E-05	45.8663	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14083 - 	CGI_10027449	superfamily	219525	1983	2019	0.000102206	42.7914	cl06646	GCC2_GCC3 superfamily	C	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#14083 - 	CGI_10027449	superfamily	111397	1630	1711	0.000154277	42.7135	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#14083 - 	CGI_10027449	superfamily	241578	1172	1211	0.000338763	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14083 - 	CGI_10027449	superfamily	241571	424	456	0.000478882	41.2439	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14083 - 	CGI_10027449	superfamily	221695	896	918	0.00177943	38.9754	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#14083 - 	CGI_10027449	superfamily	219525	1931	1976	0.00379193	38.169	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#14084 - 	CGI_10027450	superfamily	242876	50	91	4.47E-06	41.6276	cl02092	Clat_adaptor_s superfamily	NC	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#14085 - 	CGI_10027451	superfamily	242406	230	370	9.49E-23	93.8101	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#14088 - 	CGI_10027454	superfamily	241675	1012	1221	5.50E-103	326.951	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#14088 - 	CGI_10027454	superfamily	241574	728	957	2.44E-81	267.915	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#14089 - 	CGI_10027455	superfamily	216347	6	387	1.81E-102	313.318	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#14090 - 	CGI_10027456	superfamily	145726	4	67	0.00312015	34.2434	cl08353	Cu_amine_oxidN2 superfamily	N	 - 	"Copper amine oxidase, N2 domain; This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ)."
Q#14091 - 	CGI_10027457	superfamily	247856	112	174	6.52E-22	84.9069	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#14091 - 	CGI_10027457	superfamily	247856	19	97	3.67E-14	63.7209	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#14092 - 	CGI_10027458	superfamily	241677	28	194	5.05E-64	198.25	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#14093 - 	CGI_10027459	superfamily	213401	701	746	6.72E-06	44.6661	cl17098	CASP8AP2 superfamily	 - 	 - 	"Caspase 8-associated protein 2 myb-like domain; This domain is the SANT/myb-like domain of Caspase 8-associated protein 2 (CASP8AP2) / GON-4 like proteins. CASP8AP2 (aka Flice-Associated Huge Protein (FLASH)) is implicated in numerous gene regulatory roles including roles in embryogenesis, oncogenesis, down-regulation of replication-dependent histone genes, regulation of Caspase 8 activity at the death-inducing signaling complex (DISC), and as a useful marker in leukemia prognosis. Gon-4 is critical in Caenorhabditis elegans gonadogenesis. Danio rerio GON4 is a regulator of gene expression in hematopoietic development, possibly by repressing expression. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#14093 - 	CGI_10027459	superfamily	202341	1	27	0.00172787	37.0687	cl07842	PAH superfamily	N	 - 	"Paired amphipathic helix repeat; This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions."
Q#14094 - 	CGI_10027460	superfamily	220692	47	346	4.77E-09	56.0585	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#14096 - 	CGI_10027462	superfamily	247044	15	155	1.73E-42	139.614	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14097 - 	CGI_10027463	superfamily	245304	151	448	6.73E-149	436.606	cl10459	Peptidases_S8_S53 superfamily	 - 	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#14097 - 	CGI_10027463	superfamily	201820	536	626	1.63E-29	112.719	cl08326	P_proprotein superfamily	 - 	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#14097 - 	CGI_10027463	superfamily	245304	411	487	5.18E-06	47.2874	cl10459	Peptidases_S8_S53 superfamily	N	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#14098 - 	CGI_10027464	superfamily	206050	24	121	1.36E-29	114.293	cl16449	KIAA1430 superfamily	 - 	 - 	KIAA1430 homologue; This is a family of KIAA1430 homologues. The function is not known.
Q#14098 - 	CGI_10027464	superfamily	207654	743	808	5.38E-10	57.0674	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#14098 - 	CGI_10027464	superfamily	207654	671	729	5.45E-09	53.9858	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#14098 - 	CGI_10027464	superfamily	207654	900	965	7.77E-05	41.6594	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#14098 - 	CGI_10027464	superfamily	207654	404	470	0.00916958	35.4962	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#14099 - 	CGI_10027465	superfamily	216653	55	216	1.24E-11	59.5331	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#14100 - 	CGI_10027466	superfamily	216653	795	932	4.14E-21	91.1194	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#14100 - 	CGI_10027466	superfamily	216653	57	221	3.57E-17	79.5635	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#14100 - 	CGI_10027466	superfamily	207627	583	675	1.18E-15	74.2131	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#14100 - 	CGI_10027466	superfamily	207627	500	558	9.08E-15	71.5119	cl02522	Calx-beta superfamily	N	 - 	Calx-beta domain; Calx-beta domain.  
Q#14102 - 	CGI_10027468	superfamily	243051	9	115	2.20E-16	74.3365	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#14102 - 	CGI_10027468	superfamily	243051	141	304	2.85E-16	73.9241	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#14103 - 	CGI_10027469	superfamily	192566	111	186	0.00604769	35.7432	cl18180	COG5 superfamily	C	 - 	"Golgi transport complex subunit 5; The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller, B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7."
Q#14105 - 	CGI_10027471	superfamily	110440	136	163	2.50E-05	41.2393	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14105 - 	CGI_10027471	superfamily	110440	187	215	0.000490166	37.3873	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14106 - 	CGI_10027472	superfamily	247041	54	318	4.70E-76	241.452	cl15692	CE4_SF superfamily	 - 	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#14107 - 	CGI_10027473	superfamily	247041	2	192	1.69E-58	190.221	cl15692	CE4_SF superfamily	N	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#14108 - 	CGI_10027474	superfamily	247041	230	349	1.06E-19	86.9871	cl15692	CE4_SF superfamily	C	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#14110 - 	CGI_10027476	superfamily	241592	39	127	1.80E-37	124.551	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#14112 - 	CGI_10027478	superfamily	241581	127	172	0.000778517	40.4474	cl00062	FHA superfamily	N	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#14113 - 	CGI_10027479	superfamily	147570	1	189	1.45E-21	87.2698	cl09371	Siva superfamily	 - 	 - 	"Cd27 binding protein (Siva); Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1."
Q#14114 - 	CGI_10027480	superfamily	247799	167	215	7.43E-06	41.7786	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#14115 - 	CGI_10027481	superfamily	247744	9	194	5.01E-56	178.576	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#14120 - 	CGI_10027486	superfamily	245194	29	107	0.00287962	35.5465	cl09909	Cas8a1_I-A superfamily	N	 - 	"CRISPR/Cas system-associated protein Cas8a1; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as CXXC_CXXC family"
Q#14126 - 	CGI_10027494	superfamily	243072	48	171	1.60E-39	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14126 - 	CGI_10027494	superfamily	243072	18	50	0.000530506	35.9928	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14127 - 	CGI_10012699	superfamily	248097	7	69	1.29E-08	46.8746	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#14128 - 	CGI_10012700	superfamily	245226	14	181	4.98E-21	86.5856	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#14131 - 	CGI_10012703	superfamily	242406	42	113	4.31E-08	48.3565	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#14140 - 	CGI_10012712	superfamily	243134	444	567	1.38E-19	87.3196	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#14140 - 	CGI_10012712	superfamily	243134	938	1072	8.39E-19	85.0084	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#14140 - 	CGI_10012712	superfamily	243134	313	421	1.24E-17	81.5416	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#14140 - 	CGI_10012712	superfamily	243134	1090	1201	1.66E-12	66.5188	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#14140 - 	CGI_10012712	superfamily	205157	1339	1374	6.37E-08	50.9991	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#14140 - 	CGI_10012712	superfamily	205157	172	208	8.34E-06	44.8359	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#14140 - 	CGI_10012712	superfamily	205157	890	926	6.21E-05	42.5247	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#14140 - 	CGI_10012712	superfamily	205157	1378	1416	0.000813473	39.0579	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#14140 - 	CGI_10012712	superfamily	205157	811	842	0.00219967	37.9023	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#14143 - 	CGI_10012715	superfamily	242564	58	155	3.60E-38	127.761	cl01534	NDUFA12 superfamily	 - 	 - 	"NADH ubiquinone oxidoreductase subunit NDUFA12; This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologues. The family also contains a second related eukaryotic protein of unknown function, ."
Q#14144 - 	CGI_10012716	superfamily	243072	115	241	4.89E-28	110.166	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14144 - 	CGI_10012716	superfamily	243072	368	474	1.73E-23	97.069	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14144 - 	CGI_10012716	superfamily	247057	553	596	4.59E-10	56.9114	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#14145 - 	CGI_10012717	superfamily	215724	46	355	4.00E-167	472.489	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#14146 - 	CGI_10012718	superfamily	211407	12	485	0	944.125	cl16940	ST7 superfamily	 - 	 - 	"Suppression of tumorigenicity 7; ST7 is a metazoan protein that behaves as a tumor suppressor in human cancer cells. It appears to localize to the cytoplasm and plasma membrane, and may mediate tumor suppression by regulating genes that are involved in oncogenic pathways and/or maintain cellular structure. It has been suggested that the suppression of tumorigenicity is associated with a function in mediating the remodeling of the extracellular matrix. However, somatic mutations of ST7 have not been observed as being commonly associated with molecular pathogenesis in various human neoplasias."
Q#14148 - 	CGI_10012720	superfamily	248345	892	1051	1.95E-38	143.548	cl17791	SAC3_GANP superfamily	 - 	 - 	"SAC3/GANP/Nin1/mts3/eIF-3 p25 family; This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits."
Q#14148 - 	CGI_10012720	superfamily	247723	561	632	2.11E-20	88.5935	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#14148 - 	CGI_10012720	superfamily	222274	18	88	5.31E-06	47.0956	cl18658	Nucleoporin_FG superfamily	C	 - 	"Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145."
Q#14148 - 	CGI_10012720	superfamily	222274	313	400	0.00490019	37.4656	cl18658	Nucleoporin_FG superfamily	 - 	 - 	"Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145."
Q#14149 - 	CGI_10025696	superfamily	241874	182	482	0.00351796	39.5922	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#14151 - 	CGI_10025698	superfamily	247750	136	449	3.01E-156	449.131	cl17196	E1_enzyme_family superfamily	 - 	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#14152 - 	CGI_10025699	superfamily	243161	5	69	4.88E-10	54.3634	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#14157 - 	CGI_10025704	superfamily	247794	5	310	1.32E-125	364.408	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#14158 - 	CGI_10025705	superfamily	245602	262	561	1.56E-153	448.973	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#14159 - 	CGI_10025706	superfamily	241721	50	329	5.16E-107	327.266	cl00246	MTHFR superfamily	 - 	 - 	"Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease."
Q#14162 - 	CGI_10025709	superfamily	219119	45	93	5.45E-23	86.1609	cl05928	SPC12 superfamily	N	 - 	"Microsomal signal peptidase 12 kDa subunit (SPC12); This family consists of several microsomal signal peptidase 12 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 12 kDa subunit (SPC12)."
Q#14163 - 	CGI_10025710	superfamily	241575	1564	1628	0.00855099	36.4815	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#14163 - 	CGI_10025710	superfamily	202558	1	228	2.21E-118	374.373	cl03915	XRN_N superfamily	 - 	 - 	"XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalyzing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus."
Q#14167 - 	CGI_10025714	superfamily	242905	49	150	3.25E-56	173.566	cl02150	TAF10 superfamily	 - 	 - 	"The TATA Binding Protein (TBP) Associated Factor 10; The TATA Binding Protein (TBP) Associated Factor 10 (TAF 10) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of the seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. Several hypotheses are proposed for TAF functions, such as serving as activator-binding sites, being involved in core-promoter recognition, or to perform an essential catalytic activity. Each TAF - with the help of a specific activator - is required only for the expression of a subset of genes, and TAFs are not universally involved in transcription such as the GTFs. TAF10 regulates genes that are important for cell cycle progression and cell morphology. A lack of TAF10 leads to cell cycle arrest and cell death by apoptosis in mouse. In both yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF10 is part of other transcription regulatory multiprotein complexes (e.g., SAGA, TBP-free TAF-containing complex [TFTC], STAGA, and PCAF/GCN5). Several TAFs interact via histone-fold motifs. The histone fold (HFD) is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. The minimal HFD contains three alpha-helices linked by two loops. The HFD is found in core histones, TAFs and many other transcription factors. Five HF-containing TAF pairs have been described in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10."
Q#14168 - 	CGI_10025715	superfamily	243175	71	181	6.50E-45	147.755	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#14168 - 	CGI_10025715	superfamily	241832	12	63	7.12E-08	47.5665	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14171 - 	CGI_10025718	superfamily	248458	86	257	7.59E-20	89.6805	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14171 - 	CGI_10025718	superfamily	248458	315	506	1.26E-09	58.4793	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14172 - 	CGI_10025719	superfamily	199156	60	74	0.00329169	32.0409	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#14173 - 	CGI_10025720	superfamily	241913	219	333	3.92E-06	45.3124	cl00509	hot_dog superfamily	N	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#14173 - 	CGI_10025720	superfamily	241913	133	206	2.48E-05	42.5933	cl00509	hot_dog superfamily	C	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#14173 - 	CGI_10025720	superfamily	241913	353	426	0.000241956	39.5117	cl00509	hot_dog superfamily	C	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#14174 - 	CGI_10025721	superfamily	243054	692	903	1.78E-44	163.385	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	1668	1879	2.02E-40	151.444	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	153	374	5.05E-38	144.511	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	481	690	3.23E-36	139.503	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	271	480	9.04E-35	135.266	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	1457	1667	2.27E-34	134.11	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	1191	1339	2.86E-29	119.087	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	1881	2088	3.43E-29	118.702	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	247683	984	1036	1.12E-28	112.193	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#14174 - 	CGI_10025721	superfamily	243054	1987	2202	1.24E-19	90.5827	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	2101	2315	7.54E-13	69.3967	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	247856	2330	2398	1.54E-12	66.0321	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#14174 - 	CGI_10025721	superfamily	243054	15	122	1.37E-09	59.3816	cl02488	SPEC superfamily	N	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	1054	1190	4.41E-09	57.8408	cl02488	SPEC superfamily	N	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14174 - 	CGI_10025721	superfamily	243054	903	962	1.17E-09	58.4842	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14175 - 	CGI_10025722	superfamily	248012	487	618	3.31E-23	96.1884	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#14175 - 	CGI_10025722	superfamily	214507	375	428	1.91E-06	45.4988	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#14176 - 	CGI_10025723	superfamily	248012	52	183	4.14E-20	82.3213	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#14177 - 	CGI_10025724	superfamily	248012	52	183	4.80E-26	98.1144	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#14183 - 	CGI_10025730	superfamily	241593	383	535	3.96E-08	52.2638	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#14184 - 	CGI_10025731	superfamily	247743	335	452	0.00502898	37.5644	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#14184 - 	CGI_10025731	superfamily	243034	1079	1198	0.00660902	36.5892	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#14187 - 	CGI_10025734	superfamily	217473	275	436	2.72E-18	84.3389	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#14189 - 	CGI_10025737	superfamily	219911	224	432	1.07E-71	232.252	cl07255	PRP3 superfamily	 - 	 - 	pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa.
Q#14189 - 	CGI_10025737	superfamily	219080	459	590	3.15E-35	128.998	cl05851	DUF1115 superfamily	 - 	 - 	Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function.
Q#14190 - 	CGI_10025738	superfamily	243119	260	304	0.000212169	38.9541	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#14190 - 	CGI_10025738	superfamily	243119	403	447	0.000402325	38.1837	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#14190 - 	CGI_10025738	superfamily	243119	75	114	0.00365353	35.4974	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#14192 - 	CGI_10025740	superfamily	243119	216	260	2.05E-05	40.8801	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#14195 - 	CGI_10025743	superfamily	242428	1	291	7.84E-49	165.249	cl01315	NRDE superfamily	 - 	 - 	"NRDE protein; In eukaryotes this family is predicted to play a role in protein secretion and Golgi organisation. In plants this family includes Solanum habrochaites Cwp, which is involved in water permeability in the cuticles of fruit. Mouse T10 has been found to be expressed during early embryogenesis in mice. This protein contains a conserved NRDE motif."
Q#14196 - 	CGI_10025744	superfamily	245814	108	184	1.77E-07	46.5607	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14198 - 	CGI_10025746	superfamily	217518	161	266	1.07E-37	131.203	cl08388	CBM_21 superfamily	 - 	 - 	"Putative phosphatase regulatory subunit; This family consists of several eukaryotic proteins that are thought to be involved in the regulation of glycogen metabolism. For instance, the mouse PTG protein has been shown to interact with glycogen synthase, phosphorylase kinase, phosphorylase a: these three enzymes have key roles in the regulation of glycogen metabolism. PTG also binds the catalytic subunit of protein phosphatase 1 (PP1C) and localises it to glycogen. Subsets of similar interactions have been observed with several other members of this family, such as the yeast PIG1, PIG2, GAC1 and GIP2 proteins. While the precise function of these proteins is not known, they may serve a scaffold function, bringing together the key enzymes in glycogen metabolism. This family is a carbohydrate binding domain."
Q#14199 - 	CGI_10025747	superfamily	246936	634	748	4.63E-20	87.546	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#14199 - 	CGI_10025747	superfamily	246918	177	229	9.12E-13	64.9155	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14199 - 	CGI_10025747	superfamily	246918	241	300	2.80E-09	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14199 - 	CGI_10025747	superfamily	246918	305	364	3.07E-09	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14199 - 	CGI_10025747	superfamily	246918	125	165	0.00109112	38.3367	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14200 - 	CGI_10002491	superfamily	247684	37	459	1.67E-84	272.229	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14201 - 	CGI_10002589	superfamily	218847	24	170	4.90E-38	137.631	cl18479	CDO_I superfamily	 - 	 - 	Cysteine dioxygenase type I; Cysteine dioxygenase type I (EC:1.13.11.20) converts cysteine to cysteinesulphinic acid and is the rate-limiting step in sulphate production.
Q#14202 - 	CGI_10002512	superfamily	149426	132	281	2.36E-27	105.556	cl18038	SEFIR superfamily	 - 	 - 	"SEFIR domain; This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways."
Q#14203 - 	CGI_10002513	superfamily	241563	68	109	7.39E-07	46.3184	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14203 - 	CGI_10002513	superfamily	241563	21	59	0.00912112	33.992	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14204 - 	CGI_10002514	superfamily	247044	267	352	1.18E-22	90.3863	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14204 - 	CGI_10002514	superfamily	247044	121	169	1.18E-20	85.3524	cl15697	ADF_gelsolin superfamily	NC	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14204 - 	CGI_10002514	superfamily	247044	163	231	6.22E-14	66.492	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14205 - 	CGI_10002247	superfamily	248097	162	285	5.10E-29	108.121	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#14205 - 	CGI_10002247	superfamily	203593	26	109	0.00169368	36.8946	cl18243	Mod_r superfamily	C	 - 	"Modifier of rudimentary (Mod(r)) protein; This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic, and both of these regions are represented in this family. Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB). The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37). The mammalian homologue of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors."
Q#14210 - 	CGI_10002016	superfamily	247684	10	430	1.67E-97	305.356	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14217 - 	CGI_10003215	superfamily	242406	514	546	8.96E-06	44.5045	cl01271	DUF1768 superfamily	NC	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#14222 - 	CGI_10012091	superfamily	242181	7	324	6.78E-96	290.688	cl00900	Ldh_2 superfamily	 - 	 - 	"Malate/L-lactate dehydrogenase; This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyzes the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyzes the reactions: (S)-malate + NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively."
Q#14225 - 	CGI_10012094	superfamily	247755	5	150	6.73E-65	220.907	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#14225 - 	CGI_10012094	superfamily	247755	1056	1159	3.40E-64	218.981	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#14225 - 	CGI_10012094	superfamily	244201	519	560	4.94E-06	46.1268	cl05797	SMC_hinge superfamily	N	 - 	SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.
Q#14226 - 	CGI_10012095	superfamily	241645	182	250	1.09E-05	44.1802	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#14227 - 	CGI_10012096	superfamily	247743	1939	2035	9.13E-05	44.4443	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#14227 - 	CGI_10012096	superfamily	193256	2302	2563	1.90E-67	232.916	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#14227 - 	CGI_10012096	superfamily	193257	2949	3172	4.87E-51	183.648	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#14227 - 	CGI_10012096	superfamily	193253	2580	2917	4.86E-39	152.498	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#14227 - 	CGI_10012096	superfamily	247743	1605	1749	6.42E-06	47.6752	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#14229 - 	CGI_10012098	superfamily	245201	21	261	7.25E-78	240.885	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14230 - 	CGI_10012099	superfamily	243051	317	465	1.66E-18	82.4257	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#14230 - 	CGI_10012099	superfamily	245206	35	244	3.99E-60	200.197	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#14230 - 	CGI_10012099	superfamily	241583	247	299	4.76E-06	46.311	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#14233 - 	CGI_10012102	superfamily	216363	449	528	4.47E-13	65.9546	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#14234 - 	CGI_10002939	superfamily	247762	122	259	1.43E-27	104.636	cl17208	intradiol_dioxygenase superfamily	 - 	 - 	"Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear non-heme iron enzymes that catalyze the oxygenation of catecholates to aliphatic acids via the cleavage of aromatic rings. The members are intradiol-cleaving enzymes which break the catechol C1-C2 bond and utilize Fe3+, as opposed to the extradiol-cleaving enzymes which break the C2-C3 or C1-C6 bond and utilize Fe2+ and Mn+. Catechol 1,2-dioxygenases are mostly homodimers with one catalytic ferric ion per monomer. Protocatechuate 3,4-dioxygenases form more diverse oligomers."
Q#14236 - 	CGI_10024133	superfamily	247743	195	353	1.10E-22	94.9055	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#14236 - 	CGI_10024133	superfamily	216502	398	561	5.71E-33	125.012	cl03209	Peptidase_M41 superfamily	 - 	 - 	Peptidase family M41; Peptidase family M41.  
Q#14237 - 	CGI_10024134	superfamily	243035	66	105	3.27E-08	51.8518	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14238 - 	CGI_10024135	superfamily	241546	553	672	4.47E-33	124.696	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14238 - 	CGI_10024135	superfamily	242146	710	838	0.00863963	37.3276	cl00859	Cytochrome_b_N superfamily	C	 - 	"Cytochrome b (N-terminus)/b6/petB:  Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms.  Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites.  The C-terminal portion of cytochrome b is described in a separate CD."
Q#14240 - 	CGI_10024137	superfamily	241594	406	761	3.31E-164	481.294	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#14240 - 	CGI_10024137	superfamily	246669	12	135	6.21E-60	199.07	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#14240 - 	CGI_10024137	superfamily	241647	164	193	2.51E-10	56.7674	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#14240 - 	CGI_10024137	superfamily	241647	316	346	4.37E-08	50.6042	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#14240 - 	CGI_10024137	superfamily	241647	268	297	2.55E-06	45.2114	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#14241 - 	CGI_10024138	superfamily	216239	79	417	0	528.415	cl18361	IRK superfamily	 - 	 - 	Inward rectifier potassium channel; Inward rectifier potassium channel.  
Q#14243 - 	CGI_10024140	superfamily	243072	371	499	4.61E-20	85.8982	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14244 - 	CGI_10024141	superfamily	246974	32	375	1.86E-122	363.839	cl15477	diphth2_R superfamily	 - 	 - 	"diphthamide biosynthesis enzyme Dph1/Dph2 domain; Archaea and Eukaryotes, but not Eubacteria, share the property of having a covalently modified residue, 2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine, as a part of a cytosolic protein. The modified His, termed diphthamide, is part of translation elongation factor EF-2 and is the site for ADP-ribosylation by diphtheria toxin. This model includes both Dph1 and Dph2 from Saccharomyces cerevisiae, although only Dph2 is found in the Archaea (see TIGR03682). Dph2 has been shown to act analogously to the radical SAM (rSAM) family (pfam04055), with 4Fe-4S-assisted cleavage of S-adenosylmethionine to create a free radical, but a different organic radical than in rSAM."
Q#14246 - 	CGI_10024143	superfamily	245226	185	328	1.72E-62	202.33	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#14247 - 	CGI_10024144	superfamily	245226	34	224	5.82E-71	228.259	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#14247 - 	CGI_10024144	superfamily	219199	486	530	6.27E-10	55.464	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#14248 - 	CGI_10024145	superfamily	243066	9	105	1.45E-23	95.4504	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#14248 - 	CGI_10024145	superfamily	198867	110	210	1.49E-19	84.1323	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#14248 - 	CGI_10024145	superfamily	243146	342	385	3.27E-07	47.6562	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14248 - 	CGI_10024145	superfamily	243146	390	433	0.000962759	37.2558	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14249 - 	CGI_10024146	superfamily	248458	51	229	2.10E-17	82.7469	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14249 - 	CGI_10024146	superfamily	248458	471	646	5.46E-17	81.5913	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14250 - 	CGI_10024147	superfamily	241625	12	116	2.04E-08	47.9705	cl00123	PROF superfamily	 - 	 - 	"Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway."
Q#14251 - 	CGI_10024148	superfamily	247736	2465	2508	3.26E-06	47.2705	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#14251 - 	CGI_10024148	superfamily	149273	103	305	4.02E-80	265.705	cl18036	DOT1 superfamily	 - 	 - 	Histone methylation protein DOT1; The DOT1 domain regulates gene expression by methylating histone H3. H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast.
Q#14251 - 	CGI_10024148	superfamily	247999	1735	1779	0.00106952	39.5026	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#14253 - 	CGI_10024150	superfamily	247724	10	160	1.44E-73	222.702	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#14254 - 	CGI_10024151	superfamily	243082	106	474	2.85E-123	365.115	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#14254 - 	CGI_10024151	superfamily	241645	8	74	3.63E-06	44.8288	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#14259 - 	CGI_10024156	superfamily	245201	65	319	1.63E-47	162.406	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14260 - 	CGI_10024157	superfamily	207716	60	92	1.59E-09	50.3334	cl02754	zf-LITAF-like superfamily	N	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14260 - 	CGI_10024157	superfamily	207716	94	127	4.77E-09	48.7927	cl02754	zf-LITAF-like superfamily	N	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14261 - 	CGI_10024158	superfamily	207716	54	127	1.81E-17	71.9046	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14262 - 	CGI_10024159	superfamily	207716	45	118	5.55E-16	67.6674	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14263 - 	CGI_10024160	superfamily	207716	4	72	3.75E-17	69.2082	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14264 - 	CGI_10024161	superfamily	207716	57	120	5.34E-23	91.935	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14264 - 	CGI_10024161	superfamily	215754	130	224	1.08E-22	91.546	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14264 - 	CGI_10024161	superfamily	215754	236	332	8.69E-19	81.1456	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14264 - 	CGI_10024161	superfamily	215754	342	426	1.30E-15	72.286	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14265 - 	CGI_10024162	superfamily	207716	54	127	4.01E-23	86.9274	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14266 - 	CGI_10024163	superfamily	207716	26	99	1.32E-09	50.3334	cl02754	zf-LITAF-like superfamily	 - 	 - 	"LITAF-like zinc ribbon domain; Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure."
Q#14269 - 	CGI_10024166	superfamily	238076	43	170	2.78E-82	255.422	cl18938	PAX superfamily	 - 	 - 	Paired Box domain
Q#14270 - 	CGI_10024167	superfamily	247736	85	158	1.54E-08	48.8042	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#14273 - 	CGI_10024170	superfamily	192367	50	198	4.30E-73	234.422	cl10739	FPL superfamily	 - 	 - 	Uncharacterized conserved protein; This entry represents an N-terminal region of approximately 150 residues of a family of proteins of unknown function. It contains a highly conserved FPL motif.
Q#14276 - 	CGI_10024173	superfamily	243092	346	672	2.08E-29	118.206	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14278 - 	CGI_10024175	superfamily	219619	89	141	1.40E-13	64.9215	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#14278 - 	CGI_10024175	superfamily	219619	177	256	4.29E-10	55.2915	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#14281 - 	CGI_10024178	superfamily	222451	125	217	4.51E-20	85.0728	cl16470	DUF4209 superfamily	 - 	 - 	"Domain of unknown function (DUF4209); This short domain is found in bacteria and eukaryotes, though not in yeasts or Archaea. It carries a highly conserved RNxxxHG sequence motif."
Q#14287 - 	CGI_10024184	superfamily	148282	29	210	4.73E-17	78.1026	cl05873	p31comet superfamily	 - 	 - 	"Mad1 and Cdc20-bound-Mad2 binding; This family is involved in the cell-cycle surveillance mechanism called the spindle checkpoint. This mechanism monitors the proper bipolar attachment of sister chromatids to spindle microtubules and ensures the fidelity of chromosome segregation during mitosis. A key player in mitosis is Mad2, and Mad2 exhibits an unusual two-state behaviour. A Mad1-Mad2 core complex recruits cytosolic Mad2 to kinetochores through Mad2 dimerisation and converts Mad2 to a conformer amenable to Cdc20 binding. p31comet inactivates the checkpoint by binding to Mad1- or Cdc20-bound Mad2 in such a way as to stop Mad2 activation and to promote the dissociation of the Mad2-Cdc20 complex."
Q#14289 - 	CGI_10024186	superfamily	247724	20	247	5.77E-104	327.651	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#14289 - 	CGI_10024186	superfamily	243183	976	1054	5.20E-36	132.664	cl02785	Elongation_Factor_C superfamily	 - 	 - 	"Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p.  This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain.  EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown."
Q#14289 - 	CGI_10024186	superfamily	243187	673	876	2.12E-35	134.235	cl02789	EFG_like_IV superfamily	C	 - 	"Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm."
Q#14289 - 	CGI_10024186	superfamily	243185	485	586	6.92E-26	104.182	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#14289 - 	CGI_10024186	superfamily	243187	951	979	0.00129132	39.861	cl02789	EFG_like_IV superfamily	N	 - 	"Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm."
Q#14290 - 	CGI_10024187	superfamily	248030	245	772	7.29E-147	443.353	cl17476	Glyco_transf_7C superfamily	 - 	 - 	"N-terminal domain of galactosyltransferase; This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalyzed reaction."
Q#14290 - 	CGI_10024187	superfamily	190308	93	275	9.12E-10	58.4843	cl18163	Fringe superfamily	C	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#14291 - 	CGI_10024188	superfamily	243078	2	114	2.42E-20	88.4233	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#14292 - 	CGI_10024189	superfamily	248458	144	187	0.00103481	37.6785	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14293 - 	CGI_10024190	superfamily	248458	129	239	1.24E-07	52.3161	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14293 - 	CGI_10024190	superfamily	248458	380	464	0.000245251	41.9157	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14296 - 	CGI_10024193	superfamily	248458	93	218	2.44E-09	57.7089	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14296 - 	CGI_10024193	superfamily	248458	315	479	0.00118621	39.6045	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14297 - 	CGI_10024194	superfamily	241607	165	197	7.38E-07	45.3386	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#14297 - 	CGI_10024194	superfamily	241607	88	123	1.97E-06	43.7978	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#14297 - 	CGI_10024194	superfamily	241607	235	274	0.00689932	33.7826	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#14300 - 	CGI_10024197	superfamily	243175	2	41	5.63E-06	38.7878	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#14305 - 	CGI_10015492	superfamily	247684	34	397	0	746.057	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14306 - 	CGI_10015493	superfamily	218246	7	137	5.51E-43	140.932	cl12301	OST3_OST6 superfamily	 - 	 - 	"OST3 / OST6 family; The proteins in this family are part of a complex of eight ER proteins that transfers core oligosaccharide from dolichol carrier to Asn-X-Ser/Thr motifs. This family includes both OST3 and OST6, each of which contains four predicted transmembrane helices. Disruption of OST3 and OST6 leads to a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation."
Q#14308 - 	CGI_10015495	superfamily	214531	838	877	2.16E-07	49.1373	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#14308 - 	CGI_10015495	superfamily	214531	211	252	5.23E-05	42.2037	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#14308 - 	CGI_10015495	superfamily	214531	790	834	0.000331784	39.8925	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#14308 - 	CGI_10015495	superfamily	241578	314	356	0.00304586	39.2904	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14308 - 	CGI_10015495	superfamily	214531	134	155	0.00305955	37.1961	cl18310	LY superfamily	NC	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#14313 - 	CGI_10015500	superfamily	243035	5	115	0.00194385	36.0586	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14314 - 	CGI_10015501	superfamily	244881	962	1261	2.39E-131	411.201	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#14314 - 	CGI_10015501	superfamily	215788	746	837	7.19E-35	130.377	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#14314 - 	CGI_10015501	superfamily	241977	1448	1554	4.38E-27	108.675	cl00607	PUA superfamily	 - 	 - 	"PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain."
Q#14314 - 	CGI_10015501	superfamily	203720	1364	1441	1.21E-24	101.086	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#14314 - 	CGI_10015501	superfamily	216731	57	148	6.46E-16	75.7583	cl12258	A2M_N superfamily	 - 	 - 	MG2 domain; This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin.
Q#14316 - 	CGI_10015503	superfamily	243072	28	143	3.12E-34	124.803	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14316 - 	CGI_10015503	superfamily	245201	204	469	3.88E-36	134.586	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14317 - 	CGI_10015504	superfamily	241677	7	173	2.28E-93	278.757	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#14317 - 	CGI_10015504	superfamily	243034	272	336	6.84E-12	61.242	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#14318 - 	CGI_10015505	superfamily	241644	6	106	2.94E-42	139.26	cl00154	UBCc superfamily	N	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#14319 - 	CGI_10015506	superfamily	219635	403	588	7.48E-86	267.975	cl06790	Peptidase_C78 superfamily	 - 	 - 	Peptidase family C78; This family formerly known as DUF1671 has been shown to be a cysteine peptidase called (Ufm1)-specific protease.
Q#14320 - 	CGI_10015507	superfamily	247683	138	191	1.48E-25	100.811	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#14320 - 	CGI_10015507	superfamily	245201	250	507	5.95E-128	384.107	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14320 - 	CGI_10015507	superfamily	247725	5	112	2.31E-29	114.249	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#14320 - 	CGI_10015507	superfamily	247725	510	655	1.84E-21	91.9075	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#14320 - 	CGI_10015507	superfamily	246908	195	221	0.000140936	40.8465	cl15255	SH2 superfamily	C	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#14321 - 	CGI_10015508	superfamily	215754	8	97	7.97E-19	79.6048	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14321 - 	CGI_10015508	superfamily	215754	119	193	1.30E-18	78.8344	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14321 - 	CGI_10015508	superfamily	215754	213	287	1.64E-15	70.36	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14322 - 	CGI_10015509	superfamily	218839	7	165	6.57E-53	169.802	cl05501	Med7 superfamily	 - 	 - 	MED7 protein; This family consists of several eukaryotic proteins which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multi-step process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus.
Q#14324 - 	CGI_10015511	superfamily	248264	156	302	1.37E-20	85.7517	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#14327 - 	CGI_10015514	superfamily	217381	3	96	2.70E-38	127.298	cl15956	TB2_DP1_HVA22 superfamily	 - 	 - 	"TB2/DP1, HVA22 family; This family includes members from a wide variety of eukaryotes. It includes the TB2/DP1 (deleted in polyposis) protein, which in humans is deleted in severe forms of familial adenomatous polyposis, an autosomal dominant oncological inherited disease. The family also includes the plant protein of known similarity to TB2/DP1, the HVA22 abscisic acid-induced protein, which is thought to be a regulatory protein."
Q#14329 - 	CGI_10015516	superfamily	248264	320	405	6.01E-06	44.9206	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#14334 - 	CGI_10003635	superfamily	241594	711	1057	9.66E-144	437.382	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#14334 - 	CGI_10003635	superfamily	201217	165	215	3.32E-15	71.788	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#14334 - 	CGI_10003635	superfamily	201217	112	162	1.72E-14	69.862	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#14334 - 	CGI_10003635	superfamily	201217	221	267	3.63E-14	69.0916	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#14334 - 	CGI_10003635	superfamily	201217	283	318	1.15E-07	50.2168	cl08266	RCC1 superfamily	N	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#14334 - 	CGI_10003635	superfamily	201217	4	52	1.41E-07	49.8316	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#14334 - 	CGI_10003635	superfamily	201217	55	108	1.94E-07	49.4464	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#14336 - 	CGI_10003637	superfamily	245213	595	625	4.00E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14336 - 	CGI_10003637	superfamily	245213	511	545	0.000179006	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14336 - 	CGI_10003637	superfamily	245213	429	463	0.000315424	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14336 - 	CGI_10003637	superfamily	215647	1275	1469	6.13E-37	141.592	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#14336 - 	CGI_10003637	superfamily	243060	686	782	9.46E-14	70.1004	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#14336 - 	CGI_10003637	superfamily	245213	471	505	1.33E-07	50.3232	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14336 - 	CGI_10003637	superfamily	221370	1072	1235	2.46E-06	48.9069	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#14336 - 	CGI_10003637	superfamily	245213	553	593	7.42E-05	42.336	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14336 - 	CGI_10003637	superfamily	245213	633	671	0.000784209	39.1524	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14336 - 	CGI_10003637	superfamily	245814	910	978	0.000846129	39.701	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14336 - 	CGI_10003637	superfamily	221695	409	432	0.00682975	36.279	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#14337 - 	CGI_10003638	superfamily	243175	156	251	1.96E-23	91.8085	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#14338 - 	CGI_10001332	superfamily	241874	31	70	4.37E-26	98.9152	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#14339 - 	CGI_10004292	superfamily	246902	22	167	4.27E-09	54.6075	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#14340 - 	CGI_10004293	superfamily	247727	1	340	6.28E-144	412.244	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#14342 - 	CGI_10004295	superfamily	155088	148	301	6.29E-27	103.299	cl02758	AMOP superfamily	 - 	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#14342 - 	CGI_10004295	superfamily	246918	74	113	1.27E-09	53.1782	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14343 - 	CGI_10004296	superfamily	241913	34	170	4.34E-43	141.528	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#14346 - 	CGI_10004299	superfamily	245206	45	301	1.61E-93	281.012	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#14347 - 	CGI_10004300	superfamily	203458	1460	1489	2.59E-06	46.3613	cl05789	Hyd_WA superfamily	 - 	 - 	Propeller; Probable beta-propeller.
Q#14347 - 	CGI_10004300	superfamily	203458	1417	1446	1.58E-05	44.0501	cl05789	Hyd_WA superfamily	 - 	 - 	Propeller; Probable beta-propeller.
Q#14347 - 	CGI_10004300	superfamily	203458	1315	1342	4.33E-05	42.8945	cl05789	Hyd_WA superfamily	 - 	 - 	Propeller; Probable beta-propeller.
Q#14347 - 	CGI_10004300	superfamily	214782	1483	1516	9.50E-05	41.7138	cl02749	TECPR superfamily	 - 	 - 	"Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins; Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins.  "
Q#14347 - 	CGI_10004300	superfamily	203458	1149	1181	0.00851603	35.9609	cl05789	Hyd_WA superfamily	 - 	 - 	Propeller; Probable beta-propeller.
Q#14349 - 	CGI_10004302	superfamily	244681	1	57	8.29E-13	59.3068	cl07291	RNase_H2-C superfamily	N	 - 	"Ribonuclease H2-C is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; Ribonuclease H2C is one of the three protein of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder."
Q#14350 - 	CGI_10005997	superfamily	199166	82	196	1.15E-08	51.9444	cl15308	AMN1 superfamily	NC	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#14353 - 	CGI_10006000	superfamily	111646	268	404	2.94E-80	245.779	cl03707	S-AdoMet_synt_C superfamily	 - 	 - 	"S-adenosylmethionine synthetase, C-terminal domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#14353 - 	CGI_10006000	superfamily	217221	144	266	7.20E-69	215.748	cl03706	S-AdoMet_synt_M superfamily	 - 	 - 	"S-adenosylmethionine synthetase, central domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#14353 - 	CGI_10006000	superfamily	201226	32	131	1.81E-60	193.455	cl02868	S-AdoMet_synt_N superfamily	 - 	 - 	"S-adenosylmethionine synthetase, N-terminal domain; The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold."
Q#14356 - 	CGI_10006003	superfamily	247805	823	1028	2.59E-68	229.294	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#14356 - 	CGI_10006003	superfamily	247905	1040	1174	1.66E-38	141.606	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#14357 - 	CGI_10006004	superfamily	216191	69	148	1.38E-26	103.734	cl03017	UPF0004 superfamily	 - 	 - 	Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.
Q#14358 - 	CGI_10006005	superfamily	243072	13	148	3.06E-21	88.5946	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14359 - 	CGI_10006006	superfamily	241580	112	186	1.37E-31	115.344	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#14360 - 	CGI_10006007	superfamily	247724	19	139	3.39E-76	226.455	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#14361 - 	CGI_10006008	superfamily	241868	19	111	2.52E-28	102.308	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#14362 - 	CGI_10003156	superfamily	247692	31	631	0	952.139	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#14363 - 	CGI_10003157	superfamily	241698	17	171	3.61E-58	182.409	cl00220	cysteine_hydrolases superfamily	 - 	 - 	"Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function."
Q#14364 - 	CGI_10003158	superfamily	241799	566	745	2.30E-44	161.191	cl00339	SugarP_isomerase superfamily	 - 	 - 	"SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway."
Q#14364 - 	CGI_10003158	superfamily	217228	224	506	3.21E-41	154.435	cl07843	G6PD_C superfamily	 - 	 - 	"Glucose-6-phosphate dehydrogenase, C-terminal domain; Glucose-6-phosphate dehydrogenase, C-terminal domain.  "
Q#14364 - 	CGI_10003158	superfamily	215937	39	221	2.30E-40	148.419	cl02877	G6PD_N superfamily	 - 	 - 	"Glucose-6-phosphate dehydrogenase, NAD binding domain; Glucose-6-phosphate dehydrogenase, NAD binding domain.  "
Q#14364 - 	CGI_10003158	superfamily	241600	834	1036	2.40E-35	135.061	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#14367 - 	CGI_10022713	superfamily	243058	281	389	4.23E-16	76.1991	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14367 - 	CGI_10022713	superfamily	243058	396	515	1.55E-13	68.8803	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14367 - 	CGI_10022713	superfamily	243072	182	269	2.18E-08	53.5414	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14367 - 	CGI_10022713	superfamily	243058	775	870	0.000370755	39.9904	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14367 - 	CGI_10022713	superfamily	202819	46	85	1.50E-14	70.0226	cl04335	Ribosomal_L23eN superfamily	N	 - 	"Ribosomal protein L23, N-terminal domain; The N-terminal domain appears to be specific to the eukaryotic ribosomal proteins L25, L23, and L23a."
Q#14367 - 	CGI_10022713	superfamily	243058	479	589	0.00346359	37.294	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14368 - 	CGI_10022714	superfamily	241563	480	521	9.10E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14368 - 	CGI_10022714	superfamily	241563	55	97	0.000569126	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14368 - 	CGI_10022714	superfamily	241563	427	472	0.00336131	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14369 - 	CGI_10022715	superfamily	241603	52	271	5.42E-70	219.164	cl00089	NUC superfamily	 - 	 - 	DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.  They exists as monomers and homodimers.
Q#14370 - 	CGI_10022716	superfamily	241563	60	99	9.56E-06	43.0447	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14372 - 	CGI_10022718	superfamily	245835	43	142	0.00324938	37.9739	cl12013	BAR superfamily	NC	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#14375 - 	CGI_10022721	superfamily	241546	2190	2309	1.44E-52	184.401	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14375 - 	CGI_10022721	superfamily	241546	4055	4174	5.57E-52	182.476	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14375 - 	CGI_10022721	superfamily	248011	737	779	0.000122567	43.6394	cl17457	PKD superfamily	N	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#14375 - 	CGI_10022721	superfamily	243093	3279	3370	1.09E-15	76.7401	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#14375 - 	CGI_10022721	superfamily	243086	2080	2122	1.08E-08	55.0738	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#14375 - 	CGI_10022721	superfamily	248011	592	683	0.00298018	39.3566	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#14376 - 	CGI_10022722	superfamily	248011	870	918	1.86E-05	43.6394	cl17457	PKD superfamily	N	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#14376 - 	CGI_10022722	superfamily	243093	339	417	1.56E-13	67.5554	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#14376 - 	CGI_10022722	superfamily	243100	56	112	2.10E-07	49.2448	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#14377 - 	CGI_10022723	superfamily	204418	3	124	2.28E-59	187.733	cl10915	DUF2246 superfamily	N	 - 	Uncharacterized conserved protein (DUF2246); This is a family of proteins conserved from worms to humans of approximately 300 residues. The function is unknown.
Q#14378 - 	CGI_10022724	superfamily	245205	315	382	4.25E-07	48.3881	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#14381 - 	CGI_10022727	superfamily	241972	24	95	0.003651	33.7067	cl00600	Ribosomal_L7Ae superfamily	C	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#14382 - 	CGI_10022728	superfamily	241972	8	85	0.000477986	36.7883	cl00600	Ribosomal_L7Ae superfamily	C	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#14383 - 	CGI_10022729	superfamily	247684	9	182	4.36E-21	88.7999	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14384 - 	CGI_10022730	superfamily	247684	9	182	4.67E-20	86.1035	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14385 - 	CGI_10022731	superfamily	247684	10	183	7.43E-16	74.1623	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14386 - 	CGI_10022732	superfamily	247684	9	182	6.09E-17	77.2439	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14386 - 	CGI_10022732	superfamily	247684	289	319	0.00987966	36.2527	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14387 - 	CGI_10022733	superfamily	247684	9	160	1.18E-10	58.7543	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14387 - 	CGI_10022733	superfamily	217211	138	194	0.00102128	36.8786	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#14388 - 	CGI_10022734	superfamily	247727	136	194	2.78E-07	47.3716	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#14389 - 	CGI_10022735	superfamily	241843	62	179	8.34E-33	116.2	cl00402	UPF0054 superfamily	N	 - 	Uncharacterized protein family UPF0054; Uncharacterized protein family UPF0054.  
Q#14390 - 	CGI_10022736	superfamily	246748	12	166	3.51E-59	204.245	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#14391 - 	CGI_10022737	superfamily	246748	1	84	3.20E-27	102.167	cl14876	Zinc_peptidase_like superfamily	N	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#14392 - 	CGI_10022738	superfamily	246680	9	88	0.00014595	40.2628	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#14393 - 	CGI_10022739	superfamily	247683	14	68	6.41E-25	96.2656	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#14393 - 	CGI_10022739	superfamily	245674	325	380	0.00392908	35.3426	cl11531	DUF904 superfamily	N	 - 	Protein of unknown function (DUF904); This family consists of several bacterial and archaeal hypothetical proteins of unknown function.
Q#14394 - 	CGI_10022740	superfamily	247683	3	55	8.35E-27	99.2633	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#14394 - 	CGI_10022740	superfamily	247683	112	161	1.23E-22	88.1594	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#14395 - 	CGI_10022741	superfamily	244539	342	578	2.39E-63	209.731	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#14395 - 	CGI_10022741	superfamily	242849	101	174	4.97E-23	93.4224	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#14395 - 	CGI_10022741	superfamily	241659	230	316	6.83E-15	70.8236	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#14396 - 	CGI_10022742	superfamily	247057	726	781	9.57E-17	77.1585	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#14396 - 	CGI_10022742	superfamily	247057	4	64	5.08E-25	100.983	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#14396 - 	CGI_10022742	superfamily	247683	644	695	3.86E-09	54.6277	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#14396 - 	CGI_10022742	superfamily	247057	1206	1265	0.00836634	35.949	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#14397 - 	CGI_10022743	superfamily	241900	621	934	4.43E-41	154.768	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#14397 - 	CGI_10022743	superfamily	241900	931	995	2.86E-06	48.9589	cl00490	EEP superfamily	N	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#14398 - 	CGI_10022744	superfamily	245226	317	473	3.71E-14	70.4072	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#14401 - 	CGI_10022748	superfamily	227448	224	337	2.31E-17	83.9942	cl18812	BDP1 superfamily	N	 - 	"Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]"
Q#14402 - 	CGI_10022749	superfamily	241832	4	73	4.20E-34	117.65	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14402 - 	CGI_10022749	superfamily	243175	84	180	1.72E-21	85.367	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#14403 - 	CGI_10022750	superfamily	241974	536	671	8.14E-17	77.2818	cl00604	STAS superfamily	 - 	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#14403 - 	CGI_10022750	superfamily	216188	215	480	2.12E-38	143.512	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#14403 - 	CGI_10022750	superfamily	205965	72	155	3.26E-26	103.261	cl18285	Sulfate_tra_GLY superfamily	 - 	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#14404 - 	CGI_10022751	superfamily	247684	19	430	3.02E-76	250.657	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14405 - 	CGI_10022752	superfamily	216554	1	167	2.35E-39	139.922	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#14406 - 	CGI_10022753	superfamily	247684	10	428	9.85E-85	272.229	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14407 - 	CGI_10022754	superfamily	243072	102	231	8.79E-35	124.803	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14407 - 	CGI_10022754	superfamily	243072	79	104	0.000425457	37.5336	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14409 - 	CGI_10022756	superfamily	243179	111	182	6.24E-13	61.3663	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#14410 - 	CGI_10022757	superfamily	218118	64	127	0.00519347	32.9713	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#14411 - 	CGI_10022758	superfamily	244970	228	269	6.44E-07	46.2214	cl08469	tRNA_SAD superfamily	 - 	 - 	"Threonyl and Alanyl tRNA synthetase second additional domain; The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain."
Q#14412 - 	CGI_10022759	superfamily	197746	127	166	6.02E-06	41.5579	cl02624	MIR superfamily	C	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#14412 - 	CGI_10022759	superfamily	197746	4	54	1.38E-05	40.4023	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#14412 - 	CGI_10022759	superfamily	197746	65	103	1.60E-05	40.4023	cl02624	MIR superfamily	C	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#14413 - 	CGI_10022760	superfamily	241574	46	107	5.43E-25	93.1632	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#14415 - 	CGI_10010969	superfamily	241584	570	644	4.65E-08	52.1135	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14415 - 	CGI_10010969	superfamily	247724	718	802	5.79E-06	47.9256	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#14419 - 	CGI_10010973	superfamily	243066	24	104	4.48E-08	51.8493	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#14419 - 	CGI_10010973	superfamily	222150	729	753	0.00446218	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14420 - 	CGI_10010974	superfamily	217235	155	312	2.67E-97	287.519	cl18396	Gp_dh_C superfamily	 - 	 - 	"Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold."
Q#14420 - 	CGI_10010974	superfamily	248296	3	149	4.71E-71	220.058	cl17742	Gp_dh_N superfamily	 - 	 - 	"Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold."
Q#14423 - 	CGI_10010977	superfamily	245201	27	269	4.46E-71	231.742	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14424 - 	CGI_10010978	superfamily	110440	385	411	0.000946276	37.0021	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14425 - 	CGI_10010979	superfamily	243084	889	986	1.67E-27	109.952	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#14427 - 	CGI_10010981	superfamily	206097	642	729	6.79E-08	51.5279	cl16481	DUF4211 superfamily	 - 	 - 	Domain of unknown function (DUF4211); Domain of unknown function (DUF4211).  
Q#14428 - 	CGI_10010982	superfamily	220711	10	181	2.27E-39	141.183	cl18573	DUF2431 superfamily	 - 	 - 	Domain of unknown function (DUF2431); This is the N-terminal domain of a family of proteins found from plants to humans. The function is not known.
Q#14428 - 	CGI_10010982	superfamily	244928	449	543	0.000402875	38.9458	cl08386	FDX-ACB superfamily	 - 	 - 	Ferredoxin-fold anticodon binding domain; This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold.
Q#14429 - 	CGI_10010983	superfamily	241752	566	632	1.39E-19	85.4489	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#14429 - 	CGI_10010983	superfamily	241752	371	418	3.44E-16	75.8189	cl00283	ADP_ribosyl superfamily	C	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#14431 - 	CGI_10010985	superfamily	244584	606	654	4.02E-05	42.3647	cl07029	SPT2 superfamily	NC	 - 	SPT2 chromatin protein; This family includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation.
Q#14433 - 	CGI_10010987	superfamily	245864	46	486	9.22E-89	282.245	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#14435 - 	CGI_10010989	superfamily	247805	70	209	3.05E-15	70.8292	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#14436 - 	CGI_10022875	superfamily	248097	3	111	3.72E-21	82.6982	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#14437 - 	CGI_10022876	superfamily	243072	12	107	7.30E-13	61.6306	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14438 - 	CGI_10022877	superfamily	248097	71	193	4.18E-18	76.535	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#14439 - 	CGI_10022878	superfamily	241645	1	50	2.03E-16	70.436	cl00155	UBQ superfamily	C	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#14441 - 	CGI_10022880	superfamily	247769	166	286	3.03E-10	56.5789	cl17215	HDc superfamily	C	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#14441 - 	CGI_10022880	superfamily	247057	61	112	2.34E-05	41.1462	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#14443 - 	CGI_10022882	superfamily	247769	162	325	6.36E-13	66.5941	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#14444 - 	CGI_10022883	superfamily	243100	209	264	1.22E-06	45.2476	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#14450 - 	CGI_10022889	superfamily	192556	853	937	1.39E-24	100.336	cl11030	DUF2435 superfamily	 - 	 - 	Protein of unknown function (DUF2435); This is a conserved region of approximately 400 residues which is found only in eukaryotes. It is associated with HEAT domains pfam02985 in all members. The function is not known.
Q#14451 - 	CGI_10022890	superfamily	243290	246	361	0.00545072	37.261	cl03075	GrpE superfamily	C	 - 	"GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent."
Q#14454 - 	CGI_10022893	superfamily	245040	535	600	0.00115522	37.8388	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#14455 - 	CGI_10022894	superfamily	215754	215	305	1.07E-14	68.0488	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14455 - 	CGI_10022894	superfamily	215754	104	204	4.02E-13	63.8116	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14455 - 	CGI_10022894	superfamily	215754	2	90	8.19E-13	63.0412	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#14457 - 	CGI_10022896	superfamily	218182	14	213	1.42E-66	207.302	cl18445	ERG2_Sigma1R superfamily	 - 	 - 	"ERG2 and Sigma1 receptor like protein; This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyzes a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum, which interacts with endogenous steroid hormones, such as progesterone and testosterone. It also binds the sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia."
Q#14460 - 	CGI_10022899	superfamily	245225	413	679	3.22E-90	299.158	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#14460 - 	CGI_10022899	superfamily	215648	794	1033	1.02E-78	258.68	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#14460 - 	CGI_10022899	superfamily	245225	307	413	3.93E-33	133.907	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#14460 - 	CGI_10022899	superfamily	216686	90	272	1.22E-20	91.6157	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#14460 - 	CGI_10022899	superfamily	219467	713	763	2.67E-12	63.8915	cl08456	NCD3G superfamily	 - 	 - 	"Nine Cysteines Domain of family 3 GPCR; This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins."
Q#14461 - 	CGI_10022901	superfamily	241644	13	93	2.29E-23	91.4949	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#14462 - 	CGI_10022902	superfamily	243072	1164	1275	1.45E-16	78.5794	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14462 - 	CGI_10022902	superfamily	243072	1043	1206	2.84E-12	65.8678	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14462 - 	CGI_10022902	superfamily	243072	716	816	1.95E-06	47.7634	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14462 - 	CGI_10022902	superfamily	247743	19	137	0.000294838	41.8624	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#14463 - 	CGI_10022903	superfamily	243555	10	202	6.10E-12	62.0234	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#14466 - 	CGI_10022906	superfamily	247068	137	237	2.24E-18	77.7389	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14466 - 	CGI_10022906	superfamily	247068	24	127	7.62E-17	73.5017	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	1017	1111	2.86E-23	97.3841	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	496	591	9.79E-23	95.8433	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	603	694	7.32E-20	87.3689	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	169	289	4.02E-18	82.3613	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	63	161	5.84E-18	81.9761	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	702	794	1.17E-17	81.2057	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	910	1006	1.86E-17	80.4353	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	804	901	7.21E-17	78.8945	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	1119	1209	1.02E-12	66.5681	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	1329	1409	1.37E-12	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	397	487	2.50E-12	65.4125	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14467 - 	CGI_10022907	superfamily	247068	308	386	9.38E-06	45.7674	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14469 - 	CGI_10022909	superfamily	247742	72	396	5.88E-143	414.808	cl17188	enolase_like superfamily	 - 	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#14470 - 	CGI_10022910	superfamily	247044	79	191	2.89E-56	182.808	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14470 - 	CGI_10022910	superfamily	247044	205	283	8.00E-20	83.4408	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14470 - 	CGI_10022910	superfamily	247044	319	404	2.08E-21	88.0752	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14471 - 	CGI_10022911	superfamily	241563	68	109	1.37E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14471 - 	CGI_10022911	superfamily	241563	28	59	0.00373235	35.918	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14472 - 	CGI_10022912	superfamily	247044	10	58	6.02E-21	80.73	cl15697	ADF_gelsolin superfamily	C	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14474 - 	CGI_10022914	superfamily	243091	45	116	2.11E-08	52.1092	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#14477 - 	CGI_10003542	superfamily	245819	299	473	1.90E-49	175.845	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#14477 - 	CGI_10003542	superfamily	245819	843	1030	1.94E-45	164.289	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#14477 - 	CGI_10003542	superfamily	218992	516	609	5.07E-05	43.9425	cl05691	DUF1053 superfamily	 - 	 - 	Domain of Unknown Function (DUF1053); This domain is found in Adenylate cyclases.
Q#14478 - 	CGI_10003543	superfamily	241645	18	57	0.00267745	37.505	cl00155	UBQ superfamily	C	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#14480 - 	CGI_10005182	superfamily	241575	599	665	8.39E-17	76.9275	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#14480 - 	CGI_10005182	superfamily	243132	690	1077	3.18E-120	376.718	cl02661	A_deamin superfamily	 - 	 - 	"Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc."
Q#14480 - 	CGI_10005182	superfamily	207691	28	90	0.000920374	38.8565	cl02659	z-alpha superfamily	 - 	 - 	"Adenosine deaminase z-alpha domain; This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance."
Q#14483 - 	CGI_10005185	superfamily	241750	85	534	0	738.26	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#14484 - 	CGI_10005186	superfamily	247844	1	163	7.23E-59	184.82	cl17290	Methyltransf_4 superfamily	N	 - 	Putative methyltransferase; This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.
Q#14485 - 	CGI_10005187	superfamily	202474	30	113	3.20E-12	61.9009	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#14486 - 	CGI_10005188	superfamily	217293	73	261	1.94E-35	131.216	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#14486 - 	CGI_10005188	superfamily	202474	269	351	3.32E-15	73.4569	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#14486 - 	CGI_10005188	superfamily	247844	1	71	0.00825438	36.5057	cl17290	Methyltransf_4 superfamily	C	 - 	Putative methyltransferase; This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.
Q#14487 - 	CGI_10005189	superfamily	114359	13	308	8.24E-69	225.173	cl17943	DUF791 superfamily	 - 	 - 	Protein of unknown function (DUF791); This family consists of several eukaryotic proteins of unknown function.
Q#14488 - 	CGI_10005190	superfamily	245814	296	356	7.37E-06	44.0171	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14488 - 	CGI_10005190	superfamily	245814	493	556	3.50E-05	42.0911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14488 - 	CGI_10005190	superfamily	245814	196	263	0.000157573	40.3787	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14491 - 	CGI_10004188	superfamily	177822	43	290	2.99E-21	90.7497	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#14493 - 	CGI_10013832	superfamily	227453	70	270	4.67E-27	105.037	cl14331	COG5124 superfamily	 - 	 - 	Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Q#14494 - 	CGI_10013833	superfamily	243058	125	231	2.93E-14	69.2655	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14494 - 	CGI_10013833	superfamily	243058	202	323	4.64E-10	56.9391	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14494 - 	CGI_10013833	superfamily	243058	391	487	3.75E-06	45.3832	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14494 - 	CGI_10013833	superfamily	243058	282	405	3.82E-06	45.3832	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14494 - 	CGI_10013833	superfamily	201951	28	109	0.000167397	40.0566	cl03339	IBB superfamily	 - 	 - 	"Importin beta binding domain; This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain."
Q#14495 - 	CGI_10013834	superfamily	241696	221	560	4.13E-169	485.982	cl00218	Glyco_hydrolase_16 superfamily	 - 	 - 	"glycosyl hydrolase family 16; The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues."
Q#14498 - 	CGI_10013837	superfamily	241958	43	309	5.11E-37	137.262	cl00573	SDF superfamily	C	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#14499 - 	CGI_10013838	superfamily	241958	44	79	0.00372265	34.0282	cl00573	SDF superfamily	N	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#14500 - 	CGI_10013839	superfamily	248458	111	264	0.00120994	39.9897	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#14502 - 	CGI_10013841	superfamily	245213	162	196	0.00455181	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14502 - 	CGI_10013841	superfamily	245213	219	250	0.00467505	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14504 - 	CGI_10013843	superfamily	243092	3	293	1.94E-26	109.347	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14505 - 	CGI_10013844	superfamily	150957	761	869	3.30E-38	138.903	cl11034	Vps39_2 superfamily	 - 	 - 	"Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11."
Q#14505 - 	CGI_10013844	superfamily	243036	24	285	1.06E-31	125.428	cl02434	CNH superfamily	 - 	 - 	"CNH domain; Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations."
Q#14505 - 	CGI_10013844	superfamily	220718	450	552	9.13E-28	109.251	cl11033	Vps39_1 superfamily	 - 	 - 	"Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. The precise function of this domain has not been characterized."
Q#14506 - 	CGI_10013845	superfamily	247725	2274	2381	2.16E-48	170.468	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#14506 - 	CGI_10013845	superfamily	243054	637	844	3.51E-37	142.199	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	522	739	5.71E-35	135.651	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	952	1156	7.76E-34	132.569	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	1590	1801	8.07E-31	123.71	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	1802	2024	3.09E-29	119.087	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	1168	1375	7.32E-28	114.85	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	1380	1584	4.89E-27	112.539	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	241559	165	268	4.89E-24	100.463	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#14506 - 	CGI_10013845	superfamily	241559	46	149	6.30E-17	79.6623	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#14506 - 	CGI_10013845	superfamily	243054	417	501	9.90E-11	61.5658	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	847	947	1.20E-10	61.1917	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14506 - 	CGI_10013845	superfamily	243054	2013	2075	7.22E-09	55.7878	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#14507 - 	CGI_10013846	superfamily	243072	1015	1090	2.85E-10	59.3194	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14507 - 	CGI_10013846	superfamily	241645	19	93	0.00475539	36.5427	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#14508 - 	CGI_10013847	superfamily	243034	429	514	4.48E-08	51.612	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#14508 - 	CGI_10013847	superfamily	243034	290	363	1.84E-06	46.9896	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#14508 - 	CGI_10013847	superfamily	243034	333	447	6.40E-06	45.0636	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#14508 - 	CGI_10013847	superfamily	248006	569	616	4.39E-05	41.7879	cl17452	TPR_10 superfamily	 - 	 - 	Tetratricopeptide repeat; Tetratricopeptide repeat.  
Q#14510 - 	CGI_10013849	superfamily	247677	244	394	1.58E-37	135.051	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#14510 - 	CGI_10013849	superfamily	247678	4	131	1.00E-47	161.722	cl17014	eIF-5_eIF-2B superfamily	 - 	 - 	"Domain found in IF2B/IF5; This family includes the N terminus of eIF-5, and the C terminus of eIF-2 beta. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger."
Q#14511 - 	CGI_10013850	superfamily	247684	47	201	2.38E-07	49.1243	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#14515 - 	CGI_10003747	superfamily	243035	37	103	1.93E-14	65.3337	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14517 - 	CGI_10006430	superfamily	246723	83	536	0	646.158	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#14517 - 	CGI_10006430	superfamily	246723	979	1431	0	621.506	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#14517 - 	CGI_10006430	superfamily	246723	1869	2309	0	618.809	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#14519 - 	CGI_10006432	superfamily	219086	43	173	1.33E-16	73.376	cl05857	BNIP3 superfamily	 - 	 - 	"BNIP3; This family consists of several mammalian specific BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 or BNIP3 sequences. BNIP3 belongs to the Bcl-2 homology 3 (BH3)-only family, a Bcl-2-related family possessing an atypical Bcl-2 homology 3 (BH3) domain, which regulates PCD from mitochondrial sites by selective Bcl-2/Bcl-XL interactions. BNIP3 family members contain a C-terminal transmembrane domain that is required for their mitochondrial localisation, homodimerisation, as well as regulation of their pro-apoptotic activities. BNIP3-mediated apoptosis has been reported to be independent of caspase activation and cytochrome c release and is characterized by early plasma membrane and mitochondrial damage, prior to the appearance of chromatin condensation or DNA fragmentation."
Q#14520 - 	CGI_10002053	superfamily	243116	444	819	0	527.76	cl02626	DNA_pol_A superfamily	 - 	 - 	"Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase  beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains."
Q#14520 - 	CGI_10002053	superfamily	245226	252	433	1.04E-46	165.386	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#14520 - 	CGI_10002053	superfamily	246724	95	167	1.21E-29	113.263	cl14815	H3TH_StructSpec-5'-nucleases superfamily	 - 	 - 	"H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases."
Q#14520 - 	CGI_10002053	superfamily	246722	1	89	1.84E-19	87.1011	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#14521 - 	CGI_10002056	superfamily	247744	2	165	7.67E-59	184.362	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#14522 - 	CGI_10002058	superfamily	245883	119	404	6.65E-98	295.921	cl12120	SDH_alpha superfamily	 - 	 - 	Serine dehydratase alpha chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.
Q#14522 - 	CGI_10002058	superfamily	217489	1	96	2.73E-26	102.985	cl04004	SDH_beta superfamily	N	 - 	Serine dehydratase beta chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.
Q#14523 - 	CGI_10002059	superfamily	245604	3	97	1.12E-41	134.969	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#14524 - 	CGI_10002063	superfamily	241758	2	343	9.96E-133	386.107	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#14528 - 	CGI_10013713	superfamily	245040	60	89	1.18E-05	39.7648	cl09238	CY superfamily	NC	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#14529 - 	CGI_10013714	superfamily	245040	59	83	0.000183147	36.6832	cl09238	CY superfamily	NC	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#14530 - 	CGI_10013715	superfamily	245040	26	104	9.45E-06	39.5923	cl09238	CY superfamily	 - 	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#14531 - 	CGI_10013716	superfamily	245040	59	83	0.000355673	36.298	cl09238	CY superfamily	NC	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#14532 - 	CGI_10013717	superfamily	245040	26	104	5.37E-06	40.3627	cl09238	CY superfamily	 - 	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#14533 - 	CGI_10013718	superfamily	241571	17	77	7.10E-15	64.741	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14535 - 	CGI_10013720	superfamily	216981	421	542	1.03E-15	75.6469	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#14535 - 	CGI_10013720	superfamily	217473	790	849	0.000107466	44.2782	cl03978	Mab-21 superfamily	NC	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#14537 - 	CGI_10013722	superfamily	244509	31	105	6.33E-16	73.7515	cl06793	PRKCSH superfamily	 - 	 - 	"Glucosidase II beta subunit-like protein; The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain."
Q#14538 - 	CGI_10013723	superfamily	241680	20	196	2.43E-42	145.132	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#14539 - 	CGI_10013724	superfamily	241564	65	90	2.44E-10	53.0567	cl00035	BIR superfamily	N	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#14541 - 	CGI_10013726	superfamily	242326	13	94	2.04E-15	68.4823	cl01136	DUF393 superfamily	C	 - 	"Protein of unknown function, DUF393; Members of this family have two highly conserved cysteine residues near their N-terminus. The function of these proteins is unknown."
Q#14544 - 	CGI_10013729	superfamily	222150	125	149	7.45E-05	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14545 - 	CGI_10013730	superfamily	247903	279	315	0.000411659	39.2021	cl17349	Peptidase_M54 superfamily	N	 - 	"Peptidase family M54, also called archaemetzincins or archaelysins; Peptidase M54 (archaemetzincin or archaelysin) is a zinc-dependent aminopeptidase that contains the consensus zinc-binding sequence HEXXHXXGXXH/D and a conserved Met residue at the active site, and is thus classified as a metzincin. Archaemetzincins, first identified in archaea, are also found in bacteria and eukaryotes, including two human members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1 is mainly found in the liver and heart while AMZ2 is primarily expressed in testis and heart; both have been reported to degrade synthetic substrates and peptides. The Peptidase M54 family contains an extended metzincin concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that a second zinc ion is bound to four cysteines, thus resembling a zinc finger. Phylogenetic analysis of this family reveals a complex evolutionary process involving a series of lateral gene transfer, gene loss and genetic duplication events."
Q#14547 - 	CGI_10013732	superfamily	241593	135	212	0.000954491	39.9374	cl00075	HATPase_c superfamily	C	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#14547 - 	CGI_10013732	superfamily	244201	1712	1837	7.76E-06	46.4551	cl05797	SMC_hinge superfamily	 - 	 - 	SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.
Q#14551 - 	CGI_10001474	superfamily	110440	496	522	0.00398192	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14551 - 	CGI_10001474	superfamily	241563	75	110	0.00968628	35.3907	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14553 - 	CGI_10001937	superfamily	243096	312	431	8.75E-17	79.264	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#14556 - 	CGI_10010544	superfamily	243045	230	311	3.33E-07	49.1687	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#14556 - 	CGI_10010544	superfamily	241596	23	72	0.000838754	38.3491	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#14556 - 	CGI_10010544	superfamily	243045	91	148	0.0078949	35.6868	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#14558 - 	CGI_10010546	superfamily	241802	38	333	2.13E-133	386.869	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#14559 - 	CGI_10010547	superfamily	241743	21	139	1.19E-30	108.165	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#14560 - 	CGI_10010548	superfamily	241743	24	140	5.68E-33	114.328	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#14561 - 	CGI_10010549	superfamily	241743	25	153	2.51E-38	128.581	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#14562 - 	CGI_10010550	superfamily	241743	356	480	9.46E-41	143.218	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#14562 - 	CGI_10010550	superfamily	241642	214	273	6.36E-11	58.2758	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#14562 - 	CGI_10010550	superfamily	241634	36	138	4.94E-10	56.5943	cl00143	SynN superfamily	 - 	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#14563 - 	CGI_10010551	superfamily	241697	368	624	2.59E-120	377.888	cl00219	Pterin_binding superfamily	 - 	 - 	"Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH).  DHPS, a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS.  Sulfonamide drugs, which are substrate analogs of pABA, target DHPS.  Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate.  These include MeTr, a functional heterodimer, and the folate binding domain of MetH."
Q#14563 - 	CGI_10010551	superfamily	241759	668	892	1.24E-115	363.123	cl00293	B12-binding_like superfamily	 - 	 - 	"B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif."
Q#14563 - 	CGI_10010551	superfamily	246616	19	335	5.12E-128	401.3	cl14105	MetH superfamily	 - 	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#14563 - 	CGI_10010551	superfamily	111813	1084	1220	1.23E-43	156.704	cl03805	Met_synt_B12 superfamily	 - 	 - 	"Vitamin B12 dependent methionine synthase, activation domain; Vitamin B12 dependent methionine synthase, activation domain.  "
Q#14563 - 	CGI_10010551	superfamily	248312	1284	1428	4.82E-09	56.2077	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#14565 - 	CGI_10010553	superfamily	243065	1004	1160	1.53E-23	99.8237	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14565 - 	CGI_10010553	superfamily	243065	106	262	4.67E-23	98.2829	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14565 - 	CGI_10010553	superfamily	243065	555	711	4.67E-23	98.2829	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14566 - 	CGI_10010554	superfamily	243065	76	232	1.68E-23	98.6681	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14566 - 	CGI_10010554	superfamily	243065	525	681	3.45E-23	97.8977	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14567 - 	CGI_10010555	superfamily	243065	50	183	2.38E-15	69.7781	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14568 - 	CGI_10010556	superfamily	243065	435	588	9.70E-13	66.2713	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14568 - 	CGI_10010556	superfamily	205157	368	396	0.00190783	36.7467	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#14570 - 	CGI_10010558	superfamily	245332	4	341	1.90E-135	400.729	cl10557	PRK14481 superfamily	 - 	 - 	dihydroxyacetone kinase subunit DhaK; Provisional
Q#14570 - 	CGI_10010558	superfamily	243501	408	582	3.04E-37	135.755	cl03685	Dak2 superfamily	 - 	 - 	DAK2 domain; This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family.
Q#14571 - 	CGI_10010559	superfamily	245332	4	339	2.79E-100	310.207	cl10557	PRK14481 superfamily	 - 	 - 	dihydroxyacetone kinase subunit DhaK; Provisional
Q#14571 - 	CGI_10010559	superfamily	243501	408	582	5.68E-38	138.067	cl03685	Dak2 superfamily	 - 	 - 	DAK2 domain; This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family.
Q#14572 - 	CGI_10010560	superfamily	146451	72	88	0.00407828	31.9459	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#14573 - 	CGI_10010561	superfamily	243501	37	51	0.00132226	36.3739	cl03685	Dak2 superfamily	NC	 - 	DAK2 domain; This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family.
Q#14574 - 	CGI_10010562	superfamily	241599	167	225	1.06E-20	84.2172	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#14574 - 	CGI_10010562	superfamily	146451	305	321	0.00242964	35.4127	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#14575 - 	CGI_10010563	superfamily	241599	155	213	3.46E-22	88.0692	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#14575 - 	CGI_10010563	superfamily	146451	291	310	0.00699336	33.8719	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#14576 - 	CGI_10010564	superfamily	241578	1146	1307	6.53E-18	83.495	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14576 - 	CGI_10010564	superfamily	245213	329	366	2.99E-08	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	903	939	5.69E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	1061	1097	1.03E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	941	977	1.18E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	1099	1135	1.64E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	563	599	1.94E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	291	326	4.58E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	751	787	6.14E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	865	901	9.81E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	368	403	1.39E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	525	560	1.44E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	216	252	3.73E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	254	288	6.34E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	827	863	8.54E-05	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	1019	1058	0.000296629	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	979	1016	0.000803366	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	406	445	0.00234332	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	790	825	0.00528988	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	245213	680	711	0.00926151	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14576 - 	CGI_10010564	superfamily	243124	79	211	8.99E-16	76.6969	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#14577 - 	CGI_10010565	superfamily	241578	103	261	8.35E-39	142.816	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14577 - 	CGI_10010565	superfamily	245213	320	355	6.44E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	434	470	1.12E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	776	812	3.54E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	358	392	9.15E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	889	920	0.000232447	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	472	510	0.000414775	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	959	995	0.000451088	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	589	624	0.000539922	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	519	548	0.00119285	38.0014	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	395	432	0.00170164	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	851	886	0.00345784	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	550	585	0.00600963	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14577 - 	CGI_10010565	superfamily	245213	283	317	0.00896834	35.305	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14581 - 	CGI_10009654	superfamily	216049	1	85	0.0095118	33.0282	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#14582 - 	CGI_10009655	superfamily	247755	9	41	3.34E-14	62.1015	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#14583 - 	CGI_10009656	superfamily	241578	1	130	3.82E-27	100.829	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14584 - 	CGI_10009657	superfamily	241578	638	787	8.88E-36	134.727	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14584 - 	CGI_10009657	superfamily	245213	816	850	1.15E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14584 - 	CGI_10009657	superfamily	245814	874	946	3.05E-05	43.6319	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14584 - 	CGI_10009657	superfamily	245814	958	1048	6.78E-07	48.5453	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14587 - 	CGI_10021808	superfamily	217521	526	959	0	563.835	cl04032	CAS_CSE1 superfamily	 - 	 - 	"CAS/CSE protein, C-terminus; Mammalian cellular apoptosis susceptibility (CAS) proteins are homologous to the yeast chromosome-segregation protein, CSE1. This family aligns the C-terminal halves (approximately). CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localisation (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins."
Q#14587 - 	CGI_10021808	superfamily	243689	29	101	2.03E-09	55.3273	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#14590 - 	CGI_10021811	superfamily	241597	34	105	2.32E-32	116.629	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#14592 - 	CGI_10021813	superfamily	241594	159	496	6.54E-22	95.7096	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#14594 - 	CGI_10021815	superfamily	245201	18	176	4.31E-30	111.174	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14595 - 	CGI_10021816	superfamily	245201	7	125	2.86E-13	69.4709	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14596 - 	CGI_10021817	superfamily	220131	741	1044	8.98E-66	227.544	cl11721	DUF1943 superfamily	 - 	 - 	"Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined."
Q#14596 - 	CGI_10021817	superfamily	243065	2121	2282	5.13E-25	105.176	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#14597 - 	CGI_10021818	superfamily	241637	38	99	8.31E-12	61.9406	cl00146	TFIIS_I superfamily	 - 	 - 	N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Q#14598 - 	CGI_10021819	superfamily	217943	10	400	4.55E-32	125.508	cl15508	LTV superfamily	 - 	 - 	Low temperature viability protein; The low-temperature viability protein LTV1 is involved in ribosome biogenesis 40S subunit production.
Q#14600 - 	CGI_10021822	superfamily	189650	114	190	2.18E-16	72.6998	cl02913	zf-PARP superfamily	 - 	 - 	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
Q#14600 - 	CGI_10021822	superfamily	189650	215	285	5.86E-09	51.899	cl02913	zf-PARP superfamily	 - 	 - 	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
Q#14600 - 	CGI_10021822	superfamily	189650	9	52	0.00282051	35.3354	cl02913	zf-PARP superfamily	C	 - 	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
Q#14601 - 	CGI_10021823	superfamily	192472	161	224	1.34E-23	90.7808	cl10874	DUF2373 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2373); This is the C-terminal conserved region of a family of proteins found from fungi to humans. The function is not known.
Q#14603 - 	CGI_10021825	superfamily	206090	144	246	4.33E-36	134.8	cl16477	Asx-hm superfamily	 - 	 - 	"Transcriptional enhancer, Asx-hm domain; The Asx-hm domain of the additional sex combs-like 1 proteins contains two putative nuclear receptor co-regulator binding (NR box) motifs. The Asx proteins acts as an enhancer of trithorax and polycomb in displaying bidirectional homoeotic phenotypes in Drosophila, suggesting that it is required for maintenance of both activation and silencing of Hox genes. Asx is required for normal adult haematopoiesis and its function depends on its cellular context."
Q#14606 - 	CGI_10021828	superfamily	241567	51	298	4.92E-94	281.411	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#14607 - 	CGI_10021829	superfamily	241640	1242	1480	1.03E-75	252.197	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#14607 - 	CGI_10021829	superfamily	241609	391	469	2.31E-21	91.2855	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#14607 - 	CGI_10021829	superfamily	243035	76	237	3.65E-09	56.4741	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14607 - 	CGI_10021829	superfamily	241613	614	645	3.30E-08	51.8238	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#14607 - 	CGI_10021829	superfamily	241619	553	606	2.13E-07	50.5461	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#14607 - 	CGI_10021829	superfamily	241613	488	525	2.66E-05	43.3494	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#14607 - 	CGI_10021829	superfamily	243061	655	756	7.24E-38	139.399	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#14607 - 	CGI_10021829	superfamily	243061	763	861	7.10E-37	136.318	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#14607 - 	CGI_10021829	superfamily	243061	973	1071	5.54E-33	125.147	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#14607 - 	CGI_10021829	superfamily	243061	865	961	6.85E-29	113.591	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#14607 - 	CGI_10021829	superfamily	243061	1093	1194	1.57E-28	112.435	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#14607 - 	CGI_10021829	superfamily	241609	334	370	6.12E-09	55.0767	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#14607 - 	CGI_10021829	superfamily	241609	279	315	2.47E-08	53.1507	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#14607 - 	CGI_10021829	superfamily	243061	3	59	0.00298449	37.7066	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#14608 - 	CGI_10021830	superfamily	217359	241	607	3.64E-67	224.912	cl03878	Exo70 superfamily	 - 	 - 	"Exo70 exocyst complex subunit; The Exo70 protein forms one subunit of the exocyst complex. First discovered in S. cerevisiae, Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localised at the tip of the bud, the major site of exocytosis in yeast. Exo70 interacts with the Rho3 GTPase. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud). In humans, the functions of Exo70 and the exocyst complex are less well characterized: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis."
Q#14610 - 	CGI_10021832	superfamily	241580	1	67	3.80E-33	117.655	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#14611 - 	CGI_10021833	superfamily	241782	244	411	7.09E-16	78.3991	cl00321	AAT_I superfamily	NC	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#14613 - 	CGI_10021835	superfamily	207614	26	59	1.06E-11	61.5575	cl02494	SapA superfamily	 - 	 - 	Saposin A-type domain; Saposin A-type domain.  
Q#14613 - 	CGI_10021835	superfamily	207614	1083	1113	9.46E-10	56.1647	cl02494	SapA superfamily	 - 	 - 	Saposin A-type domain; Saposin A-type domain.  
Q#14613 - 	CGI_10021835	superfamily	112314	674	708	1.88E-06	46.4057	cl08395	SapB_2 superfamily	 - 	 - 	"Saposin-like type B, region 2; Saposin-like type B, region 2.  "
Q#14613 - 	CGI_10021835	superfamily	112314	762	796	1.88E-06	46.4057	cl08395	SapB_2 superfamily	 - 	 - 	"Saposin-like type B, region 2; Saposin-like type B, region 2.  "
Q#14613 - 	CGI_10021835	superfamily	112314	850	884	1.88E-06	46.4057	cl08395	SapB_2 superfamily	 - 	 - 	"Saposin-like type B, region 2; Saposin-like type B, region 2.  "
Q#14613 - 	CGI_10021835	superfamily	112314	367	401	3.27E-06	45.6353	cl08395	SapB_2 superfamily	 - 	 - 	"Saposin-like type B, region 2; Saposin-like type B, region 2.  "
Q#14613 - 	CGI_10021835	superfamily	191220	431	469	1.70E-05	43.7394	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#14613 - 	CGI_10021835	superfamily	191220	632	670	1.82E-05	43.7394	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#14613 - 	CGI_10021835	superfamily	112314	1012	1046	3.22E-05	42.9389	cl08395	SapB_2 superfamily	 - 	 - 	"Saposin-like type B, region 2; Saposin-like type B, region 2.  "
Q#14613 - 	CGI_10021835	superfamily	191220	970	1008	3.62E-05	42.5838	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#14613 - 	CGI_10021835	superfamily	191220	912	950	3.71E-05	42.5838	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#14613 - 	CGI_10021835	superfamily	191220	810	846	4.04E-05	42.5838	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#14613 - 	CGI_10021835	superfamily	191220	722	758	4.04E-05	42.5838	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#14613 - 	CGI_10021835	superfamily	112314	566	599	7.98E-05	41.7833	cl08395	SapB_2 superfamily	 - 	 - 	"Saposin-like type B, region 2; Saposin-like type B, region 2.  "
Q#14613 - 	CGI_10021835	superfamily	191220	525	561	0.000212361	40.6578	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#14613 - 	CGI_10021835	superfamily	112314	473	507	0.000749293	38.7017	cl08395	SapB_2 superfamily	 - 	 - 	"Saposin-like type B, region 2; Saposin-like type B, region 2.  "
Q#14615 - 	CGI_10021837	superfamily	241584	2	71	1.10E-11	60.9731	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14615 - 	CGI_10021837	superfamily	241584	86	179	1.24E-06	45.9503	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14616 - 	CGI_10021838	superfamily	247042	96	238	4.13E-10	58.7897	cl15693	Sema superfamily	N	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#14616 - 	CGI_10021838	superfamily	247999	32	86	0.00724187	33.618	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#14618 - 	CGI_10021840	superfamily	198867	137	235	5.67E-45	155.009	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#14618 - 	CGI_10021840	superfamily	243066	26	129	5.37E-35	127.348	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#14618 - 	CGI_10021840	superfamily	243146	370	414	4.39E-13	64.605	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14618 - 	CGI_10021840	superfamily	243146	286	332	4.91E-13	64.5019	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14618 - 	CGI_10021840	superfamily	243146	321	360	7.63E-13	63.8346	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14618 - 	CGI_10021840	superfamily	243146	476	521	1.50E-11	60.2647	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14618 - 	CGI_10021840	superfamily	243146	510	555	1.40E-10	57.2862	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14618 - 	CGI_10021840	superfamily	243146	436	474	4.85E-10	56.0275	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14619 - 	CGI_10021841	superfamily	243072	57	149	4.26E-12	60.0898	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14621 - 	CGI_10021843	superfamily	243064	24	190	1.48E-15	70.5222	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#14622 - 	CGI_10021844	superfamily	222150	796	818	4.32E-05	42.3789	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14622 - 	CGI_10021844	superfamily	222150	768	793	5.89E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14622 - 	CGI_10021844	superfamily	246975	756	776	0.00527977	36.1709	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#14623 - 	CGI_10003298	superfamily	241647	89	116	5.05E-10	56.3822	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#14623 - 	CGI_10003298	superfamily	241647	127	157	2.12E-07	48.6782	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#14623 - 	CGI_10003298	superfamily	207669	262	311	1.49E-12	64.0026	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#14623 - 	CGI_10003298	superfamily	207669	615	663	7.35E-06	44.3574	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#14623 - 	CGI_10003298	superfamily	207669	395	453	0.000688965	38.7089	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#14624 - 	CGI_10003299	superfamily	216423	28	406	1.07E-138	412.785	cl18367	Glyco_hydro_35 superfamily	 - 	 - 	Glycosyl hydrolases family 35; Glycosyl hydrolases family 35.  
Q#14626 - 	CGI_10003301	superfamily	222258	499	545	4.04E-05	43.7108	cl18656	AAA_30 superfamily	C	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#14627 - 	CGI_10004441	superfamily	110440	134	160	0.00136103	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14629 - 	CGI_10004443	superfamily	219542	56	163	5.52E-35	129.669	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#14629 - 	CGI_10004443	superfamily	219541	447	618	1.60E-21	91.7611	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#14629 - 	CGI_10004443	superfamily	215896	223	352	2.31E-14	71.172	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#14631 - 	CGI_10004445	superfamily	219541	232	405	2.15E-25	101.391	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#14631 - 	CGI_10004445	superfamily	219542	1	63	3.00E-20	86.5267	cl18517	Cu-oxidase_3 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#14631 - 	CGI_10004445	superfamily	215896	66	137	2.31E-11	61.542	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#14632 - 	CGI_10000662	superfamily	216315	185	274	0.000575883	39.3318	cl18364	ART superfamily	N	 - 	NAD:arginine ADP-ribosyltransferase; NAD:arginine ADP-ribosyltransferase.  
Q#14633 - 	CGI_10013311	superfamily	246723	4	123	5.21E-48	163.628	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#14636 - 	CGI_10013314	superfamily	247825	71	346	7.12E-37	135.614	cl17271	BcrAD_BadFG superfamily	 - 	 - 	"BadF/BadG/BcrA/BcrD ATPase family; This family includes the BadF and BadG proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase. An uncharacterized protein from Aquifex aeolicus contains two copies of this region suggesting that the family may structurally dimerise. This family appears to be related to pfam00370."
Q#14637 - 	CGI_10013315	superfamily	218809	14	114	1.71E-25	93.6569	cl05468	DUF872 superfamily	 - 	 - 	Eukaryotic protein of unknown function (DUF872); This family consists of several uncharacterized eukaryotic proteins. The function of this family is unknown.
Q#14639 - 	CGI_10013317	superfamily	245864	4	431	8.88E-98	303.431	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#14640 - 	CGI_10013318	superfamily	243083	522	617	1.22E-41	149.004	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#14640 - 	CGI_10013318	superfamily	241597	194	245	8.56E-05	41.8356	cl00082	HMG-box superfamily	C	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#14640 - 	CGI_10013318	superfamily	243091	716	834	2.36E-38	140.547	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#14640 - 	CGI_10013318	superfamily	243083	2	114	7.24E-24	98.6125	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#14640 - 	CGI_10013318	superfamily	197795	661	710	1.73E-09	55.4834	cl02673	AWS superfamily	 - 	 - 	associated with SET domains; subdomain of PRESET
Q#14640 - 	CGI_10013318	superfamily	247999	477	516	7.30E-07	47.8704	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#14643 - 	CGI_10013321	superfamily	128778	199	323	1.34E-10	59.5859	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#14643 - 	CGI_10013321	superfamily	243109	543	740	1.10E-07	51.1296	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#14643 - 	CGI_10013321	superfamily	241563	143	191	0.00420593	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14644 - 	CGI_10013322	superfamily	243092	205	481	4.43E-39	144.015	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14646 - 	CGI_10013324	superfamily	245316	29	120	2.72E-34	118.862	cl10502	nitrobindin superfamily	C	 - 	"nitrobindin heme-binding domain; Nitrobindin is a heme-containing lipocalin that may reversibly bind nitric oxide. This heme-binding domain forms a beta barrel structure, and in a small family of proteins from tetrapods, it is found C-terminal to a THAP zinc finger domain (a sequence-specific DNA binding domain). Members of this group are putatively related to fatty acid-binding proteins (FABPs)."
Q#14647 - 	CGI_10013325	superfamily	245598	1	238	4.24E-113	354.062	cl11396	Patatin_and_cPLA2 superfamily	C	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#14647 - 	CGI_10013325	superfamily	245598	324	581	1.63E-98	315.927	cl11396	Patatin_and_cPLA2 superfamily	N	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#14648 - 	CGI_10013326	superfamily	246669	28	126	7.53E-29	103.111	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#14649 - 	CGI_10013327	superfamily	245213	1320	1357	2.21E-08	53.4094	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1397	1434	2.51E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	943	979	3.82E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1627	1663	5.35E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1436	1472	9.17E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	2112	2149	1.65E-06	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1244	1280	1.70E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	449	484	1.73E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1130	1165	2.16E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1474	1510	2.29E-06	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1589	1625	2.30E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	867	903	2.31E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	487	523	4.37E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	563	599	5.61E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1778	1814	6.29E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	639	675	7.50E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1551	1587	9.15E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	525	561	1.05E-05	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1703	1739	1.12E-05	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	2188	2223	1.29E-05	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	601	636	1.44E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	715	750	1.71E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1359	1395	2.28E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	373	408	2.46E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	829	864	2.66E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1513	1549	3.60E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1168	1204	3.74E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	753	788	4.81E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1206	1242	4.93E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	905	941	5.51E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1092	1128	0.00010381	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1055	1089	0.000130017	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1282	1318	0.000169292	41.8534	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	2001	2036	0.000241122	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	2151	2185	0.000396351	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1018	1052	0.000472853	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	2038	2072	0.00051723	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	411	446	0.000812117	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1665	1700	0.00087505	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	791	826	0.00108156	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1964	1998	0.00125924	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1853	1887	0.00547321	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	2075	2109	0.00584228	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1927	1961	0.00618091	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	245213	1890	1924	0.00762863	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14649 - 	CGI_10013327	superfamily	243060	192	275	6.17E-06	46.9884	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#14649 - 	CGI_10013327	superfamily	243060	2352	2430	1.09E-05	46.218	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#14649 - 	CGI_10013327	superfamily	243060	2231	2300	2.28E-05	45.4476	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#14649 - 	CGI_10013327	superfamily	243119	2642	2690	0.00100187	39.7245	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#14651 - 	CGI_10013329	superfamily	245864	56	150	1.31E-32	120.846	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#14652 - 	CGI_10013330	superfamily	243072	1	113	1.21E-16	71.6458	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14653 - 	CGI_10013331	superfamily	243072	36	152	6.93E-25	95.9134	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14654 - 	CGI_10013332	superfamily	243072	1	108	1.05E-26	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14656 - 	CGI_10001118	superfamily	248054	11	53	2.87E-07	43.3529	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#14658 - 	CGI_10001230	superfamily	241874	12	167	1.29E-46	159.954	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#14659 - 	CGI_10002821	superfamily	248097	39	159	3.66E-18	76.1498	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#14660 - 	CGI_10002822	superfamily	247912	32	101	9.54E-15	67.5264	cl17358	Beta-lactamase superfamily	C	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#14663 - 	CGI_10000380	superfamily	241733	1	63	2.29E-26	93.0053	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#14664 - 	CGI_10000455	superfamily	246723	7	207	7.64E-129	375.363	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#14665 - 	CGI_10000581	superfamily	216301	20	237	1.57E-55	177.841	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#14666 - 	CGI_10003924	superfamily	245213	397	434	5.19E-08	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	475	512	4.05E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	319	354	5.13E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	357	394	6.75E-07	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	596	634	8.88E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	554	594	1.20E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	437	473	1.02E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	637	672	0.00190312	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245213	515	551	0.00723549	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14666 - 	CGI_10003924	superfamily	245814	240	304	0.000372967	39.6976	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14667 - 	CGI_10000790	superfamily	245201	3	132	3.32E-55	176.188	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14669 - 	CGI_10011388	superfamily	218284	26	197	2.97E-45	149.712	cl04786	SOUL superfamily	 - 	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#14670 - 	CGI_10011389	superfamily	218284	51	106	1.08E-10	54.1827	cl04786	SOUL superfamily	C	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#14671 - 	CGI_10011390	superfamily	247085	274	391	3.44E-11	60.597	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#14671 - 	CGI_10011390	superfamily	245596	3	260	2.37E-97	300.66	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#14671 - 	CGI_10011390	superfamily	218284	395	552	4.67E-34	126.6	cl04786	SOUL superfamily	 - 	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#14672 - 	CGI_10011391	superfamily	218284	1	109	2.90E-25	94.6287	cl04786	SOUL superfamily	N	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#14674 - 	CGI_10011393	superfamily	246681	1	240	1.97E-51	168.476	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#14677 - 	CGI_10011396	superfamily	222269	49	245	8.46E-45	152.478	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#14679 - 	CGI_10011398	superfamily	241570	245	357	2.59E-34	123.59	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#14679 - 	CGI_10011398	superfamily	241570	123	236	2.38E-27	104.33	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#14679 - 	CGI_10011398	superfamily	213107	5	43	6.21E-14	65.3447	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#14682 - 	CGI_10011401	superfamily	243066	17	70	0.000542659	34.0657	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#14683 - 	CGI_10011402	superfamily	247041	7	273	9.69E-89	283.054	cl15692	CE4_SF superfamily	 - 	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#14683 - 	CGI_10011402	superfamily	247041	524	787	3.11E-59	202.932	cl15692	CE4_SF superfamily	 - 	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#14685 - 	CGI_10011405	superfamily	241580	13	90	2.43E-47	155.404	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#14686 - 	CGI_10011406	superfamily	192535	43	145	8.77E-05	42.583	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#14689 - 	CGI_10023926	superfamily	152088	131	213	9.21E-17	72.2355	cl13155	DUF3259 superfamily	 - 	 - 	Protein of unknown function (DUF3259); This eukaryotic family of proteins has no known function.
Q#14691 - 	CGI_10023928	superfamily	218493	429	571	1.89E-38	138.259	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#14691 - 	CGI_10023928	superfamily	248054	28	57	0.00663554	35.1404	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#14692 - 	CGI_10023929	superfamily	246669	283	416	2.69E-46	157.36	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#14692 - 	CGI_10023929	superfamily	246669	149	275	1.19E-30	114.284	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#14693 - 	CGI_10023930	superfamily	218387	12	229	2.76E-91	278.41	cl18452	Phytochelatin superfamily	 - 	 - 	"Phytochelatin synthase; Phytochelatin synthase is the enzyme responsible for the synthesis of heavy-metal-binding peptides (phytochelatins) from glutathione and related thiols. The crystal structure of a member of this family shows it to possess a papain fold. The enzyme catalyzes the deglycination of a GSH donor molecule. The enzyme contains a catalytic triad of cysteine, histidine and aspartate residues."
Q#14694 - 	CGI_10023931	superfamily	246751	132	372	1.41E-64	209.407	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#14695 - 	CGI_10023932	superfamily	246751	99	337	5.86E-62	201.318	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#14696 - 	CGI_10023933	superfamily	198867	254	353	3.48E-18	81.2336	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#14696 - 	CGI_10023933	superfamily	243066	138	245	2.70E-15	73.0353	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#14696 - 	CGI_10023933	superfamily	243146	577	623	2.34E-09	54.5898	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14696 - 	CGI_10023933	superfamily	243146	539	588	1.75E-06	46.0123	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14697 - 	CGI_10023934	superfamily	219000	103	246	3.26E-28	113.51	cl05717	Drf_FH3 superfamily	 - 	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#14697 - 	CGI_10023934	superfamily	219001	4	97	8.87E-18	82.7419	cl05720	Drf_GBD superfamily	N	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#14700 - 	CGI_10023937	superfamily	219428	1	18	6.35E-07	43.0187	cl06499	PPI_Ypi1 superfamily	NC	 - 	"Protein phosphatase inhibitor; These proteins include Ypi1, , a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor and ppp1r11/hcgv, annotated as having protein phosphatase inhibitor activity."
Q#14701 - 	CGI_10023938	superfamily	243058	535	621	8.68E-10	56.9391	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14701 - 	CGI_10023938	superfamily	243058	264	367	1.32E-05	44.2276	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#14705 - 	CGI_10023942	superfamily	151147	26	55	1.03E-08	50.935	cl11240	DUF2475 superfamily	C	 - 	Protein of unknown function (DUF2475); This family of proteins has no known function.
Q#14705 - 	CGI_10023942	superfamily	151147	259	283	3.49E-05	40.9198	cl11240	DUF2475 superfamily	C	 - 	Protein of unknown function (DUF2475); This family of proteins has no known function.
Q#14706 - 	CGI_10023943	superfamily	243072	181	337	1.30E-26	106.314	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14707 - 	CGI_10023944	superfamily	216981	1	28	0.00776577	32.8898	cl17087	OTU superfamily	NC	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#14709 - 	CGI_10023946	superfamily	248264	235	351	4.05E-09	54.1654	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#14711 - 	CGI_10023948	superfamily	152683	8	100	7.45E-09	48.4381	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#14712 - 	CGI_10023949	superfamily	241589	92	219	1.26E-25	98.0899	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#14713 - 	CGI_10023950	superfamily	241589	8	127	7.57E-43	145.469	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#14713 - 	CGI_10023950	superfamily	241589	170	305	1.95E-32	117.735	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#14716 - 	CGI_10023953	superfamily	145533	60	159	1.15E-47	162.148	cl03592	Ski_Sno superfamily	 - 	 - 	"SKI/SNO/DAC family; This family contains a presumed domain that is about 100 amino acids long. All members of this family contain a conserved CLPQ motif. The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation. Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli. Dachshund also contains this domain. It is involved in various aspects of development."
Q#14717 - 	CGI_10023954	superfamily	146346	98	331	3.70E-101	300.902	cl04200	UPF0121 superfamily	 - 	 - 	Uncharacterized protein family (UPF0121); Uncharacterized integral membrane protein family.
Q#14718 - 	CGI_10023955	superfamily	241596	91	148	1.45E-16	71.4763	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#14720 - 	CGI_10023957	superfamily	247792	10	61	1.94E-06	44.744	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#14721 - 	CGI_10023958	superfamily	220249	31	95	1.01E-12	60.6968	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#14721 - 	CGI_10023958	superfamily	220249	174	241	2.04E-12	59.9264	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#14722 - 	CGI_10023959	superfamily	220249	54	116	3.78E-13	59.9264	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#14723 - 	CGI_10023960	superfamily	241567	13	231	1.70E-82	248.669	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#14724 - 	CGI_10023961	superfamily	246680	27	103	1.44E-14	69.1802	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#14724 - 	CGI_10023961	superfamily	246680	136	217	5.08E-06	44.5225	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#14724 - 	CGI_10023961	superfamily	246680	278	331	0.00379101	35.7742	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#14725 - 	CGI_10023962	superfamily	220691	66	299	0.00902285	36.4418	cl18569	7TM_GPCR_Srv superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#14727 - 	CGI_10023964	superfamily	243072	1	122	2.93E-09	52.3858	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14728 - 	CGI_10023966	superfamily	243146	82	130	4.49E-08	47.6691	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14732 - 	CGI_10001204	superfamily	241563	78	114	2.47E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14732 - 	CGI_10001204	superfamily	245027	111	217	0.00160265	37.758	cl09176	FlgN superfamily	C	 - 	FlgN protein; This family includes the FlgN protein and export chaperone involved in flagellar synthesis.
Q#14734 - 	CGI_10001493	superfamily	242164	20	117	3.99E-30	108.578	cl00878	Ribosomal_S24e superfamily	C	 - 	Ribosomal protein S24e; Ribosomal protein S24e.  
Q#14735 - 	CGI_10001494	superfamily	220695	96	237	1.70E-05	44.4919	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#14736 - 	CGI_10001495	superfamily	217293	10	144	7.49E-17	77.2879	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#14736 - 	CGI_10001495	superfamily	202474	151	201	6.28E-10	57.2785	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#14738 - 	CGI_10001521	superfamily	243067	110	205	4.06E-08	51.6444	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#14738 - 	CGI_10001521	superfamily	243053	315	524	2.39E-22	94.9189	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#14739 - 	CGI_10001522	superfamily	243179	128	196	2.08E-19	83.1217	cl02781	tetraspanin_LEL superfamily	C	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#14739 - 	CGI_10001522	superfamily	248019	259	317	0.000667719	40.6387	cl17465	DAGK_cat superfamily	N	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#14740 - 	CGI_10001337	superfamily	248028	44	155	9.68E-06	42.4905	cl17474	Steroid_dh superfamily	C	 - 	"3-oxo-5-alpha-steroid 4-dehydrogenase; This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development."
Q#14743 - 	CGI_10020256	superfamily	242280	53	82	0.000204109	34.5818	cl01066	Trm112p superfamily	N	 - 	"Trm112p-like protein; The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices."
Q#14744 - 	CGI_10020257	superfamily	241647	23	40	0.00485621	34.0406	cl00157	WW superfamily	N	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#14745 - 	CGI_10020258	superfamily	241647	8	39	5.91E-07	46.7522	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#14746 - 	CGI_10020259	superfamily	241644	52	143	1.48E-17	75.4084	cl00154	UBCc superfamily	N	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#14747 - 	CGI_10020260	superfamily	248338	159	279	0.000808358	39.5069	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#14748 - 	CGI_10020261	superfamily	244824	49	507	0	617.706	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#14749 - 	CGI_10020262	superfamily	241559	40	154	3.45E-22	87.7515	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#14751 - 	CGI_10020264	superfamily	243092	381	683	1.51E-35	140.163	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14751 - 	CGI_10020264	superfamily	243035	2694	2812	6.34E-28	112.713	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	2250	2364	3.35E-27	110.402	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	245847	1993	2134	1.74E-26	109.364	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#14751 - 	CGI_10020264	superfamily	243035	2988	3098	3.91E-26	107.32	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	2537	2658	7.38E-26	106.55	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	2842	2959	6.70E-24	100.772	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	245847	1842	1977	6.67E-23	98.9636	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#14751 - 	CGI_10020264	superfamily	243035	3125	3245	2.85E-22	96.1497	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	1567	1670	2.39E-21	93.4533	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	245847	1678	1822	5.62E-20	90.104	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#14751 - 	CGI_10020264	superfamily	243035	984	1112	7.64E-20	88.9285	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	2392	2507	8.46E-20	88.8309	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	1413	1531	1.18E-19	88.4457	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	1263	1384	6.93E-19	86.5197	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	243035	1132	1248	3.26E-13	69.5709	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14751 - 	CGI_10020264	superfamily	247856	53	117	7.54E-07	49.4685	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#14751 - 	CGI_10020264	superfamily	243092	556	862	1.87E-20	94.7092	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14751 - 	CGI_10020264	superfamily	243093	2144	2222	2.86E-12	66.0146	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#14751 - 	CGI_10020264	superfamily	243092	196	539	3.11E-12	68.9008	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14752 - 	CGI_10020265	superfamily	241568	108	160	1.46E-06	47.8428	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14752 - 	CGI_10020265	superfamily	245213	1667	1699	0.000214159	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14752 - 	CGI_10020265	superfamily	245213	1278	1320	0.000291575	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14752 - 	CGI_10020265	superfamily	245213	1500	1532	0.000667711	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14752 - 	CGI_10020265	superfamily	219525	1698	1742	8.25E-07	48.5693	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#14752 - 	CGI_10020265	superfamily	241578	1454	1497	8.74E-06	47.7648	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14752 - 	CGI_10020265	superfamily	241578	1233	1273	1.31E-05	47.3796	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14752 - 	CGI_10020265	superfamily	241578	1758	1798	4.55E-05	45.8388	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14752 - 	CGI_10020265	superfamily	219525	2003	2039	8.74E-05	42.7914	cl06646	GCC2_GCC3 superfamily	C	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#14752 - 	CGI_10020265	superfamily	219525	2071	2119	0.000211637	41.6358	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#14752 - 	CGI_10020265	superfamily	241578	1796	1838	0.000553478	42.372	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14752 - 	CGI_10020265	superfamily	221695	1646	1670	0.000901014	39.3606	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#14752 - 	CGI_10020265	superfamily	222150	718	743	0.00114938	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14752 - 	CGI_10020265	superfamily	221695	1562	1585	0.00152551	38.5902	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#14752 - 	CGI_10020265	superfamily	241578	1362	1403	0.00204813	40.446	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14752 - 	CGI_10020265	superfamily	241568	51	103	0.00339288	37.8913	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14752 - 	CGI_10020265	superfamily	241578	1837	1880	0.00449847	39.6756	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14753 - 	CGI_10020266	superfamily	248022	19	429	1.94E-40	150.121	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#14754 - 	CGI_10020267	superfamily	247792	16	66	5.10E-08	50.9072	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#14754 - 	CGI_10020267	superfamily	241563	165	195	0.000430471	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14755 - 	CGI_10020268	superfamily	241868	171	282	1.47E-51	169.023	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#14759 - 	CGI_10020274	superfamily	247755	159	379	6.06E-135	388.39	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#14760 - 	CGI_10020275	superfamily	243092	726	993	6.05E-14	72.3676	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14760 - 	CGI_10020275	superfamily	243092	550	831	3.84E-06	48.4852	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14760 - 	CGI_10020275	superfamily	243092	366	444	5.55E-06	48.1	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14761 - 	CGI_10020276	superfamily	247856	55	92	0.00244352	33.2901	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#14765 - 	CGI_10002114	superfamily	219579	23	69	9.75E-06	44.0966	cl16001	Afi1 superfamily	 - 	 - 	"Docking domain of Afi1 for Arf3 in vesicle trafficking; This domain occurs at the N-terminal of Afi1, a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3. Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalisation. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth."
Q#14767 - 	CGI_10002116	superfamily	242748	209	280	0.00267773	36.6905	cl01853	COG4467 superfamily	C	 - 	"Regulator of replication initiation timing [Replication,    recombination, and repair]"
Q#14770 - 	CGI_10020281	superfamily	243072	1	98	1.87E-18	76.2682	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14771 - 	CGI_10020282	superfamily	243082	225	240	3.62E-05	43.3155	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#14772 - 	CGI_10020283	superfamily	241594	1509	1828	1.00E-88	295.243	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#14772 - 	CGI_10020283	superfamily	243072	851	980	3.81E-19	86.2834	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	757	869	2.65E-16	78.1942	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	670	816	1.94E-15	75.4978	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	994	1102	2.54E-15	75.1126	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	617	707	7.98E-11	62.0158	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	1176	1264	8.01E-10	58.9342	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	86	199	4.53E-05	43.9115	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	189	304	0.000279223	41.6003	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	281	404	0.00081694	40.0595	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14772 - 	CGI_10020283	superfamily	243072	1298	1371	0.00175482	38.9039	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14773 - 	CGI_10020284	superfamily	245864	27	418	9.07E-95	310.75	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#14773 - 	CGI_10020284	superfamily	243068	624	895	4.20E-10	60.2516	cl02523	Zona_pellucida superfamily	 - 	 - 	Zona pellucida-like domain; Zona pellucida-like domain.  
Q#14774 - 	CGI_10020285	superfamily	247725	18	235	2.31E-30	121.307	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#14774 - 	CGI_10020285	superfamily	247725	236	423	3.30E-18	85.4833	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#14775 - 	CGI_10020286	superfamily	247727	51	159	7.85E-06	44.7283	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#14775 - 	CGI_10020286	superfamily	247727	474	587	0.000905784	38.1799	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#14776 - 	CGI_10020287	superfamily	242206	43	158	2.59E-31	115.588	cl00938	Rieske superfamily	 - 	 - 	"Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis."
Q#14777 - 	CGI_10020288	superfamily	242206	124	239	2.91E-33	121.751	cl00938	Rieske superfamily	 - 	 - 	"Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis."
Q#14779 - 	CGI_10020290	superfamily	243035	849	960	8.52E-26	104.624	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14779 - 	CGI_10020290	superfamily	243035	977	1088	5.42E-23	96.5349	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14779 - 	CGI_10020290	superfamily	245213	507	537	0.00213745	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14779 - 	CGI_10020290	superfamily	246918	658	710	4.53E-14	68.7675	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14779 - 	CGI_10020290	superfamily	246918	716	768	1.37E-12	64.5303	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14779 - 	CGI_10020290	superfamily	246918	618	653	0.00249469	37.1811	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14780 - 	CGI_10020291	superfamily	246918	178	230	1.09E-11	60.2931	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14780 - 	CGI_10020291	superfamily	246918	292	343	3.11E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14780 - 	CGI_10020291	superfamily	246918	235	287	1.58E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14780 - 	CGI_10020291	superfamily	246918	121	173	2.45E-10	56.4411	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14780 - 	CGI_10020291	superfamily	246918	357	401	6.96E-06	43.7295	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14780 - 	CGI_10020291	superfamily	246918	64	93	0.000319552	38.7219	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14780 - 	CGI_10020291	superfamily	246918	7	36	0.000373196	38.3367	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14781 - 	CGI_10020292	superfamily	243035	116	227	3.35E-28	110.402	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14781 - 	CGI_10020292	superfamily	243035	2	99	5.79E-21	89.6013	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14781 - 	CGI_10020292	superfamily	246918	578	629	3.92E-12	62.6043	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14781 - 	CGI_10020292	superfamily	246918	407	459	1.43E-10	57.9819	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14781 - 	CGI_10020292	superfamily	246918	302	345	3.50E-08	51.0483	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14781 - 	CGI_10020292	superfamily	246918	635	686	2.71E-05	42.5739	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14781 - 	CGI_10020292	superfamily	246918	530	558	0.000207214	40.2627	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14781 - 	CGI_10020292	superfamily	246918	253	288	0.0014021	37.5663	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14782 - 	CGI_10020294	superfamily	246918	14	66	1.72E-14	64.1451	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14783 - 	CGI_10020295	superfamily	216653	354	494	5.73E-20	86.1118	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#14783 - 	CGI_10020295	superfamily	216653	100	181	9.13E-17	76.8671	cl08331	Na_Ca_ex superfamily	C	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#14784 - 	CGI_10020296	superfamily	219086	2	144	7.65E-18	76.0724	cl05857	BNIP3 superfamily	 - 	 - 	"BNIP3; This family consists of several mammalian specific BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 or BNIP3 sequences. BNIP3 belongs to the Bcl-2 homology 3 (BH3)-only family, a Bcl-2-related family possessing an atypical Bcl-2 homology 3 (BH3) domain, which regulates PCD from mitochondrial sites by selective Bcl-2/Bcl-XL interactions. BNIP3 family members contain a C-terminal transmembrane domain that is required for their mitochondrial localisation, homodimerisation, as well as regulation of their pro-apoptotic activities. BNIP3-mediated apoptosis has been reported to be independent of caspase activation and cytochrome c release and is characterized by early plasma membrane and mitochondrial damage, prior to the appearance of chromatin condensation or DNA fragmentation."
Q#14785 - 	CGI_10020297	superfamily	238012	220	271	1.38E-10	58.5198	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#14785 - 	CGI_10020297	superfamily	238012	120	172	8.71E-08	50.4306	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#14785 - 	CGI_10020297	superfamily	238012	173	212	4.04E-05	42.3414	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#14785 - 	CGI_10020297	superfamily	245201	732	935	9.50E-51	180.04	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14785 - 	CGI_10020297	superfamily	247038	306	402	8.09E-07	47.9893	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#14785 - 	CGI_10020297	superfamily	247038	404	464	1.34E-05	44.3301	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#14792 - 	CGI_10020304	superfamily	243073	311	354	0.00215091	35.5491	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#14793 - 	CGI_10001789	superfamily	241584	802	882	5.92E-10	59.0471	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14793 - 	CGI_10001789	superfamily	241584	693	767	2.63E-06	47.8763	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14793 - 	CGI_10001789	superfamily	241584	1475	1560	1.96E-05	45.1799	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14793 - 	CGI_10001789	superfamily	241584	331	420	5.35E-05	44.0243	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14793 - 	CGI_10001789	superfamily	241584	926	1018	0.000263697	41.7131	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14793 - 	CGI_10001789	superfamily	241584	425	514	0.000996139	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14793 - 	CGI_10001789	superfamily	241832	2001	2125	0.00130823	39.527	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14793 - 	CGI_10001789	superfamily	241584	1046	1131	0.00482509	37.5941	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14794 - 	CGI_10003044	superfamily	243092	70	107	1.52E-05	42.2994	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14794 - 	CGI_10003044	superfamily	243092	377	439	0.000943363	39.6256	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14796 - 	CGI_10007526	superfamily	241563	135	171	0.00103409	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14797 - 	CGI_10007527	superfamily	243092	157	276	0.000682227	39.6256	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14798 - 	CGI_10007528	superfamily	217953	43	285	8.62E-66	210.055	cl04440	DUF410 superfamily	 - 	 - 	Protein of unknown function (DUF410); This family of proteins is from Caenorhabditis elegans and has no known function. The protein has some GO references indicating that the protein has a positive regulation of growth rate and is involved in nematode larval development.
Q#14799 - 	CGI_10007529	superfamily	241599	104	162	9.77E-25	95.388	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#14802 - 	CGI_10007533	superfamily	241568	49	77	0.00345078	34.4245	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#14803 - 	CGI_10007534	superfamily	214531	293	333	4.90E-10	54.5301	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#14803 - 	CGI_10007534	superfamily	215683	267	307	7.80E-06	42.5423	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#14807 - 	CGI_10002798	superfamily	242889	208	277	2.50E-12	61.1039	cl02111	PCI superfamily	N	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#14810 - 	CGI_10003195	superfamily	241578	1065	1226	1.57E-40	150.52	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	41	202	1.05E-38	145.127	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	664	825	1.05E-38	145.127	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	1902	2063	3.03E-31	123.556	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	2770	2934	8.56E-24	101.599	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	1291	1436	1.94E-22	97.7474	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	241	401	2.48E-20	91.5842	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	2128	2279	3.94E-20	91.199	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	452	606	2.70E-18	85.421	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	1704	1844	1.58E-17	83.495	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	1492	1648	3.35E-17	82.3394	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	245213	2085	2120	2.54E-12	64.9654	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14810 - 	CGI_10003195	superfamily	245213	2310	2345	3.80E-11	61.4986	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14810 - 	CGI_10003195	superfamily	241578	2578	2747	1.92E-39	147.433	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	860	1012	2.89E-24	103.622	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	241578	2353	2507	8.95E-20	90.2064	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14810 - 	CGI_10003195	superfamily	245213	2538	2571	1.38E-07	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14812 - 	CGI_10003771	superfamily	217643	1	262	1.25E-134	391.906	cl04182	Solute_trans_a superfamily	 - 	 - 	"Organic solute transporter Ostalpha; This family is a transmembrane organic solute transport protein. In vertebrates these proteins form a complex with Ostbeta, and function as bile transporters. In plants they may transport brassinosteroid-like compounds and act as regulators of cell death."
Q#14813 - 	CGI_10003772	superfamily	219226	338	535	5.66E-36	132.423	cl06118	Senescence superfamily	 - 	 - 	"Senescence-associated protein; This family contains a number of plant senescence-associated proteins of approximately 450 residues in length. In Hemerocallis, petals have a genetically based program that leads to senescence and cell death approximately 24 hours after the flower opens, and it is believed that senescence proteins produced around that time have a role in this program. This family extends to the higher vertebrates where the full-length protein is often a Spartin, associated with mitochondrial membranes and transportation along microtubules."
Q#14813 - 	CGI_10003772	superfamily	241764	40	115	6.79E-06	44.1907	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#14814 - 	CGI_10003773	superfamily	247068	1771	1871	6.53E-31	121.266	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1980	2076	3.30E-30	118.955	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1667	1763	3.83E-29	115.874	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2195	2291	1.94E-28	113.948	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2936	3033	1.59E-26	108.555	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	997	1092	2.45E-26	107.784	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1315	1410	2.59E-26	107.784	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1209	1307	8.24E-26	106.244	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1883	1972	2.90E-25	104.703	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2085	2186	1.13E-23	100.081	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2506	2606	1.90E-23	99.3101	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	584	684	2.49E-23	99.3101	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	479	575	4.22E-23	98.5397	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1420	1519	1.16E-21	94.3025	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2829	2924	7.06E-21	91.9913	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1100	1201	7.95E-21	91.9913	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	3041	3141	8.45E-21	91.9913	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	3257	3354	4.12E-20	89.6801	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2613	2710	2.04E-19	87.7541	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247907	3833	3998	5.35E-19	88.244	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#14814 - 	CGI_10003773	superfamily	247068	3150	3248	7.96E-19	86.2133	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2406	2498	5.31E-18	83.5169	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	252	356	1.45E-17	82.3613	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	370	470	1.68E-17	82.3613	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	245213	3753	3789	7.26E-17	78.8326	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14814 - 	CGI_10003773	superfamily	247068	796	885	7.28E-16	77.3537	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	1570	1658	3.61E-15	75.4277	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	3364	3465	3.85E-15	75.4277	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2717	2820	2.29E-14	73.1165	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	144	244	2.77E-14	72.7313	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	693	783	1.54E-13	70.8053	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	896	988	1.72E-11	64.6421	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	44	131	1.11E-10	62.3309	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247068	2308	2391	4.18E-10	60.4049	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#14814 - 	CGI_10003773	superfamily	247907	4064	4224	6.58E-10	60.8949	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#14814 - 	CGI_10003773	superfamily	245213	3793	3827	4.07E-08	53.4094	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14814 - 	CGI_10003773	superfamily	245213	4027	4059	8.03E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14814 - 	CGI_10003773	superfamily	245213	3728	3751	0.000983907	40.3126	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14815 - 	CGI_10003774	superfamily	241578	22	192	8.89E-38	133.507	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14816 - 	CGI_10001913	superfamily	245847	24	165	1.92E-09	55.5863	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#14817 - 	CGI_10002289	superfamily	201885	59	226	1.72E-37	131.206	cl12249	I_LWEQ superfamily	 - 	 - 	"I/LWEQ domain; I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin and yeast Sla2p interact with F-actin. I/LWEQ domains can be placed into four major groups based on sequence similarity: (1) Metazoan talin; (2) Dictyostelium TalA/TalB and SLA110; (3) metazoan Hip1p; and (4) yeast Sla2p. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks."
Q#14818 - 	CGI_10001177	superfamily	222313	109	160	1.62E-08	51.4238	cl18662	Methyltransf_32 superfamily	C	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#14820 - 	CGI_10007313	superfamily	247725	154	274	1.57E-66	218.763	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#14820 - 	CGI_10007313	superfamily	246669	40	135	0.000346526	40.1279	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#14820 - 	CGI_10007313	superfamily	218976	470	562	2.57E-36	133.728	cl05671	DUF1041 superfamily	 - 	 - 	"Domain of Unknown Function (DUF1041); This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains."
Q#14823 - 	CGI_10003433	superfamily	247727	49	111	2.08E-25	96.3757	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#14824 - 	CGI_10003434	superfamily	205431	296	478	1.07E-61	208.704	cl16184	DUF4042 superfamily	 - 	 - 	"Domain of unknown function (DUF4042); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 180 amino acids in length."
Q#14825 - 	CGI_10003435	superfamily	222150	456	480	2.06E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14825 - 	CGI_10003435	superfamily	222150	428	449	2.32E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14825 - 	CGI_10003435	superfamily	222150	343	367	3.33E-05	42.3789	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14825 - 	CGI_10003435	superfamily	222150	370	395	8.94E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14825 - 	CGI_10003435	superfamily	222150	569	594	0.000533044	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14825 - 	CGI_10003435	superfamily	222150	398	421	0.00733108	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#14828 - 	CGI_10004692	superfamily	219669	196	279	3.45E-07	46.6171	cl06832	Integrin_B_tail superfamily	 - 	 - 	Integrin beta tail domain; This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
Q#14829 - 	CGI_10004693	superfamily	248247	53	123	0.00158819	37.3001	cl17693	Integrin_beta superfamily	C	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#14830 - 	CGI_10004694	superfamily	246723	370	1004	0	791.774	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#14831 - 	CGI_10004695	superfamily	243109	1	164	1.29E-115	327.923	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#14833 - 	CGI_10003065	superfamily	241691	417	537	0.000204367	41.3436	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#14835 - 	CGI_10026021	superfamily	247724	512	714	4.58E-35	134.069	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#14835 - 	CGI_10026021	superfamily	248054	6	221	3.00E-10	59.6235	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#14836 - 	CGI_10026022	superfamily	248363	7	131	7.21E-39	129.27	cl17809	Sedlin_N superfamily	 - 	 - 	"Sedlin, N-terminal conserved region; Mutations in this protein are associated with the X-linked spondyloepiphyseal dysplasia tarda syndrome (OMIM:313400). This family represents an N-terminal conserved region."
Q#14837 - 	CGI_10026023	superfamily	243173	389	603	1.22E-113	350.101	cl02774	Topoisomer_IB_N superfamily	 - 	 - 	"Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into:  topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes.  Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts.  In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topos I play putative roles in organizing the kinetoplast DNA network unique to these parasites.  This family may represent more than one structural domain."
Q#14837 - 	CGI_10026023	superfamily	241691	613	812	6.63E-78	254.114	cl00213	DNA_BRE_C superfamily	 - 	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#14837 - 	CGI_10026023	superfamily	206538	867	938	1.55E-36	133.121	cl16833	Topo_C_assoc superfamily	 - 	 - 	C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.
Q#14838 - 	CGI_10026024	superfamily	203031	97	157	3.10E-05	40.3892	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#14839 - 	CGI_10026025	superfamily	241748	178	411	1.51E-92	296.95	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#14839 - 	CGI_10026025	superfamily	219951	521	681	3.98E-68	225.191	cl07315	SPT16 superfamily	 - 	 - 	FACT complex subunit (SPT16/CDC68); Proteins in this family are subunits the FACT complex. The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin.
Q#14839 - 	CGI_10026025	superfamily	247725	798	888	8.97E-27	106.456	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#14843 - 	CGI_10026029	superfamily	245213	168	204	6.90E-08	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14843 - 	CGI_10026029	superfamily	245213	130	166	1.99E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14843 - 	CGI_10026029	superfamily	245213	207	242	2.56E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#14845 - 	CGI_10026031	superfamily	247755	50	259	1.20E-72	235.628	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#14845 - 	CGI_10026031	superfamily	247789	386	593	5.85E-30	117.745	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#14848 - 	CGI_10026034	superfamily	246908	179	260	6.42E-05	42.4427	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#14848 - 	CGI_10026034	superfamily	246680	972	1048	0.00465668	36.5446	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#14848 - 	CGI_10026034	superfamily	247724	326	558	1.77E-14	72.3687	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#14848 - 	CGI_10026034	superfamily	246908	56	147	0.00128676	38.3639	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#14848 - 	CGI_10026034	superfamily	247803	244	359	0.00850285	36.5938	cl17249	YlqF_related_GTPase superfamily	 - 	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#14849 - 	CGI_10026035	superfamily	243072	15	158	6.09E-27	103.617	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14849 - 	CGI_10026035	superfamily	247792	333	369	0.00974259	33.5732	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#14849 - 	CGI_10026035	superfamily	247792	242	285	3.69E-08	49.6856	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#14849 - 	CGI_10026035	superfamily	247792	195	238	1.90E-05	41.5964	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#14850 - 	CGI_10026036	superfamily	243072	501	620	8.59E-32	120.566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#14850 - 	CGI_10026036	superfamily	241760	94	138	2.61E-26	102.537	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#14850 - 	CGI_10026036	superfamily	115363	26	85	1.19E-24	98.2129	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#14850 - 	CGI_10026036	superfamily	115363	165	232	3.59E-24	97.0573	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#14852 - 	CGI_10026038	superfamily	242206	8	99	1.88E-15	67.8991	cl00938	Rieske superfamily	 - 	 - 	"Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis."
Q#14853 - 	CGI_10026039	superfamily	246597	18	312	3.39E-86	263.001	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#14855 - 	CGI_10026041	superfamily	241607	483	519	1.77E-06	45.7238	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#14855 - 	CGI_10026041	superfamily	241607	532	559	0.000338376	39.1754	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#14855 - 	CGI_10026041	superfamily	241607	626	643	0.000548575	38.405	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#14855 - 	CGI_10026041	superfamily	217473	46	333	7.49E-06	46.9745	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#14857 - 	CGI_10026043	superfamily	247724	46	222	6.66E-122	346.958	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#14860 - 	CGI_10026046	superfamily	243092	141	263	4.09E-08	52.7224	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14861 - 	CGI_10026047	superfamily	247058	34	227	1.29E-74	228.984	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#14862 - 	CGI_10026048	superfamily	241832	363	464	8.60E-51	170.045	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14862 - 	CGI_10026048	superfamily	241832	25	124	8.25E-41	142.75	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14862 - 	CGI_10026048	superfamily	241832	135	227	2.32E-21	88.9338	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14862 - 	CGI_10026048	superfamily	241832	272	341	3.21E-15	71.5338	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14863 - 	CGI_10026049	superfamily	150787	32	540	9.20E-153	450.041	cl10851	DUF2362 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2362); This is a family of proteins conserved from nematodes to humans. The function is not known.
Q#14865 - 	CGI_10026051	superfamily	245599	522	695	2.70E-38	140.436	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#14865 - 	CGI_10026051	superfamily	207662	42	114	8.06E-35	127.293	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#14866 - 	CGI_10026052	superfamily	218721	39	291	3.18E-32	126.462	cl05344	TROVE superfamily	C	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#14866 - 	CGI_10026052	superfamily	218721	282	479	3.07E-13	69.8374	cl05344	TROVE superfamily	N	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#14867 - 	CGI_10026053	superfamily	218721	13	351	3.24E-51	178.078	cl05344	TROVE superfamily	 - 	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#14868 - 	CGI_10026054	superfamily	218721	2	341	7.16E-58	197.724	cl05344	TROVE superfamily	 - 	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#14868 - 	CGI_10026054	superfamily	241578	345	478	5.24E-05	42.4416	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14869 - 	CGI_10026055	superfamily	242102	1	129	6.75E-32	115.837	cl00801	FlaRed superfamily	 - 	 - 	"Flavin Reductases; Flavin reductase catalyzes the reduction of FMN or FAD using NAD(P)H as a cofactor. It is part of a two-component enzyme system, composed of a smaller component (flavin reductase) and a larger component (an oxidase), which uses the reduced flavin to hydroxylate substrates."
Q#14870 - 	CGI_10026056	superfamily	245212	484	526	4.82E-07	47.6294	cl09940	S4 superfamily	C	 - 	"S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site;  Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes."
Q#14870 - 	CGI_10026056	superfamily	215762	385	483	1.80E-26	103.559	cl02814	Ribosomal_S4 superfamily	 - 	 - 	Ribosomal protein S4/S9 N-terminal domain; This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.
Q#14872 - 	CGI_10026058	superfamily	245087	4	256	1.49E-98	291.07	cl09515	PCNA superfamily	 - 	 - 	"Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea.  These polymerase processivity factors play a role in DNA replication and repair.  PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.   PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY]."
Q#14874 - 	CGI_10026060	superfamily	246680	825	907	1.61E-39	142.073	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#14874 - 	CGI_10026060	superfamily	194336	490	589	5.75E-25	101.168	cl02517	ZU5 superfamily	 - 	 - 	ZU5 domain; Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
Q#14874 - 	CGI_10026060	superfamily	245814	76	160	3.78E-16	75.5093	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#14874 - 	CGI_10026060	superfamily	246918	222	270	4.58E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14874 - 	CGI_10026060	superfamily	246918	173	217	2.10E-08	52.2039	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14878 - 	CGI_10026064	superfamily	245206	10	340	5.58E-162	461.202	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#14879 - 	CGI_10026065	superfamily	245206	88	271	1.77E-78	245.876	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#14879 - 	CGI_10026065	superfamily	245206	12	84	1.77E-05	44.2971	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#14881 - 	CGI_10026067	superfamily	110440	475	502	0.000532649	37.7725	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14881 - 	CGI_10026067	superfamily	241563	50	86	0.00564561	35.0055	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14882 - 	CGI_10026068	superfamily	245201	18	269	9.87E-71	227.403	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14882 - 	CGI_10026068	superfamily	248058	357	485	4.41E-60	195.35	cl17504	CaMKII_AD superfamily	 - 	 - 	Calcium/calmodulin dependent protein kinase II Association; This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
Q#14883 - 	CGI_10026069	superfamily	246918	46	98	5.26E-14	64.9155	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14883 - 	CGI_10026069	superfamily	246918	160	212	4.10E-13	62.6043	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14883 - 	CGI_10026069	superfamily	246918	103	155	5.36E-11	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#14884 - 	CGI_10026070	superfamily	243035	340	415	5.12E-15	71.1117	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14884 - 	CGI_10026070	superfamily	243035	212	321	3.02E-22	91.2121	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#14886 - 	CGI_10026072	superfamily	246597	38	342	0	682.492	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#14887 - 	CGI_10026074	superfamily	215647	620	819	2.31E-11	63.3964	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#14889 - 	CGI_10026076	superfamily	241584	944	1029	7.60E-05	42.0983	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#14889 - 	CGI_10026076	superfamily	216686	10	187	3.48E-46	165.574	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#14889 - 	CGI_10026076	superfamily	222429	216	270	4.88E-06	45.6944	cl18676	Myb_DNA-bind_5 superfamily	N	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#14889 - 	CGI_10026076	superfamily	241571	884	938	2.88E-05	43.5551	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14889 - 	CGI_10026076	superfamily	241571	695	785	3.43E-05	43.5328	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14889 - 	CGI_10026076	superfamily	241571	537	619	0.00230641	37.7771	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14890 - 	CGI_10026077	superfamily	245248	102	566	1.21E-69	233.659	cl10080	RPE65 superfamily	 - 	 - 	"Retinal pigment epithelial membrane protein; This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria."
Q#14891 - 	CGI_10026078	superfamily	241599	387	444	8.12E-25	97.6992	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#14891 - 	CGI_10026078	superfamily	217293	28	229	4.35E-30	116.963	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#14891 - 	CGI_10026078	superfamily	202474	236	313	1.91E-12	65.7529	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#14892 - 	CGI_10026079	superfamily	247727	123	220	2.96E-15	68.6106	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#14894 - 	CGI_10026081	superfamily	241750	573	770	2.12E-27	111.991	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#14895 - 	CGI_10026082	superfamily	241749	7	144	5.46E-33	115.561	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#14898 - 	CGI_10005949	superfamily	241638	76	198	1.56E-10	55.0669	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#14901 - 	CGI_10005952	superfamily	221377	208	350	5.68E-07	47.8487	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#14903 - 	CGI_10005954	superfamily	219127	69	367	2.08E-81	253.772	cl05943	MIG-14_Wnt-bd superfamily	 - 	 - 	"Wnt-binding factor required for Wnt secretion; MIG-14 is a Wnt-binding factor. Newly synthesised EGL-20/Wnt binds to MIG-14 in the Golgi, targetting the Wnt to the cell membrane for secretion. AP-2-mediated endocytosis and retromer retrieval at the sorting endosome would recycle MIG-14 to the Golgi, where it can bind to EGL-20/Wnt for next cycle of secretion."
Q#14907 - 	CGI_10017411	superfamily	110440	82	108	8.81E-05	37.0021	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#14909 - 	CGI_10017413	superfamily	241563	65	106	5.27E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14910 - 	CGI_10017414	superfamily	241563	62	103	1.86E-05	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14911 - 	CGI_10017415	superfamily	246664	201	233	5.27E-08	51.5418	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#14912 - 	CGI_10017416	superfamily	246664	104	562	2.71E-128	392.829	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#14914 - 	CGI_10017418	superfamily	245227	13	653	0	1204.09	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#14915 - 	CGI_10017419	superfamily	245660	171	270	0.00086872	41.0534	cl11493	PQQ_DH_like superfamily	C	 - 	"PQQ-dependent dehydrogenases and related proteins; This family is composed of dehydrogenases with pyrroloquinoline quinone (PQQ) as a cofactor, such as ethanol, methanol, and membrane-bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller, and the family also includes distantly related proteins which are not enzymatically active and do not bind PQQ."
Q#14916 - 	CGI_10017420	superfamily	242406	1	67	6.60E-10	52.2085	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#14917 - 	CGI_10017421	superfamily	247736	79	154	7.17E-07	46.0208	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#14921 - 	CGI_10017425	superfamily	246664	56	150	1.66E-23	95.4545	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#14922 - 	CGI_10017426	superfamily	246664	316	693	1.20E-136	411.968	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#14924 - 	CGI_10017428	superfamily	241563	61	96	0.00597391	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14928 - 	CGI_10008012	superfamily	241867	25	187	8.05E-07	46.3926	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#14929 - 	CGI_10008013	superfamily	241867	29	188	7.43E-16	71.8158	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#14930 - 	CGI_10008014	superfamily	217309	56	610	0	682.501	cl09289	EMP70 superfamily	 - 	 - 	Endomembrane protein 70; Endomembrane protein 70.  
Q#14931 - 	CGI_10008015	superfamily	248372	7	114	1.61E-18	76.084	cl17818	Nuc_deoxyrib_tr superfamily	 - 	 - 	Nucleoside 2-deoxyribosyltransferase; Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyzes the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides.
Q#14932 - 	CGI_10008016	superfamily	202014	285	489	2.44E-60	203.417	cl03387	RB_A superfamily	 - 	 - 	Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
Q#14932 - 	CGI_10008016	superfamily	216744	563	681	6.37E-33	124.801	cl18378	RB_B superfamily	 - 	 - 	"Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B domain. The B domain has a cyclin fold."
Q#14932 - 	CGI_10008016	superfamily	149868	684	783	3.06E-13	68.4437	cl07508	Rb_C superfamily	C	 - 	"Rb C-terminal domain; The Rb C-terminal domain is required for high-affinity binding to E2F-DP complexes and for maximal repression of E2F-responsive promoters, thereby acting as a growth suppressor by blocking the G1-S transition of the cell cycle. This domain has a strand-loop-helix structure, which directly interacts with both E2F1 and DP1, followed by a tail segment that lacks regular secondary structure."
Q#14932 - 	CGI_10008016	superfamily	221325	76	167	0.000143104	41.5334	cl13385	DUF3452 superfamily	N	 - 	"Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with pfam01858, pfam01857. This domain has a single completely conserved residue W that may be functionally important."
Q#14935 - 	CGI_10008019	superfamily	219145	73	230	1.45E-57	182.445	cl05974	SPC25 superfamily	 - 	 - 	"Microsomal signal peptidase 25 kDa subunit (SPC25); This family consists of several microsomal signal peptidase 25 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 25 kDa subunit (SPC25)."
Q#14939 - 	CGI_10009361	superfamily	216363	3	64	1.27E-05	38.2202	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#14945 - 	CGI_10025908	superfamily	241563	68	105	9.20E-06	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#14945 - 	CGI_10025908	superfamily	128778	113	235	0.00115999	38.0147	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#14946 - 	CGI_10025909	superfamily	246908	286	387	1.11E-38	135.788	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#14947 - 	CGI_10025910	superfamily	245201	30	303	0	560.865	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#14948 - 	CGI_10025911	superfamily	198867	91	190	1.40E-41	144.994	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#14948 - 	CGI_10025911	superfamily	243146	382	429	4.66E-14	67.1983	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14948 - 	CGI_10025911	superfamily	243146	287	333	1.65E-13	65.6575	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14948 - 	CGI_10025911	superfamily	243146	418	462	6.40E-13	63.8346	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14948 - 	CGI_10025911	superfamily	243146	478	524	9.38E-13	63.3463	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14948 - 	CGI_10025911	superfamily	243146	322	367	8.28E-11	57.6714	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14948 - 	CGI_10025911	superfamily	243146	241	286	4.92E-10	55.6423	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14948 - 	CGI_10025911	superfamily	243066	27	86	0.000139872	40.3669	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#14949 - 	CGI_10025912	superfamily	241559	5	97	0.0005966	40.3404	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#14953 - 	CGI_10025916	superfamily	217958	102	192	0.00100928	39.8644	cl04445	Birna_RdRp superfamily	C	 - 	"Birnavirus RNA dependent RNA polymerase (VP1); Birnaviruses are dsRNA viruses. This family corresponds to the RNA dependent RNA polymerase. This protein is also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps."
Q#14957 - 	CGI_10025920	superfamily	241583	60	251	1.09E-48	168.904	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#14957 - 	CGI_10025920	superfamily	241571	293	412	8.37E-17	77.0674	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#14959 - 	CGI_10025922	superfamily	247948	65	116	7.85E-16	69.245	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#14960 - 	CGI_10025923	superfamily	216152	21	369	3.18E-69	226.041	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#14961 - 	CGI_10025924	superfamily	241578	364	609	1.48E-106	333.086	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#14961 - 	CGI_10025924	superfamily	218277	711	813	5.44E-28	109.928	cl04773	Sec23_helical superfamily	 - 	 - 	"Sec23/Sec24 helical domain; COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices."
Q#14961 - 	CGI_10025924	superfamily	219707	614	697	4.35E-26	104.135	cl06871	Sec23_BS superfamily	 - 	 - 	Sec23/Sec24 beta-sandwich domain; Sec23/Sec24 beta-sandwich domain.  
Q#14961 - 	CGI_10025924	superfamily	203092	287	325	9.89E-15	70.2819	cl04769	zf-Sec23_Sec24 superfamily	 - 	 - 	"Sec23/Sec24 zinc finger; COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain."
Q#14961 - 	CGI_10025924	superfamily	247044	831	884	2.79E-09	55.3836	cl15697	ADF_gelsolin superfamily	C	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#14963 - 	CGI_10025926	superfamily	247743	1305	1343	0.000126305	42.5183	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#14963 - 	CGI_10025926	superfamily	149859	18	103	1.27E-26	107.441	cl07498	MAPKK1_Int superfamily	N	 - 	Mitogen-activated protein kinase kinase 1 interacting; Mitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer.
Q#14964 - 	CGI_10025927	superfamily	220618	247	519	2.06E-16	78.38	cl10873	DUF2369 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2369); This is a proline-rich region of a group of proteins found from plants to fungi. The function is not known.
Q#14968 - 	CGI_10025931	superfamily	243066	21	125	1.74E-28	109.244	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#14968 - 	CGI_10025931	superfamily	198867	133	217	2.01E-23	95.3031	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#14968 - 	CGI_10025931	superfamily	243146	414	460	0.00155242	36.8707	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14968 - 	CGI_10025931	superfamily	243146	318	359	0.00230538	36.4855	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14968 - 	CGI_10025931	superfamily	243146	503	538	0.00669503	34.8951	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14968 - 	CGI_10025931	superfamily	243146	363	414	0.00780338	34.7314	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#14970 - 	CGI_10025933	superfamily	152105	205	252	0.00190178	36.3567	cl13169	WBP-1 superfamily	C	 - 	"WW domain-binding protein 1; This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain."
Q#14971 - 	CGI_10025934	superfamily	243092	7	311	1.85E-88	269.205	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14972 - 	CGI_10025935	superfamily	246597	12	296	0	615.774	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#14974 - 	CGI_10025937	superfamily	241832	46	155	7.12E-59	186.18	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#14975 - 	CGI_10025938	superfamily	241810	635	760	1.06E-65	217.442	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#14975 - 	CGI_10025938	superfamily	247805	136	267	8.77E-23	96.6375	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#14975 - 	CGI_10025938	superfamily	247905	359	503	7.37E-06	45.6917	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#14975 - 	CGI_10025938	superfamily	219729	846	1025	4.11E-77	250.981	cl06956	DSHCT superfamily	 - 	 - 	DSHCT (NUC185) domain; This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases.
Q#14976 - 	CGI_10025939	superfamily	216212	356	858	8.46E-90	296.51	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#14976 - 	CGI_10025939	superfamily	241651	150	313	5.96E-08	51.9422	cl00163	PTS_IIA_fru superfamily	 - 	 - 	"PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation."
Q#14977 - 	CGI_10025940	superfamily	245835	10	267	2.34E-117	358.963	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#14977 - 	CGI_10025940	superfamily	245456	612	820	1.24E-65	220.747	cl10970	AP_MHD_Cterm superfamily	 - 	 - 	"C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15."
Q#14978 - 	CGI_10025941	superfamily	243310	40	272	1.19E-74	230.973	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#14979 - 	CGI_10025942	superfamily	147693	43	107	3.54E-14	63.5391	cl05311	NDUF_B7 superfamily	 - 	 - 	"NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7); This family consists of several NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organisms. Oxidative phosphorylation is the well-characterized process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of human mitochondrial encephalomyopathies."
Q#14980 - 	CGI_10025943	superfamily	243092	8	308	1.45E-31	120.132	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#14982 - 	CGI_10025945	superfamily	241546	476	594	5.52E-50	174.28	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14982 - 	CGI_10025945	superfamily	241546	1044	1164	2.51E-48	169.658	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14982 - 	CGI_10025945	superfamily	241645	93	166	5.09E-16	75.3036	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#14982 - 	CGI_10025945	superfamily	241645	231	305	1.03E-14	71.8368	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#14982 - 	CGI_10025945	superfamily	241546	350	466	2.98E-30	117.656	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14982 - 	CGI_10025945	superfamily	241546	919	1033	8.78E-13	67.1948	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14982 - 	CGI_10025945	superfamily	241546	1284	1333	1.12E-12	66.8096	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14982 - 	CGI_10025945	superfamily	241546	1188	1272	2.03E-05	44.468	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14982 - 	CGI_10025945	superfamily	241579	623	726	0.000248762	40.9696	cl00060	FGF superfamily	 - 	 - 	"Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate embryogenesis, and has neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate one of four cell surface FGF receptors. Upon binding to FGF, the receptors dimerize and their intracellular tyrosine kinase domains become active. FGFs have internal pseudo-threefold symmetry (beta-trefoil topology)."
Q#14983 - 	CGI_10025946	superfamily	241546	164	282	2.33E-41	150.398	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	1606	1723	1.35E-36	136.916	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	673	789	2.36E-27	109.952	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	943	1043	3.55E-27	109.567	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	421	522	1.40E-16	78.7508	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	36	152	2.09E-16	78.3656	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	1107	1198	3.17E-12	66.0392	cl00011	PLAT superfamily	N	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	1210	1260	1.30E-10	61.0316	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	306	393	2.48E-08	54.098	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	834	931	6.68E-08	52.6632	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	1541	1595	2.92E-05	44.6373	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14983 - 	CGI_10025946	superfamily	241546	549	639	0.00319591	38.0257	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#14988 - 	CGI_10025951	superfamily	243091	3	33	0.000556469	34.6176	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#14990 - 	CGI_10025953	superfamily	245206	40	286	7.30E-120	347.532	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#14991 - 	CGI_10025954	superfamily	245206	50	286	4.84E-55	181.654	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#14992 - 	CGI_10025955	superfamily	248318	2	52	6.61E-14	68.2313	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#14992 - 	CGI_10025955	superfamily	216371	502	912	4.27E-165	491.568	cl18365	ERG4_ERG24 superfamily	 - 	 - 	Ergosterol biosynthesis ERG4/ERG24 family; Ergosterol biosynthesis ERG4/ERG24 family.  
Q#14993 - 	CGI_10025956	superfamily	245596	148	443	0	522.92	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#14993 - 	CGI_10025956	superfamily	247085	463	575	1.15E-20	88.3314	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#14994 - 	CGI_10025957	superfamily	147298	1003	1214	1.29E-44	162.69	cl04904	Pecanex_C superfamily	 - 	 - 	Pecanex protein (C-terminus); This family consists of C terminal region of the pecanex protein homologues. The pecanex protein is a maternal-effect neurogenic gene found in Drosophila.
Q#14995 - 	CGI_10025958	superfamily	220605	10	462	2.01E-56	199.124	cl10853	Med17 superfamily	 - 	 - 	Subunit 17 of Mediator complex; This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures.
Q#14998 - 	CGI_10025961	superfamily	247057	40	98	2.15E-07	46.4637	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#14999 - 	CGI_10025962	superfamily	245596	100	199	3.83E-28	110.475	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#14999 - 	CGI_10025962	superfamily	245596	200	239	3.47E-10	58.4732	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15001 - 	CGI_10025964	superfamily	243035	84	158	7.52E-05	39.5254	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15002 - 	CGI_10025965	superfamily	247057	285	331	2.32E-06	44.9229	cl15755	SAM_superfamily superfamily	C	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#15002 - 	CGI_10025965	superfamily	247057	215	272	7.04E-06	43.4409	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#15003 - 	CGI_10025966	superfamily	245596	75	199	8.91E-31	113.942	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15006 - 	CGI_10025969	superfamily	217473	115	339	3.02E-28	114.77	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#15007 - 	CGI_10025970	superfamily	241574	38	125	2.62E-28	111.138	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15007 - 	CGI_10025970	superfamily	241574	126	178	2.38E-16	76.8557	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15007 - 	CGI_10025970	superfamily	241574	240	416	5.21E-16	76.0853	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15008 - 	CGI_10025971	superfamily	245201	33	67	0.00613036	34.9102	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15011 - 	CGI_10005414	superfamily	243250	80	359	2.11E-85	269.133	cl02959	Glyco_hydro_9 superfamily	C	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#15013 - 	CGI_10005416	superfamily	245814	283	371	0.00223113	36.9451	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15015 - 	CGI_10005418	superfamily	248097	6	136	1.05E-15	68.831	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15016 - 	CGI_10005419	superfamily	248097	216	347	5.53E-21	86.5502	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15016 - 	CGI_10005419	superfamily	221533	89	151	0.00169806	36.1356	cl13726	TMF_DNA_bd superfamily	C	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#15017 - 	CGI_10005094	superfamily	204985	3	119	1.56E-45	146.933	cl14987	Chorein_N superfamily	 - 	 - 	"N-terminal region of Chorein, a TM vesicle-mediated sorter; Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport."
Q#15018 - 	CGI_10005095	superfamily	241610	83	135	8.69E-16	67.275	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15019 - 	CGI_10005096	superfamily	241646	40	69	4.01E-06	45.9039	cl00156	WAP superfamily	N	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#15020 - 	CGI_10005097	superfamily	241610	344	397	3.96E-20	83.0682	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15020 - 	CGI_10005097	superfamily	241832	42	87	0.000768036	37.3852	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15020 - 	CGI_10005097	superfamily	241646	271	319	8.63E-05	39.7414	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#15022 - 	CGI_10005099	superfamily	243035	42	67	0.000329761	34.883	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15023 - 	CGI_10005100	superfamily	243035	26	99	1.25E-13	61.6232	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15025 - 	CGI_10006637	superfamily	247724	13	181	1.61E-62	193.914	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15027 - 	CGI_10006639	superfamily	247038	425	511	5.75E-16	76.7245	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	1442	1496	2.10E-13	69.4057	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	1196	1267	1.84E-10	60.5461	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	2036	2118	7.36E-10	59.0053	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	1273	1350	1.39E-08	55.16	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	1867	1943	3.66E-08	53.6125	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	1772	1847	7.29E-08	52.8421	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	191	291	4.26E-05	44.3677	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	241629	92	164	2.73E-22	96.4285	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#15027 - 	CGI_10006639	superfamily	244965	492	632	1.40E-09	58.962	cl08459	PA14 superfamily	 - 	 - 	"PA14 domain; This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding."
Q#15027 - 	CGI_10006639	superfamily	247038	1972	2030	7.17E-05	43.5852	cl15674	IPT superfamily	N	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15027 - 	CGI_10006639	superfamily	247038	1679	1742	0.000187355	42.4296	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15028 - 	CGI_10006640	superfamily	247095	60	505	4.23E-168	484.082	cl15837	alkPPc superfamily	 - 	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#15030 - 	CGI_10006642	superfamily	241872	62	162	4.63E-06	43.7593	cl00453	CDP-OH_P_transf superfamily	 - 	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#15031 - 	CGI_10006643	superfamily	216050	19	103	7.38E-06	42.6763	cl18357	rve superfamily	C	 - 	Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.
Q#15032 - 	CGI_10006644	superfamily	241594	433	496	1.45E-05	45.7592	cl00077	HECTc superfamily	N	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#15035 - 	CGI_10005789	superfamily	248281	1	60	3.39E-07	44.5687	cl17727	GT1 superfamily	N	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#15037 - 	CGI_10005791	superfamily	245205	82	164	1.78E-06	44.1509	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#15039 - 	CGI_10005793	superfamily	245213	227	260	0.000111331	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15039 - 	CGI_10005793	superfamily	245213	179	224	0.000176961	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15040 - 	CGI_10005794	superfamily	246910	503	612	2.58E-60	198.68	cl15257	GIY-YIG_SF superfamily	 - 	 - 	"GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions."
Q#15040 - 	CGI_10005794	superfamily	243072	1	77	1.84E-13	67.7938	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15040 - 	CGI_10005794	superfamily	243125	406	440	9.74E-12	60.881	cl02649	LEM superfamily	 - 	 - 	"LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins; The family corresponds to a group of inner nuclear membrane proteins containing LEM domain. Emerin occurs in four phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy. Emerin interacts with A-type and B-type lamins. Man1, also termed LEM domain-containing protein 3 (LEMD3) is an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and post-mitotic reassembly. Some LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are non-membrane nuclear polypeptides. This family also contains LEM domain-containing protein LEMP-1 and LEM2. LEMP-1, also termed cancer/testis antigen 50 (CT50), is encoded by LEMD1, a novel testis-specific gene expressed in colorectal cancers. LEMP-1 may function as a cancer-testis antigen for immunotherapy of colorectal carcinoma (CRC). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization while its binding to lamin C plays an important role in the organization of lamin A/C complexes. Some uncharacterized LEM domain-containing proteins are also included in this family. Unlike other family members, these harbor an ankyrin repeat region that may mediate protein-protein interactions."
Q#15042 - 	CGI_10003981	superfamily	241551	77	138	1.89E-21	83.8875	cl00016	Cyt_c_Oxidase_Vb superfamily	N	 - 	"Cytochrome c oxidase subunit Vb.  Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome.  Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region.  Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A.  The abnormally extended conformation is stable only in the CcO assembly."
Q#15043 - 	CGI_10003982	superfamily	243058	43	128	1.71E-07	47.3091	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#15044 - 	CGI_10003983	superfamily	245201	24	270	1.53E-75	242.04	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15044 - 	CGI_10003983	superfamily	247694	400	555	3.17E-37	134.128	cl17070	AMPKA_C_like superfamily	 - 	 - 	"C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha subunit and similar domains; This family is composed of AMPKs, microtubule-associated protein/microtubule affinity regulating kinases (MARKs), yeast Kcc4p-like proteins, plant calcineurin B-Like (CBL)-interacting protein kinases (CIPKs), and similar proteins. They are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. AMPKs act as sensors for the energy status of the cell and are activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. MARKs phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Kcc4p and related proteins are septin-associated proteins that are involved in septin organization and in the yeast morphogenesis checkpoint coordinating the cell cycle with bud formation. CIPKs interact with the calcineurin B-like (CBL) calcium sensors to form a signaling network that decode specific calcium signals triggered by a variety of environmental stimuli including salinity, drought, cold, light, and mechanical perturbation, among others. All members of this family contain an N-terminal catalytic kinase domain and a C-terminal regulatory domain which is also called kinase associated domain 1 (KA1) in some cases. The C-terminal regulatory domain serves as a protein interaction domain in AMPKs and CIPKs. In MARKs and Kcc4p-like proteins, this domain binds phospholipids and may be involved in membrane localization."
Q#15045 - 	CGI_10003984	superfamily	247755	439	644	1.80E-82	259.779	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15045 - 	CGI_10003984	superfamily	241940	57	338	2.48E-123	370.022	cl00549	ABC_membrane_2 superfamily	 - 	 - 	ABC transporter transmembrane region 2; This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with pfam00664. Mutations in this domain in human ABCD3 (PMP70) are believed responsible for Zellweger Syndrome-2; mutations in human ABCD1 (ALD) are responsible for recessive X-linked adrenoleukodystrophy. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids.
Q#15046 - 	CGI_10019421	superfamily	243098	479	517	0.00139307	37.9628	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15046 - 	CGI_10019421	superfamily	241565	768	832	0.00173292	37.6863	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#15048 - 	CGI_10019423	superfamily	242199	48	261	6.75E-95	281.698	cl00931	Ribosomal_S6e superfamily	 - 	 - 	Ribosomal protein S6e; Ribosomal protein S6e.  
Q#15050 - 	CGI_10019425	superfamily	241832	15	103	2.48E-32	109.937	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15051 - 	CGI_10019426	superfamily	241832	15	103	4.39E-27	96.4547	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15054 - 	CGI_10019429	superfamily	247856	91	139	1.00E-07	51.0093	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#15058 - 	CGI_10019433	superfamily	243100	96	140	3.12E-05	40.3659	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#15060 - 	CGI_10019435	superfamily	241754	4	363	1.12E-174	516.094	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#15060 - 	CGI_10019435	superfamily	241581	452	543	2.05E-05	43.9142	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#15060 - 	CGI_10019435	superfamily	221571	659	699	3.17E-05	42.8751	cl13810	KIF1B superfamily	 - 	 - 	"Kinesin protein 1B; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00225, pfam00498. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells."
Q#15062 - 	CGI_10019437	superfamily	247787	8	191	8.62E-39	135.404	cl17233	RecA-like_NTPases superfamily	N	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#15063 - 	CGI_10019438	superfamily	242899	7	156	3.18E-51	162.345	cl02135	TRAPP superfamily	 - 	 - 	"Transport protein particle (TRAPP) component; TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterized TRAPP proteins and has a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi."
Q#15064 - 	CGI_10019439	superfamily	202351	92	215	4.92E-14	69.448	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#15064 - 	CGI_10019439	superfamily	202351	388	477	8.17E-07	47.8768	cl03662	Na_Pi_cotrans superfamily	N	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#15065 - 	CGI_10019440	superfamily	202351	128	251	1.08E-13	68.6776	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#15065 - 	CGI_10019440	superfamily	202351	374	502	4.49E-12	64.0552	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#15066 - 	CGI_10019441	superfamily	202351	27	150	8.80E-12	62.1292	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#15066 - 	CGI_10019441	superfamily	202351	181	314	6.64E-06	44.41	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#15067 - 	CGI_10019442	superfamily	241782	42	408	2.40E-169	482.106	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#15068 - 	CGI_10019443	superfamily	241884	5	217	8.77E-142	399.348	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#15069 - 	CGI_10019444	superfamily	241666	60	299	6.39E-50	178.745	cl00184	CAS_like superfamily	 - 	 - 	"Clavaminic acid synthetase (CAS) -like;  CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to succinate and CO2"
Q#15069 - 	CGI_10019444	superfamily	190398	656	980	1.72E-52	188.115	cl03672	DUF221 superfamily	 - 	 - 	"Domain of unknown function DUF221; This family consists of hypothetical transmembrane proteins none of which have any function, the aligned region is at 538 residues at maximum length."
Q#15069 - 	CGI_10019444	superfamily	222479	429	500	0.0029925	38.2608	cl16507	RSN1_TM superfamily	N	 - 	"Late exocytosis, associated with Golgi transport; This family represents the first three transmembrane regions of 11-TM proteins involved in vesicle transport. In S. cerevisiae these proteins are members of the yeast facilitator superfamily and are integral membrane proteins localised to the cell periphery, in particular to the bud-neck region. The distribution is consistent with a role in late exocytosis which is in agreement with the proteins' ability to substitute for the function of Sro7p, required for the sorting of the protein Enap1 into Golgi-derived vesicles destined for the cell surface."
Q#15071 - 	CGI_10019446	superfamily	241616	59	140	7.61E-30	111.583	cl00109	MADS superfamily	 - 	 - 	"MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers.  Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals.  Also found in fungi."
Q#15072 - 	CGI_10019447	superfamily	246748	53	307	1.87E-117	343.815	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#15074 - 	CGI_10019449	superfamily	243050	15	67	1.59E-21	85.8924	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#15074 - 	CGI_10019449	superfamily	241599	160	218	1.42E-19	80.3652	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#15074 - 	CGI_10019449	superfamily	243050	74	128	1.98E-14	66.7022	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#15075 - 	CGI_10019450	superfamily	243050	10	62	7.58E-22	87.048	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#15075 - 	CGI_10019450	superfamily	241599	155	211	2.80E-18	77.2836	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#15075 - 	CGI_10019450	superfamily	243050	70	124	3.61E-15	69.0134	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#15076 - 	CGI_10019451	superfamily	247069	101	157	4.13E-08	48.3972	cl15787	SEC14 superfamily	C	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#15076 - 	CGI_10019451	superfamily	247643	21	71	1.49E-07	44.8849	cl16919	CRAL_TRIO_N superfamily	 - 	 - 	"CRAL/TRIO, N-terminal domain; This all-alpha domain is found to the N-terminus of pfam00650."
Q#15080 - 	CGI_10019455	superfamily	241832	49	70	1.93E-05	40.2477	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15080 - 	CGI_10019455	superfamily	243175	115	172	2.29E-10	54.1958	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#15081 - 	CGI_10019456	superfamily	241832	7	78	3.64E-17	72.9896	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15081 - 	CGI_10019456	superfamily	243175	153	210	6.47E-09	51.1142	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#15082 - 	CGI_10019457	superfamily	241645	185	268	4.77E-29	106.904	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#15085 - 	CGI_10005856	superfamily	245596	409	638	8.40E-78	256.466	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15085 - 	CGI_10005856	superfamily	245596	298	358	6.52E-06	47.6876	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15085 - 	CGI_10005856	superfamily	242144	696	803	0.00769055	38.0842	cl00857	DUF63 superfamily	C	 - 	Membrane protein of unknown function DUF63; Proteins found in Archaebacteria of unknown function. These proteins are probably transmembrane proteins.
Q#15086 - 	CGI_10005857	superfamily	241609	46	113	2.11E-21	83.9667	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#15086 - 	CGI_10005857	superfamily	241609	1	34	3.69E-14	64.3338	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#15088 - 	CGI_10005859	superfamily	245596	156	269	1.11E-18	81.5852	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15089 - 	CGI_10005860	superfamily	245596	517	766	2.95E-77	252.999	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15090 - 	CGI_10005861	superfamily	248458	202	381	9.25E-09	55.3977	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#15091 - 	CGI_10005862	superfamily	243035	66	155	9.78E-15	71.8821	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15091 - 	CGI_10005862	superfamily	241613	158	187	4.05E-07	47.9718	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#15091 - 	CGI_10005862	superfamily	215647	459	528	6.44E-15	74.5672	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#15091 - 	CGI_10005862	superfamily	215647	398	473	3.47E-09	56.8481	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#15094 - 	CGI_10008331	superfamily	247068	461	558	3.45E-14	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15094 - 	CGI_10008331	superfamily	247068	369	449	5.03E-06	45.7674	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15094 - 	CGI_10008331	superfamily	247068	587	667	2.06E-05	43.8414	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15094 - 	CGI_10008331	superfamily	247068	676	751	0.000443427	39.5872	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15095 - 	CGI_10008332	superfamily	241832	273	401	2.17E-66	210.671	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15095 - 	CGI_10008332	superfamily	241832	26	125	1.73E-59	191.731	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15095 - 	CGI_10008332	superfamily	241832	160	263	1.03E-56	184.412	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15097 - 	CGI_10008334	superfamily	220792	4	41	2.66E-10	58.5715	cl11150	EPL1 superfamily	N	 - 	Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.
Q#15097 - 	CGI_10008334	superfamily	191602	364	487	9.12E-10	58.0843	cl06011	E_Pc_C superfamily	C	 - 	"Enhancer of Polycomb C-terminus; This family represents the C-terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation. This family contains several conserved motifs."
Q#15098 - 	CGI_10008335	superfamily	241599	1026	1082	1.25E-09	56.0977	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#15102 - 	CGI_10008339	superfamily	219225	1	177	4.22E-79	235.82	cl06114	FAIM1 superfamily	 - 	 - 	"Fas apoptotic inhibitory molecule (FAIM1); This family consists of several fas apoptotic inhibitory molecule (FAIM1) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM1 is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology."
Q#15104 - 	CGI_10008341	superfamily	241696	121	446	8.79E-173	490.99	cl00218	Glyco_hydrolase_16 superfamily	 - 	 - 	"glycosyl hydrolase family 16; The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues."
Q#15105 - 	CGI_10011981	superfamily	242093	170	252	0.00404417	37.1089	cl00788	MttA_Hcf106 superfamily	N	 - 	mttA/Hcf106 family; Members of this protein family are involved in a sec independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts. Members of this family in E.coli are involved in export of redox proteins with a "twin arginine" leader motif.
Q#15106 - 	CGI_10011982	superfamily	247792	18	69	9.27E-08	49.3664	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15108 - 	CGI_10011984	superfamily	243092	111	353	0.000687666	39.6256	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15109 - 	CGI_10011985	superfamily	247792	18	69	2.61E-09	53.9888	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15109 - 	CGI_10011985	superfamily	243092	387	583	0.00633063	37.6996	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15110 - 	CGI_10011986	superfamily	248097	356	478	1.34E-24	98.4914	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15111 - 	CGI_10011987	superfamily	241563	68	109	9.70E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15112 - 	CGI_10011988	superfamily	246875	183	312	7.48E-48	158.596	cl15166	RRP7_like superfamily	 - 	 - 	"RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A (Rrp7A), and similar proteins; This CD corresponds to the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7A, also termed gastric cancer antigen Zg14, is the Rrp7p homolog mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Both Rrp7p and Rrp7A harbor an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain."
Q#15112 - 	CGI_10011988	superfamily	247723	89	191	2.16E-35	125.114	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15113 - 	CGI_10011989	superfamily	241563	60	98	0.000320083	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15114 - 	CGI_10011990	superfamily	247724	313	481	1.78E-85	262.657	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15114 - 	CGI_10011990	superfamily	128778	179	277	2.00E-11	61.1266	cl17972	BBC superfamily	N	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#15114 - 	CGI_10011990	superfamily	241563	34	75	0.0001149	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15115 - 	CGI_10011991	superfamily	241563	68	109	5.35E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15115 - 	CGI_10011991	superfamily	241563	28	59	0.00536719	35.1476	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15116 - 	CGI_10011992	superfamily	247724	8	108	5.21E-44	142.86	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15117 - 	CGI_10011993	superfamily	241563	68	109	0.000120925	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15118 - 	CGI_10011994	superfamily	241563	31	72	3.51E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15119 - 	CGI_10011995	superfamily	241563	111	152	0.00275704	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15120 - 	CGI_10011996	superfamily	241563	68	109	0.00012948	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15121 - 	CGI_10011997	superfamily	241563	68	109	0.000131488	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15122 - 	CGI_10011998	superfamily	241563	68	109	0.000518184	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15122 - 	CGI_10011998	superfamily	241563	21	59	0.00213879	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15123 - 	CGI_10011999	superfamily	241563	68	109	0.000542421	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15123 - 	CGI_10011999	superfamily	241563	22	59	0.00696747	34.7624	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15124 - 	CGI_10012000	superfamily	243095	368	578	4.02E-85	267.623	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#15124 - 	CGI_10012000	superfamily	241566	304	352	5.32E-09	53.2648	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#15125 - 	CGI_10012001	superfamily	207546	277	337	3.41E-32	116.366	cl02165	CBFB_NFYA superfamily	 - 	 - 	CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B.  
Q#15126 - 	CGI_10012002	superfamily	242882	3	98	1.12E-63	192.803	cl02102	S10_plectin superfamily	 - 	 - 	Plectin/S10 domain; This presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.
Q#15127 - 	CGI_10012003	superfamily	244913	1	454	5.47E-165	489.02	cl08327	Glyco_hydro_47 superfamily	 - 	 - 	"Glycosyl hydrolase family 47; Members of this family are alpha-mannosidases that catalyze the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2)."
Q#15129 - 	CGI_10004216	superfamily	245040	26	89	3.49E-05	38.5633	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#15137 - 	CGI_10008292	superfamily	215686	11	145	0.00638987	34.3153	cl18340	Lipocalin superfamily	 - 	 - 	"Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel."
Q#15138 - 	CGI_10008293	superfamily	247068	591	687	3.55E-15	73.1165	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15138 - 	CGI_10008293	superfamily	247068	378	466	3.72E-09	55.3974	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15138 - 	CGI_10008293	superfamily	247068	270	367	2.75E-06	46.5378	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15138 - 	CGI_10008293	superfamily	245213	805	843	6.87E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15138 - 	CGI_10008293	superfamily	247068	493	582	0.000118104	41.5302	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15138 - 	CGI_10008293	superfamily	216265	874	985	1.79E-24	101.225	cl03079	Cadherin_C superfamily	 - 	 - 	Cadherin cytoplasmic region; Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
Q#15138 - 	CGI_10008293	superfamily	214565	767	813	0.000737598	39.0829	cl18312	VWC_out superfamily	 - 	 - 	von Willebrand factor (vWF) type C domain; von Willebrand factor (vWF) type C domain.  
Q#15139 - 	CGI_10008294	superfamily	234583	1	365	1.61E-135	398.382	cl18873	PRK00029 superfamily	N	 - 	hypothetical protein; Validated
Q#15140 - 	CGI_10008295	superfamily	241831	19	81	4.21E-23	85.3006	cl00386	BolA superfamily	 - 	 - 	BolA-like protein; This family consist of the morphoprotein BolA from E. coli and its various homologues. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5.
Q#15144 - 	CGI_10008299	superfamily	248024	194	370	2.75E-17	79.6345	cl17470	SBF superfamily	 - 	 - 	"Sodium Bile acid symporter family; This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae, this is a putative transmembrane protein involved in resistance to arsenic compounds."
Q#15145 - 	CGI_10008300	superfamily	247648	165	255	2.24E-32	116.081	cl16941	NTP-PPase superfamily	 - 	 - 	"Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; This superfamily contains enzymes that hydrolyze the alpha-beta phosphodiester bond of all canonical NTPs into monophosphate derivatives and pyrophosphate (PPi). Divalent ions, such as Mg2+ ion(s), are essential to activate a proposed water nucleophile and stabilize the charged intermediates to facilitate catalysis. These enzymes share a conserved divalent ion-binding motif EXX[E/D] in their active sites. They also share a highly conserved four-helix bundle, where one face forms the active site, while the other participates in oligomer assembly. The four-helix bundle consists of two central antiparallel alpha-helices that can be contained within a single protomer or form upon dimerization. The superfamily members include dimeric dUTP pyrophosphatases (dUTPases; EC 3.6.1.23), the nonspecific NTP-PPase MazG proteins, HisE-encoded phosphoribosyl ATP pyrophosphohydolase (PRA-PH), fungal histidine biosynthesis trifunctional proteins, and several uncharacterized protein families."
Q#15145 - 	CGI_10008300	superfamily	247648	41	131	5.67E-31	112.229	cl16941	NTP-PPase superfamily	 - 	 - 	"Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; This superfamily contains enzymes that hydrolyze the alpha-beta phosphodiester bond of all canonical NTPs into monophosphate derivatives and pyrophosphate (PPi). Divalent ions, such as Mg2+ ion(s), are essential to activate a proposed water nucleophile and stabilize the charged intermediates to facilitate catalysis. These enzymes share a conserved divalent ion-binding motif EXX[E/D] in their active sites. They also share a highly conserved four-helix bundle, where one face forms the active site, while the other participates in oligomer assembly. The four-helix bundle consists of two central antiparallel alpha-helices that can be contained within a single protomer or form upon dimerization. The superfamily members include dimeric dUTP pyrophosphatases (dUTPases; EC 3.6.1.23), the nonspecific NTP-PPase MazG proteins, HisE-encoded phosphoribosyl ATP pyrophosphohydolase (PRA-PH), fungal histidine biosynthesis trifunctional proteins, and several uncharacterized protein families."
Q#15149 - 	CGI_10001752	superfamily	247743	13	166	5.85E-14	68.7119	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#15150 - 	CGI_10001753	superfamily	243176	1	311	1.76E-89	278.956	cl02777	chaperonin_like superfamily	N	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#15151 - 	CGI_10001755	superfamily	243116	398	773	7.30E-161	474.217	cl02626	DNA_pol_A superfamily	 - 	 - 	"Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase  beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains."
Q#15151 - 	CGI_10001755	superfamily	246724	90	162	4.57E-29	111.337	cl14815	H3TH_StructSpec-5'-nucleases superfamily	 - 	 - 	"H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases."
Q#15151 - 	CGI_10001755	superfamily	246722	1	82	1.87E-10	59.7519	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#15151 - 	CGI_10001755	superfamily	245226	246	389	8.85E-08	51.4963	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#15152 - 	CGI_10001757	superfamily	241550	58	216	4.78E-36	132.303	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#15152 - 	CGI_10001757	superfamily	245839	257	419	8.21E-34	124.249	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#15155 - 	CGI_10011828	superfamily	241886	93	308	4.48E-57	188.537	cl00470	Aldo_ket_red superfamily	C	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#15156 - 	CGI_10011829	superfamily	245603	311	397	2.16E-20	85.7767	cl11403	pepsin_retropepsin_like superfamily	 - 	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#15157 - 	CGI_10011831	superfamily	246925	153	281	2.06E-05	46.1946	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15158 - 	CGI_10011832	superfamily	247683	226	280	2.88E-24	94.6856	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15158 - 	CGI_10011832	superfamily	247683	31	81	6.17E-24	94.0221	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15158 - 	CGI_10011832	superfamily	246908	335	427	1.29E-34	124.549	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15158 - 	CGI_10011832	superfamily	247683	140	193	9.79E-22	88.0911	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15159 - 	CGI_10011833	superfamily	241599	789	847	1.76E-21	90.3804	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#15159 - 	CGI_10011833	superfamily	199908	231	291	2.71E-08	52.2579	cl16908	DnaJ_zf superfamily	 - 	 - 	"Zinc finger domain of DnaJ and HSP40; Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. Hsp40 proteins are characterized by the presence of an N-terminal J domain, which mediates the interaction with Hsp70. This central domain contains four repeats of a CxxCxGxG motif and binds to two Zinc ions. It has been implicated in substrate binding."
Q#15159 - 	CGI_10011833	superfamily	199908	583	635	1.83E-06	46.8651	cl16908	DnaJ_zf superfamily	N	 - 	"Zinc finger domain of DnaJ and HSP40; Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. Hsp40 proteins are characterized by the presence of an N-terminal J domain, which mediates the interaction with Hsp70. This central domain contains four repeats of a CxxCxGxG motif and binds to two Zinc ions. It has been implicated in substrate binding."
Q#15160 - 	CGI_10011834	superfamily	241596	256	294	4.16E-06	43.3567	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#15162 - 	CGI_10011836	superfamily	248097	21	158	1.67E-22	87.7058	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15163 - 	CGI_10011837	superfamily	248097	46	183	3.27E-23	93.0986	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15163 - 	CGI_10011837	superfamily	248097	251	388	8.12E-23	92.3282	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15164 - 	CGI_10011838	superfamily	217293	43	232	4.20E-37	135.068	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15164 - 	CGI_10011838	superfamily	202474	239	343	7.70E-12	63.4417	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#15165 - 	CGI_10011839	superfamily	217293	1	153	1.21E-28	110.8	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15165 - 	CGI_10011839	superfamily	202474	160	256	5.58E-09	54.5821	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#15166 - 	CGI_10011840	superfamily	217293	35	225	1.14E-35	134.683	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15166 - 	CGI_10011840	superfamily	217293	425	552	6.22E-17	80.3695	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15166 - 	CGI_10011840	superfamily	202474	232	328	1.49E-08	54.5821	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#15166 - 	CGI_10011840	superfamily	202474	559	629	3.06E-07	50.7301	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#15168 - 	CGI_10011842	superfamily	217293	464	667	2.05E-24	102.711	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15168 - 	CGI_10011842	superfamily	217293	31	231	2.65E-24	102.326	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15169 - 	CGI_10011843	superfamily	217293	25	212	8.48E-38	136.994	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15169 - 	CGI_10011843	superfamily	247741	300	335	0.00186076	38.4317	cl17187	Aldolase_Class_I superfamily	NC	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#15170 - 	CGI_10011844	superfamily	217293	22	216	1.69E-25	102.711	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15170 - 	CGI_10011844	superfamily	202474	223	436	2.83E-11	61.9009	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#15171 - 	CGI_10011845	superfamily	217293	33	232	1.38E-28	111.185	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15173 - 	CGI_10011847	superfamily	216554	147	329	1.72E-32	120.662	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#15174 - 	CGI_10011848	superfamily	243072	121	245	3.15E-32	121.722	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15174 - 	CGI_10011848	superfamily	243072	36	147	1.33E-21	91.6762	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15174 - 	CGI_10011848	superfamily	243072	330	457	5.85E-21	89.7502	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15174 - 	CGI_10011848	superfamily	243072	439	556	3.60E-20	87.439	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15174 - 	CGI_10011848	superfamily	243073	617	654	2.04E-07	48.6205	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#15176 - 	CGI_10011850	superfamily	248054	5	86	1.06E-06	47.6823	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#15177 - 	CGI_10011851	superfamily	241580	120	197	8.03E-49	162.338	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#15178 - 	CGI_10012996	superfamily	177822	35	215	9.17E-18	79.1937	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#15179 - 	CGI_10012997	superfamily	247727	218	299	0.00261428	36.6391	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#15179 - 	CGI_10012997	superfamily	177822	352	591	1.32E-21	95.3721	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#15180 - 	CGI_10012998	superfamily	241575	20	87	4.48E-11	59.5935	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#15180 - 	CGI_10012998	superfamily	241575	109	175	3.40E-09	54.2007	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#15180 - 	CGI_10012998	superfamily	241575	211	278	1.78E-07	49.1931	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#15180 - 	CGI_10012998	superfamily	243132	302	667	3.68E-126	381.341	cl02661	A_deamin superfamily	 - 	 - 	"Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc."
Q#15181 - 	CGI_10012999	superfamily	241563	64	100	2.34E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15182 - 	CGI_10013000	superfamily	241900	33	285	1.01E-101	306.087	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#15183 - 	CGI_10013001	superfamily	241900	37	292	2.67E-106	318.028	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#15185 - 	CGI_10013003	superfamily	243082	306	487	4.88E-39	143.778	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#15185 - 	CGI_10013003	superfamily	243082	133	226	2.62E-07	50.9446	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#15186 - 	CGI_10013004	superfamily	246675	388	678	2.14E-143	435.697	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#15186 - 	CGI_10013004	superfamily	246669	710	838	4.09E-58	197.379	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#15186 - 	CGI_10013004	superfamily	247725	97	205	2.74E-53	182.843	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15186 - 	CGI_10013004	superfamily	150071	306	387	6.57E-21	89.555	cl08538	efhand_like superfamily	 - 	 - 	"Phosphoinositide-specific phospholipase C, efhand-like; Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme."
Q#15188 - 	CGI_10013006	superfamily	245201	33	267	2.60E-67	221.24	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15188 - 	CGI_10013006	superfamily	243239	394	481	1.15E-44	154.016	cl02916	POLO_box superfamily	 - 	 - 	"Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides."
Q#15188 - 	CGI_10013006	superfamily	243239	496	577	1.11E-36	131.55	cl02916	POLO_box superfamily	 - 	 - 	"Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides."
Q#15189 - 	CGI_10013007	superfamily	243107	22	68	1.84E-11	60.2514	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#15190 - 	CGI_10013008	superfamily	241900	538	866	0	545.834	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#15190 - 	CGI_10013008	superfamily	217007	58	354	1.52E-102	329.946	cl11995	Syja_N superfamily	 - 	 - 	SacI homology domain; This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
Q#15190 - 	CGI_10013008	superfamily	247723	865	1004	5.19E-34	129.833	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15192 - 	CGI_10013010	superfamily	247755	1	222	2.83E-70	227.819	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15192 - 	CGI_10013010	superfamily	247789	340	546	5.12E-32	123.138	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#15195 - 	CGI_10013013	superfamily	152787	122	186	1.03E-13	63.0005	cl18053	V-SNARE_C superfamily	 - 	 - 	Snare region anchored in the vesicle membrane C-terminus; Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle pfam05008.
Q#15196 - 	CGI_10013014	superfamily	218028	166	299	2.01E-14	68.4931	cl04479	AAA_4 superfamily	 - 	 - 	"Divergent AAA domain; This family is related to the pfam00004 family, and presumably has the same function (ATP-binding)."
Q#15197 - 	CGI_10002545	superfamily	245201	24	216	1.49E-32	122.345	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15199 - 	CGI_10002547	superfamily	243689	29	95	9.51E-07	47.6233	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#15200 - 	CGI_10002548	superfamily	241563	62	97	0.000351578	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15200 - 	CGI_10002548	superfamily	110440	483	510	0.00444607	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#15200 - 	CGI_10002548	superfamily	241563	8	53	0.00716296	34.6203	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15201 - 	CGI_10011741	superfamily	243058	513	592	1.51E-05	44.2276	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#15201 - 	CGI_10011741	superfamily	197676	19	41	0.00343878	36.6749	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#15203 - 	CGI_10011743	superfamily	207637	1	87	2.58E-17	75.267	cl02541	CIDE_N superfamily	 - 	 - 	"CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein."
Q#15203 - 	CGI_10011743	superfamily	150043	108	324	1.32E-74	231.936	cl07748	DFF40 superfamily	 - 	 - 	DNA fragmentation factor 40 kDa; Members of this family of eukaryotic apoptotic proteins induce DNA fragmentation and chromatin condensation during apoptosis.
Q#15204 - 	CGI_10011744	superfamily	245603	213	336	2.14E-77	239.377	cl11403	pepsin_retropepsin_like superfamily	 - 	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#15204 - 	CGI_10011744	superfamily	241645	3	70	3.18E-24	95.5144	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#15204 - 	CGI_10011744	superfamily	241643	410	445	0.000158045	39.3647	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#15207 - 	CGI_10011747	superfamily	245213	63	93	0.000489897	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15209 - 	CGI_10011749	superfamily	243034	97	168	0.0054774	34.278	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#15210 - 	CGI_10011750	superfamily	219016	64	119	1.18E-19	83.0795	cl05757	DUF1077 superfamily	N	 - 	Protein of unknown function (DUF1077); This family consists of several hypothetical eukaryotic proteins of unknown function.
Q#15211 - 	CGI_10011751	superfamily	247723	60	127	3.65E-32	115.398	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15211 - 	CGI_10011751	superfamily	206083	205	231	0.00993402	33.3504	cl16471	zf-C2H2_6 superfamily	 - 	 - 	C2H2-type zinc finger; C2H2-type zinc finger.  
Q#15212 - 	CGI_10011752	superfamily	243109	88	242	7.70E-80	246.716	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#15212 - 	CGI_10011752	superfamily	247805	273	418	4.25E-30	115.274	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15212 - 	CGI_10011752	superfamily	247805	1	66	3.15E-16	76.3693	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15214 - 	CGI_10019660	superfamily	241754	6	334	6.05E-156	446.633	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#15215 - 	CGI_10019661	superfamily	246918	32	82	8.22E-09	53.3595	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#15215 - 	CGI_10019661	superfamily	245814	673	732	2.38E-08	52.4091	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15215 - 	CGI_10019661	superfamily	246918	580	641	0.00205425	37.5663	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#15215 - 	CGI_10019661	superfamily	246918	318	347	0.0056273	36.2294	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#15215 - 	CGI_10019661	superfamily	246918	793	813	0.00639939	36.0255	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#15216 - 	CGI_10019662	superfamily	245201	1	240	2.20E-176	511.07	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15216 - 	CGI_10019662	superfamily	243036	501	807	6.18E-79	258.82	cl02434	CNH superfamily	 - 	 - 	"CNH domain; Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations."
Q#15217 - 	CGI_10019663	superfamily	245201	2	287	0	609.372	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15218 - 	CGI_10019664	superfamily	247745	155	446	3.70E-148	439.008	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#15218 - 	CGI_10019664	superfamily	245003	463	524	1.46E-09	55.6658	cl08536	Alpha-mann_mid superfamily	N	 - 	"Alpha mannosidase, middle domain; Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase."
Q#15219 - 	CGI_10019665	superfamily	187403	4	356	0	549.251	cl14649	BRO1_Alix_like superfamily	 - 	 - 	"Protein-interacting Bro1-like domain of mammalian Alix and related domains; This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, HD-PTP, and Brox) and Snf7 (in the case of yeast Bro1, and Rim20). The single domain protein human Brox, and the isolated Bro1-like domains of Alix, HD-PTP and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V) domain, which in the case of Alix, has been shown to be a dimerization domain and to contain a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in this superfamily. Alix, HD-PTP and Bro1 also have a proline-rich region (PRR); the Alix PRR binds multiple partners. Rhophilin-1, and -2, in addition to this Bro1-like domain, have an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This protein has a C-terminal, catalytically inactive tyrosine phosphatase domain."
Q#15220 - 	CGI_10019666	superfamily	241640	381	504	1.22E-11	62.5901	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#15222 - 	CGI_10019668	superfamily	241599	412	466	9.99E-12	60.72	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#15222 - 	CGI_10019668	superfamily	202226	290	367	5.44E-35	125.869	cl08348	CUT superfamily	 - 	 - 	"CUT domain; The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein ."
Q#15226 - 	CGI_10019672	superfamily	243034	423	527	8.67E-08	51.2268	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#15226 - 	CGI_10019672	superfamily	243034	101	175	3.61E-06	46.2192	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#15226 - 	CGI_10019672	superfamily	243072	320	396	0.00781027	36.2075	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15228 - 	CGI_10019674	superfamily	246723	108	747	0	699.441	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#15229 - 	CGI_10019675	superfamily	243161	5	75	4.32E-11	57.0598	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#15231 - 	CGI_10019677	superfamily	243033	75	185	1.33E-11	58.4837	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#15232 - 	CGI_10019678	superfamily	243161	86	150	3.72E-11	55.9042	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#15234 - 	CGI_10019680	superfamily	222090	1	113	1.28E-10	55.3566	cl18636	Methyltransf_22 superfamily	NC	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#15235 - 	CGI_10019681	superfamily	246723	281	811	0	550.369	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#15235 - 	CGI_10019681	superfamily	243033	92	189	1.21E-09	56.9429	cl02428	Ependymin superfamily	N	 - 	Ependymin; Ependymin.  
Q#15237 - 	CGI_10019683	superfamily	247068	40	137	2.25E-06	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15237 - 	CGI_10019683	superfamily	247068	145	237	1.76E-05	42.3006	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15237 - 	CGI_10019683	superfamily	247068	4	32	0.0070485	34.5966	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15238 - 	CGI_10019684	superfamily	247068	145	219	9.58E-06	43.4562	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15238 - 	CGI_10019684	superfamily	247068	348	393	0.00419147	35.367	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15239 - 	CGI_10019685	superfamily	247724	34	211	1.70E-105	310.308	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15240 - 	CGI_10019686	superfamily	245206	562	803	1.15E-106	330.335	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15242 - 	CGI_10019688	superfamily	191369	1	182	3.68E-46	153.417	cl05372	DUF837 superfamily	 - 	 - 	Protein of unknown function (DUF837); This family consists of several eukaryotic proteins of unknown function. One of the family members is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke).
Q#15243 - 	CGI_10019689	superfamily	243072	408	532	1.07E-34	129.426	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15243 - 	CGI_10019689	superfamily	243072	572	697	2.45E-33	125.574	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15243 - 	CGI_10019689	superfamily	243072	638	763	3.28E-31	119.411	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15243 - 	CGI_10019689	superfamily	243072	385	412	0.0014659	37.5336	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15243 - 	CGI_10019689	superfamily	243072	547	575	0.00174975	37.1484	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15244 - 	CGI_10009217	superfamily	248012	478	598	1.02E-10	59.5945	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#15244 - 	CGI_10009217	superfamily	214507	356	393	0.000239298	39.3356	cl15307	LRRCT superfamily	C	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#15246 - 	CGI_10009219	superfamily	241624	22	286	1.12E-91	275.744	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#15247 - 	CGI_10009220	superfamily	217492	97	629	4.47E-104	327.693	cl18413	GH3 superfamily	 - 	 - 	GH3 auxin-responsive promoter; GH3 auxin-responsive promoter.  
Q#15248 - 	CGI_10009221	superfamily	242849	6	104	2.98E-11	55.2877	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#15249 - 	CGI_10009222	superfamily	218485	410	519	4.50E-63	204.292	cl04974	ETF_QO superfamily	 - 	 - 	"Electron transfer flavoprotein-ubiquinone oxidoreductase; Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane. The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64-kDa monomer."
Q#15249 - 	CGI_10009222	superfamily	248054	19	61	1.35E-05	43.2296	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#15250 - 	CGI_10009223	superfamily	220657	1	196	4.85E-55	193.335	cl10940	RAI16-like superfamily	N	 - 	Retinoic acid induced 16-like protein; This is the conserved N-terminal 450 residues of a family of proteins described as retinoic acid-induced protein 16-like proteins. The exact function is not known. The proteins are found from worms to humans.
Q#15252 - 	CGI_10009225	superfamily	247683	173	226	1.36E-25	101.257	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15252 - 	CGI_10009225	superfamily	247792	11	56	6.80E-12	61.6928	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15252 - 	CGI_10009225	superfamily	247683	368	422	1.88E-26	103.628	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15252 - 	CGI_10009225	superfamily	247683	112	163	5.28E-25	99.3584	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15252 - 	CGI_10009225	superfamily	247683	728	782	9.64E-25	98.6923	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15256 - 	CGI_10009229	superfamily	243035	321	363	7.11E-05	41.4314	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15257 - 	CGI_10009230	superfamily	241763	16	194	2.65E-85	253.7	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#15258 - 	CGI_10009231	superfamily	241763	52	263	1.07E-112	326.118	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#15258 - 	CGI_10009231	superfamily	244586	5	25	0.000309094	37.6083	cl07031	Inhibitor_I29 superfamily	N	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#15259 - 	CGI_10000914	superfamily	247684	1	289	1.45E-65	217.145	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15261 - 	CGI_10009331	superfamily	220692	116	330	0.000221135	41.4209	cl18570	7TM_GPCR_Srw superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#15263 - 	CGI_10009333	superfamily	247724	27	81	6.97E-13	61.703	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15265 - 	CGI_10009844	superfamily	247743	246	389	1.19E-23	97.9871	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#15265 - 	CGI_10009844	superfamily	216502	451	654	4.70E-52	179.71	cl03209	Peptidase_M41 superfamily	 - 	 - 	Peptidase family M41; Peptidase family M41.  
Q#15266 - 	CGI_10009845	superfamily	150442	199	319	2.52E-54	175.737	cl10750	Tmemb_18A superfamily	 - 	 - 	"Transmembrane protein 188; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#15266 - 	CGI_10009845	superfamily	218118	80	140	2.68E-09	53.0017	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#15267 - 	CGI_10009846	superfamily	247723	126	194	1.86E-27	103.842	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15268 - 	CGI_10009847	superfamily	219120	297	428	0.00243526	39.8035	cl05929	Mycoplasma_p37 superfamily	NC	 - 	"High affinity transport system protein p37; This family consists of several high affinity transport system protein p37 sequences which are specific to Mycoplasma species. The p37 gene is part of an operon encoding two additional proteins which are highly similar to components of the periplasmic binding-protein-dependent transport systems of Gram-negative bacteria.It has been suggested that p37 is part of a homologous, high-affinity transport system in M. hyorhinis, a Gram-positive bacterium."
Q#15269 - 	CGI_10009848	superfamily	243176	87	313	1.80E-13	69.1785	cl02777	chaperonin_like superfamily	N	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#15269 - 	CGI_10009848	superfamily	243176	34	96	4.35E-09	56.1418	cl02777	chaperonin_like superfamily	C	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#15270 - 	CGI_10009849	superfamily	243072	500	612	1.25E-28	113.633	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15270 - 	CGI_10009849	superfamily	246925	1074	1307	4.14E-08	55.4394	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15272 - 	CGI_10009851	superfamily	222150	317	342	0.000770835	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#15272 - 	CGI_10009851	superfamily	246975	303	324	0.00546096	34.6301	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#15274 - 	CGI_10009853	superfamily	241628	978	1158	4.12E-89	287.99	cl00130	PseudoU_synth superfamily	 - 	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#15274 - 	CGI_10009853	superfamily	245212	945	1002	0.000398787	40.3106	cl09940	S4 superfamily	N	 - 	"S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site;  Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes."
Q#15274 - 	CGI_10009853	superfamily	241628	1292	1326	9.18E-08	52.6327	cl00130	PseudoU_synth superfamily	N	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#15274 - 	CGI_10009853	superfamily	209898	37	53	0.000909565	38.8607	cl14787	MORN superfamily	C	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#15274 - 	CGI_10009853	superfamily	209898	226	248	0.00150415	38.1534	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#15275 - 	CGI_10009854	superfamily	201479	155	284	3.06E-30	118.115	cl02994	Transglut_N superfamily	 - 	 - 	Transglutaminase family; Transglutaminase family.  
Q#15275 - 	CGI_10009854	superfamily	201479	975	1096	1.10E-26	108.1	cl02994	Transglut_N superfamily	 - 	 - 	Transglutaminase family; Transglutaminase family.  
Q#15275 - 	CGI_10009854	superfamily	247916	1250	1345	4.88E-18	81.275	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#15275 - 	CGI_10009854	superfamily	247916	433	527	2.83E-17	79.349	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#15275 - 	CGI_10009854	superfamily	216198	1592	1680	2.71E-08	53.4716	cl08295	Transglut_C superfamily	 - 	 - 	"Transglutaminase family, C-terminal ig like domain; Transglutaminase family, C-terminal ig like domain.  "
Q#15275 - 	CGI_10009854	superfamily	216198	777	871	3.10E-06	47.3084	cl08295	Transglut_C superfamily	 - 	 - 	"Transglutaminase family, C-terminal ig like domain; Transglutaminase family, C-terminal ig like domain.  "
Q#15275 - 	CGI_10009854	superfamily	247916	519	563	2.95E-05	43.9107	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#15277 - 	CGI_10009856	superfamily	247724	199	407	8.51E-35	128.676	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15279 - 	CGI_10009858	superfamily	147626	77	106	0.000824751	36.0791	cl05227	DUF1519 superfamily	N	 - 	Protein of unknown function (DUF1519); This family consists of several putative homing endonuclease proteins of around 245 residues in length which appear to be found exclusively in Naegleria species. The function of this family is unclear.
Q#15280 - 	CGI_10009859	superfamily	241739	220	548	0	577.614	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#15280 - 	CGI_10009859	superfamily	245205	108	217	2.58E-48	164.573	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#15281 - 	CGI_10009860	superfamily	243092	52	155	9.45E-20	82.3828	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15284 - 	CGI_10001064	superfamily	241594	258	517	2.80E-12	66.1747	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#15286 - 	CGI_10001464	superfamily	217316	111	185	0.00155685	37.2208	cl03832	DUF234 superfamily	 - 	 - 	Archaea bacterial proteins of unknown function; Archaea bacterial proteins of unknown function.  
Q#15287 - 	CGI_10001465	superfamily	110440	394	420	0.00399928	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#15288 - 	CGI_10001466	superfamily	245106	134	259	3.30E-68	209.423	cl09615	UBA_e1_C superfamily	 - 	 - 	Ubiquitin-activating enzyme e1 C-terminal domain; This presumed domain found at the C-terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterized.
Q#15288 - 	CGI_10001466	superfamily	202124	69	95	2.27E-05	40.9936	cl08340	UBACT superfamily	C	 - 	Repeat in ubiquitin-activating (UBA) protein; Repeat in ubiquitin-activating (UBA) protein.  
Q#15290 - 	CGI_10018405	superfamily	216897	2	80	7.29E-22	86.9665	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#15290 - 	CGI_10018405	superfamily	248097	160	273	1.67E-15	70.3718	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15292 - 	CGI_10018407	superfamily	241563	69	110	3.16E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15293 - 	CGI_10018408	superfamily	216897	81	159	3.50E-23	88.5072	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#15294 - 	CGI_10018409	superfamily	216897	2	80	1.87E-23	90.4332	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#15294 - 	CGI_10018409	superfamily	248097	95	210	7.08E-16	70.757	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15295 - 	CGI_10018411	superfamily	248097	1	103	8.69E-12	56.8898	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15296 - 	CGI_10018412	superfamily	216897	103	181	1.02E-24	93.5148	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#15299 - 	CGI_10018415	superfamily	221897	115	320	1.06E-44	158.317	cl16028	Maelstrom superfamily	 - 	 - 	"piRNA pathway germ-plasm component; Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species. The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains. Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, pfam00929); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely "active site switch", has been proposed, in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteristics of both 3'-5' exonuclease and Maelstrom domains."
Q#15299 - 	CGI_10018415	superfamily	241597	1	51	1.77E-05	43.1936	cl00082	HMG-box superfamily	N	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#15301 - 	CGI_10018417	superfamily	241597	10	80	5.51E-31	106.999	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#15303 - 	CGI_10018419	superfamily	243082	65	359	2.89E-50	172.075	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#15305 - 	CGI_10018421	superfamily	241868	295	384	1.66E-47	162.706	cl00447	Nudix_Hydrolase superfamily	C	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#15305 - 	CGI_10018421	superfamily	245010	401	532	1.67E-22	93.4483	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#15305 - 	CGI_10018421	superfamily	243072	21	99	1.42E-15	73.5718	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15305 - 	CGI_10018421	superfamily	204192	252	280	5.51E-05	41.0606	cl07801	zf-NADH-PPase superfamily	 - 	 - 	NADH pyrophosphatase zinc ribbon domain; This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Q#15305 - 	CGI_10018421	superfamily	220167	184	249	0.00122019	37.3861	cl07800	NUDIX-like superfamily	N	 - 	"NADH pyrophosphatase-like rudimentary NUDIX domain; The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP."
Q#15309 - 	CGI_10018425	superfamily	247684	13	387	0	556.153	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15310 - 	CGI_10018426	superfamily	243035	1	112	1.98E-20	83.4381	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15313 - 	CGI_10018429	superfamily	241578	11	169	3.64E-38	136.653	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15313 - 	CGI_10018429	superfamily	241578	244	409	5.97E-38	136.262	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15314 - 	CGI_10018430	superfamily	243051	274	420	1.02E-16	77.8033	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#15314 - 	CGI_10018430	superfamily	241578	11	176	4.64E-41	146.278	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15315 - 	CGI_10018431	superfamily	115363	208	266	2.56E-08	51.989	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#15315 - 	CGI_10018431	superfamily	115363	766	823	5.46E-08	51.2186	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#15315 - 	CGI_10018431	superfamily	241578	445	534	7.67E-08	51.9572	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15315 - 	CGI_10018431	superfamily	115363	692	737	2.62E-06	46.211	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#15319 - 	CGI_10020401	superfamily	245864	57	148	3.50E-09	53.051	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#15320 - 	CGI_10020402	superfamily	245864	11	247	1.59E-39	143.958	cl12078	p450 superfamily	NC	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#15321 - 	CGI_10020403	superfamily	247792	691	736	1.30E-08	52.448	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15321 - 	CGI_10020403	superfamily	245201	390	586	1.16E-103	323.918	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15321 - 	CGI_10020403	superfamily	246908	12	107	4.31E-39	141.378	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15321 - 	CGI_10020403	superfamily	246908	154	255	2.72E-24	99.2252	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15323 - 	CGI_10020405	superfamily	241760	264	312	4.60E-22	90.8781	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#15323 - 	CGI_10020405	superfamily	149946	167	254	6.89E-28	108.896	cl07621	efhand_2 superfamily	 - 	 - 	"EF-hand; Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding."
Q#15325 - 	CGI_10020407	superfamily	147569	9	118	5.36E-38	125.922	cl05167	eIF_4EBP superfamily	 - 	 - 	"Eukaryotic translation initiation factor 4E binding protein (EIF4EBP); This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1,2 and 3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F."
Q#15326 - 	CGI_10020408	superfamily	245818	14	371	1.21E-128	374.609	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#15327 - 	CGI_10020409	superfamily	241780	2	281	9.30E-105	321.704	cl00319	Gn_AT_II superfamily	 - 	 - 	"Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate.  Asparagine synthetase B  synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the formation of the beta-lactam ring in the beta-lactamase inhibitor clavulanic acid. GltS synthesizes L-glutamate from 2-oxoglutarate and L-glutamine. These enzymes are generally dimers, but GPATase also exists as a homotetramer."
Q#15327 - 	CGI_10020409	superfamily	241833	365	490	1.65E-58	195.023	cl00389	SIS superfamily	 - 	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#15327 - 	CGI_10020409	superfamily	241833	527	664	3.46E-52	178.225	cl00389	SIS superfamily	 - 	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#15328 - 	CGI_10020410	superfamily	241782	19	482	7.00E-113	344.167	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#15330 - 	CGI_10020412	superfamily	247724	30	345	3.25E-159	451.596	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15331 - 	CGI_10020413	superfamily	247684	9	182	2.02E-16	78.0143	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15331 - 	CGI_10020413	superfamily	247684	402	576	1.22E-15	75.7031	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15337 - 	CGI_10020419	superfamily	192109	3	49	8.33E-09	50.2741	cl07313	U3_assoc_6 superfamily	N	 - 	U3 small nucleolar RNA-associated protein 6; This is a family of U3 nucleolar RNA-associated proteins which are involved in nucleolar processing of pre-18S ribosomal RNA.
Q#15341 - 	CGI_10020424	superfamily	198867	117	217	4.13E-36	129.971	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#15341 - 	CGI_10020424	superfamily	243066	5	108	4.48E-31	116.563	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#15341 - 	CGI_10020424	superfamily	243146	446	492	3.32E-12	61.9086	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15341 - 	CGI_10020424	superfamily	243146	494	540	3.58E-11	59.2122	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15341 - 	CGI_10020424	superfamily	243146	350	395	1.88E-10	56.901	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15341 - 	CGI_10020424	superfamily	243146	315	361	1.84E-06	45.6271	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15341 - 	CGI_10020424	superfamily	243146	399	447	0.000861034	37.813	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15342 - 	CGI_10020425	superfamily	247755	1675	1890	2.63E-95	309.05	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15342 - 	CGI_10020425	superfamily	247755	790	1000	3.08E-80	266.293	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15343 - 	CGI_10020426	superfamily	246598	233	414	1.05E-67	217.52	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#15343 - 	CGI_10020426	superfamily	241571	102	196	3.07E-05	42.3772	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15344 - 	CGI_10020427	superfamily	243051	58	127	1.26E-08	49.2713	cl02479	MAM superfamily	NC	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#15345 - 	CGI_10020428	superfamily	215647	560	823	3.23E-70	234.81	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#15345 - 	CGI_10020428	superfamily	216897	48	130	2.62E-24	98.9076	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#15345 - 	CGI_10020428	superfamily	221370	283	493	1.29E-20	92.4344	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#15345 - 	CGI_10020428	superfamily	243086	504	545	2.05E-14	69.7113	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#15345 - 	CGI_10020428	superfamily	243029	211	270	7.40E-08	51.3612	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#15345 - 	CGI_10020428	superfamily	243029	144	198	7.34E-05	42.1164	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#15350 - 	CGI_10020433	superfamily	216411	127	214	0.000258874	38.7971	cl15974	MARVEL superfamily	N	 - 	"Membrane-associating domain; MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis."
Q#15351 - 	CGI_10020434	superfamily	242232	122	178	4.16E-15	69.9982	cl00984	TM2 superfamily	C	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#15351 - 	CGI_10020434	superfamily	242232	267	338	5.05E-11	58.4422	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#15351 - 	CGI_10020434	superfamily	242232	44	93	3.55E-09	52.5604	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#15351 - 	CGI_10020434	superfamily	242232	197	246	9.04E-09	52.279	cl00984	TM2 superfamily	C	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#15352 - 	CGI_10020435	superfamily	216411	55	93	0.00624306	33.4043	cl15974	MARVEL superfamily	N	 - 	"Membrane-associating domain; MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis."
Q#15353 - 	CGI_10020436	superfamily	241636	257	476	3.22E-108	325.696	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#15354 - 	CGI_10020437	superfamily	241636	88	282	5.57E-120	347.653	cl00145	TBOX superfamily	 - 	 - 	"T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors."
Q#15355 - 	CGI_10020438	superfamily	247724	5	164	1.50E-87	258.636	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15356 - 	CGI_10020439	superfamily	247725	126	223	1.59E-12	65.3165	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15356 - 	CGI_10020439	superfamily	247725	4	118	1.85E-09	56.3213	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15358 - 	CGI_10020441	superfamily	219936	200	303	1.18E-29	111.188	cl18534	SPA superfamily	 - 	 - 	Stabilisation of polarity axis; Yeast AFI1 (ARF3-interaction protein 1) has been shown to interact with the outer plaque of the spindle pole body. In Aspergillus nidulans the protein member is necessary for stabilisation of the polarity axes during septation. and in S. cerevisiae it functions as a polarisation-specific docking factor.
Q#15358 - 	CGI_10020441	superfamily	219579	47	99	1.69E-10	56.8082	cl16001	Afi1 superfamily	 - 	 - 	"Docking domain of Afi1 for Arf3 in vesicle trafficking; This domain occurs at the N-terminal of Afi1, a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3. Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalisation. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth."
Q#15359 - 	CGI_10020442	superfamily	246722	20	190	2.82E-79	256.81	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#15359 - 	CGI_10020442	superfamily	216112	455	781	1.17E-96	309.227	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#15361 - 	CGI_10020444	superfamily	243088	118	227	1.64E-55	179.142	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#15362 - 	CGI_10020445	superfamily	241571	28	132	6.83E-11	57.8074	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15362 - 	CGI_10020445	superfamily	241613	139	170	0.000492956	37.1862	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#15363 - 	CGI_10020446	superfamily	243058	256	370	1.01E-13	67.7247	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#15363 - 	CGI_10020446	superfamily	243058	338	453	5.73E-12	62.3319	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#15363 - 	CGI_10020446	superfamily	243058	48	162	5.85E-12	62.3319	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#15363 - 	CGI_10020446	superfamily	243058	130	285	6.37E-08	50.3907	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#15364 - 	CGI_10002339	superfamily	248139	624	1135	0	654.253	cl17585	RNA_pol_B_RPB2 superfamily	N	 - 	"RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation."
Q#15364 - 	CGI_10002339	superfamily	248139	332	517	1.24E-52	198.561	cl17585	RNA_pol_B_RPB2 superfamily	NC	 - 	"RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation."
Q#15364 - 	CGI_10002339	superfamily	248139	32	227	1.13E-45	176.99	cl17585	RNA_pol_B_RPB2 superfamily	C	 - 	"RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation."
Q#15364 - 	CGI_10002339	superfamily	219216	562	620	2.39E-18	81.4734	cl06098	RNA_pol_Rpa2_4 superfamily	 - 	 - 	"RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability."
Q#15364 - 	CGI_10002339	superfamily	218151	182	357	4.41E-12	65.8225	cl15858	RNA_pol_Rpb2_2 superfamily	 - 	 - 	"RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI)."
Q#15365 - 	CGI_10002340	superfamily	220809	15	246	6.88E-49	166.096	cl11190	UPF0565 superfamily	 - 	 - 	Uncharacterized protein family UPF0565; This family of proteins has no known function.
Q#15366 - 	CGI_10002341	superfamily	247755	352	546	1.15E-52	177.641	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15366 - 	CGI_10002341	superfamily	247755	224	298	2.19E-32	121.402	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15366 - 	CGI_10002341	superfamily	247755	80	132	1.61E-10	58.9992	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15366 - 	CGI_10002341	superfamily	221805	292	335	4.13E-10	56.8218	cl14896	ABC_tran_2 superfamily	C	 - 	ABC transporter; This domain is related to pfam00005.
Q#15366 - 	CGI_10002341	superfamily	247755	182	251	7.71E-06	45.9967	cl17201	ABC_ATPase superfamily	NC	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#15370 - 	CGI_10024351	superfamily	202234	4	85	4.65E-21	83.8949	cl03577	Viral_Rep superfamily	 - 	 - 	Putative viral replication protein; This is a family of viral ORFs from various plant and animal ssDNA circoviruses. Published evidence to support the annotated function "viral replication associated protein" has not be found.
Q#15376 - 	CGI_10024357	superfamily	218222	367	767	0	611.039	cl04696	Pellino superfamily	 - 	 - 	"Pellino; Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase."
Q#15376 - 	CGI_10024357	superfamily	242350	72	173	3.22E-15	73.8982	cl01182	SprT superfamily	N	 - 	"SprT homologues; Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function."
Q#15379 - 	CGI_10024360	superfamily	245201	39	143	1.65E-19	81.1289	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15380 - 	CGI_10024361	superfamily	216599	46	115	1.20E-23	93.4935	cl18372	B56 superfamily	C	 - 	"Protein phosphatase 2A regulatory B subunit (B56 family); Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also pfam01240), this family is called the B56 family."
Q#15381 - 	CGI_10024362	superfamily	243421	17	136	1.15E-29	107.696	cl03428	MAS20 superfamily	 - 	 - 	MAS20 protein import receptor; MAS20 protein import receptor.  
Q#15382 - 	CGI_10024363	superfamily	246748	233	431	3.64E-101	305.654	cl14876	Zinc_peptidase_like superfamily	N	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#15382 - 	CGI_10024363	superfamily	244870	95	221	6.04E-58	188.608	cl08238	PA superfamily	 - 	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#15382 - 	CGI_10024363	superfamily	246748	12	117	6.16E-30	116.907	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#15383 - 	CGI_10024364	superfamily	219188	78	363	8.03E-89	274.548	cl18498	Lung_7-TM_R superfamily	 - 	 - 	Lung seven transmembrane receptor; This family represents a conserved region with eukaryotic lung seven transmembrane receptors and related proteins.
Q#15384 - 	CGI_10024365	superfamily	244509	75	160	8.28E-12	60.2695	cl06793	PRKCSH superfamily	 - 	 - 	"Glucosidase II beta subunit-like protein; The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain."
Q#15384 - 	CGI_10024365	superfamily	244509	247	304	1.91E-07	47.9431	cl06793	PRKCSH superfamily	 - 	 - 	"Glucosidase II beta subunit-like protein; The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain."
Q#15385 - 	CGI_10024366	superfamily	247637	2	351	1.83E-175	494.599	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#15387 - 	CGI_10024368	superfamily	219001	36	216	1.06E-53	186.361	cl05720	Drf_GBD superfamily	 - 	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#15387 - 	CGI_10024368	superfamily	219000	219	408	3.45E-53	185.543	cl05717	Drf_FH3 superfamily	 - 	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#15388 - 	CGI_10024369	superfamily	245456	890	1166	1.25E-110	348.97	cl10970	AP_MHD_Cterm superfamily	 - 	 - 	"C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15."
Q#15388 - 	CGI_10024369	superfamily	241754	5	306	9.72E-134	413.417	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#15389 - 	CGI_10024370	superfamily	247724	136	354	3.57E-124	368.156	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15389 - 	CGI_10024370	superfamily	243184	465	551	1.59E-34	125.818	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#15389 - 	CGI_10024370	superfamily	243185	370	456	1.13E-32	120.787	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#15391 - 	CGI_10024372	superfamily	247856	140	163	0.00223842	36.102	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#15393 - 	CGI_10024374	superfamily	248279	49	137	2.06E-20	83.5699	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#15394 - 	CGI_10024375	superfamily	241686	13	71	1.41E-12	59.5417	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#15394 - 	CGI_10024375	superfamily	242173	88	194	5.02E-23	90.389	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#15395 - 	CGI_10024376	superfamily	246925	174	362	9.72E-26	107.441	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15398 - 	CGI_10024379	superfamily	204741	5	61	1.39E-10	51.994	cl13257	DUF3317 superfamily	 - 	 - 	"Protein of unknown function (DUF3317); This is a short family of proteins conserved from fungi and plants to human. One each of the human and mouse members is annotated as being androgen down-regulated protein expressed in mouse prostate, with a potential signal transduction function, and all appear to be membrane proteins."
Q#15399 - 	CGI_10024380	superfamily	247856	117	178	6.54E-15	66.0321	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#15399 - 	CGI_10024380	superfamily	247856	44	104	2.50E-08	47.5425	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#15400 - 	CGI_10024381	superfamily	247856	219	280	4.36E-06	43.6905	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#15400 - 	CGI_10024381	superfamily	247856	295	353	1.29E-05	42.1497	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#15400 - 	CGI_10024381	superfamily	247856	46	87	5.32E-05	40.6089	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#15401 - 	CGI_10024382	superfamily	243183	825	902	6.87E-27	106.073	cl02785	Elongation_Factor_C superfamily	 - 	 - 	"Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p.  This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain.  EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown."
Q#15401 - 	CGI_10024382	superfamily	247792	37	69	0.000783488	38.5808	cl17238	RING superfamily	N	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15401 - 	CGI_10024382	superfamily	241677	378	444	7.19E-25	102.72	cl00197	cyclophilin superfamily	C	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#15403 - 	CGI_10024384	superfamily	241664	48	162	2.38E-40	138.487	cl00182	Mth938-like superfamily	 - 	 - 	"Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer.  2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined."
Q#15405 - 	CGI_10024386	superfamily	241610	1665	1717	1.15E-19	86.535	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	1288	1341	1.97E-18	82.683	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	2315	2368	3.47E-16	76.5198	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	1730	1782	4.42E-16	76.1346	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	1919	1972	6.29E-16	75.7494	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	1123	1175	7.56E-16	75.3642	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	1865	1915	3.47E-15	73.4382	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	1542	1594	1.16E-14	71.8974	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241584	2094	2190	1.62E-13	69.8327	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#15405 - 	CGI_10024386	superfamily	241610	1224	1279	4.04E-13	67.6602	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	2206	2256	3.87E-12	64.5786	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241610	1604	1644	9.76E-12	63.423	cl00101	KU superfamily	C	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#15405 - 	CGI_10024386	superfamily	241584	1347	1434	4.14E-11	62.5139	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#15405 - 	CGI_10024386	superfamily	241613	1976	2008	6.34E-06	46.0458	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#15405 - 	CGI_10024386	superfamily	241613	2018	2051	1.34E-05	45.2754	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#15405 - 	CGI_10024386	superfamily	241613	2057	2090	3.27E-05	44.1198	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#15405 - 	CGI_10024386	superfamily	245814	2621	2694	8.56E-13	67.5304	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15405 - 	CGI_10024386	superfamily	245814	2524	2592	2.87E-10	59.8264	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15405 - 	CGI_10024386	superfamily	245814	2457	2514	1.13E-06	49.229	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15405 - 	CGI_10024386	superfamily	204025	2704	2737	0.0020949	38.7717	cl07344	PLAC superfamily	 - 	 - 	PLAC (protease and lacunin) domain; The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins. It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin.
Q#15406 - 	CGI_10024387	superfamily	245864	63	498	1.29E-117	357.359	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#15408 - 	CGI_10024389	superfamily	241607	461	512	1.54E-15	71.9517	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#15408 - 	CGI_10024389	superfamily	220617	108	147	0.00946021	35.8877	cl10871	DUF2371 superfamily	N	 - 	Uncharacterized conserved protein (DUF2371); This is a family of proteins conserved from nematodes to humans. The function is not known.
Q#15409 - 	CGI_10024390	superfamily	247725	11	123	2.79E-43	149.003	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15409 - 	CGI_10024390	superfamily	147416	318	413	5.65E-39	137.14	cl04988	Sprouty superfamily	 - 	 - 	"Sprouty protein (Spry); This family consists of eukaryotic Sprouty protein homologues. Sprouty proteins have been revealed as inhibitors of the Ras/mitogen-activated protein kinase (MAPK) cascade, a pathway crucial for developmental processes initiated by activation of various receptor tyrosine kinases. The sprouty gene has found to be expressed in the the brain, cochlea, nasal organs, teeth, salivary gland, lungs, digestive tract, kidneys and limb buds in mice."
Q#15411 - 	CGI_10024392	superfamily	247805	519	670	1.19E-18	84.6964	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15411 - 	CGI_10024392	superfamily	247905	856	989	7.47E-12	64.1812	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#15411 - 	CGI_10024392	superfamily	221155	1069	1192	7.83E-17	78.9488	cl13152	RIG-I_C-RD superfamily	 - 	 - 	"C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity."
Q#15411 - 	CGI_10024392	superfamily	213148	731	862	3.35E-12	65.0258	cl17041	helicase_insert_domain superfamily	 - 	 - 	"helical domain inserted in SF2-type helicase domain in Hef-, MDA5- and FancM-like proteins; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex."
Q#15411 - 	CGI_10024392	superfamily	246680	168	252	4.22E-08	52.3038	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#15411 - 	CGI_10024392	superfamily	246680	73	155	1.60E-05	44.5998	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#15412 - 	CGI_10024393	superfamily	247805	105	260	1.10E-19	86.6224	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15412 - 	CGI_10024393	superfamily	247905	323	457	1.50E-14	71.1148	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#15412 - 	CGI_10024393	superfamily	243035	565	649	3.00E-05	42.9922	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15417 - 	CGI_10024398	superfamily	248458	98	478	8.96E-34	130.126	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#15418 - 	CGI_10024399	superfamily	216686	109	258	3.68E-29	112.031	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#15419 - 	CGI_10024400	superfamily	202668	441	544	1.43E-22	95.0386	cl04110	BK_channel_a superfamily	 - 	 - 	Calcium-activated BK potassium channel alpha subunit; Calcium-activated BK potassium channel alpha subunit.  
Q#15419 - 	CGI_10024400	superfamily	219619	215	288	3.67E-11	61.4547	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#15420 - 	CGI_10024401	superfamily	186602	79	318	7.41E-84	260.717	cl03849	PSS superfamily	 - 	 - 	Phosphatidyl serine synthase; Phosphatidyl serine synthase is also known as serine exchange enzyme. This family represents eukaryotic PSS I and II which are membrane bound proteins which catalyzes the replacement of the head group of a phospholipid (phosphotidylcholine or phosphotidylethanolamine) by L-serine.
Q#15422 - 	CGI_10024403	superfamily	241733	6	81	3.19E-24	88.0866	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#15424 - 	CGI_10024405	superfamily	241680	39	246	1.27E-60	193.624	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#15427 - 	CGI_10001558	superfamily	244824	2	282	9.79E-59	198.737	cl07893	AmyAc_family superfamily	N	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#15428 - 	CGI_10001559	superfamily	241574	94	309	5.68E-84	260.981	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15430 - 	CGI_10002463	superfamily	248264	119	170	6.70E-08	48.0022	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#15431 - 	CGI_10010363	superfamily	243093	396	447	0.00470643	35.969	cl02568	WSC superfamily	N	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#15436 - 	CGI_10010368	superfamily	245201	17	228	1.74E-64	213.638	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15436 - 	CGI_10010368	superfamily	247694	542	636	8.91E-29	110.782	cl17070	AMPKA_C_like superfamily	 - 	 - 	"C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha subunit and similar domains; This family is composed of AMPKs, microtubule-associated protein/microtubule affinity regulating kinases (MARKs), yeast Kcc4p-like proteins, plant calcineurin B-Like (CBL)-interacting protein kinases (CIPKs), and similar proteins. They are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. AMPKs act as sensors for the energy status of the cell and are activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. MARKs phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Kcc4p and related proteins are septin-associated proteins that are involved in septin organization and in the yeast morphogenesis checkpoint coordinating the cell cycle with bud formation. CIPKs interact with the calcineurin B-like (CBL) calcium sensors to form a signaling network that decode specific calcium signals triggered by a variety of environmental stimuli including salinity, drought, cold, light, and mechanical perturbation, among others. All members of this family contain an N-terminal catalytic kinase domain and a C-terminal regulatory domain which is also called kinase associated domain 1 (KA1) in some cases. The C-terminal regulatory domain serves as a protein interaction domain in AMPKs and CIPKs. In MARKs and Kcc4p-like proteins, this domain binds phospholipids and may be involved in membrane localization."
Q#15445 - 	CGI_10003259	superfamily	243072	52	201	2.17E-07	49.6894	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15450 - 	CGI_10020797	superfamily	247683	302	354	2.07E-11	58.4803	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15451 - 	CGI_10020798	superfamily	245596	24	239	3.87E-106	308.742	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15452 - 	CGI_10020799	superfamily	245596	131	346	1.34E-109	321.839	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15453 - 	CGI_10020800	superfamily	216363	185	280	1.55E-15	70.1918	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#15455 - 	CGI_10020803	superfamily	243072	20	133	4.59E-21	87.8242	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15456 - 	CGI_10020804	superfamily	204080	169	274	1.29E-07	50.3485	cl18252	BAAT_C superfamily	C	 - 	BAAT / Acyl-CoA thioester hydrolase C terminal; This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT).
Q#15457 - 	CGI_10020805	superfamily	241566	29	78	9.04E-15	70.2135	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#15457 - 	CGI_10020805	superfamily	241566	161	211	8.93E-11	58.6576	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#15457 - 	CGI_10020805	superfamily	241566	92	139	2.37E-05	42.8644	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#15457 - 	CGI_10020805	superfamily	243037	638	777	1.18E-62	208.195	cl02440	DAGK_acc superfamily	 - 	 - 	Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
Q#15457 - 	CGI_10020805	superfamily	248019	487	612	3.02E-46	161.31	cl17465	DAGK_cat superfamily	 - 	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#15457 - 	CGI_10020805	superfamily	241645	350	446	5.74E-29	112.166	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#15458 - 	CGI_10020806	superfamily	247723	131	212	1.20E-50	170.92	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15458 - 	CGI_10020806	superfamily	247723	51	128	1.63E-46	159.262	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15458 - 	CGI_10020806	superfamily	247723	226	301	7.21E-33	121.578	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15461 - 	CGI_10020809	superfamily	248097	140	266	4.99E-15	68.831	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15462 - 	CGI_10020810	superfamily	152088	126	206	3.99E-12	59.1387	cl13155	DUF3259 superfamily	 - 	 - 	Protein of unknown function (DUF3259); This eukaryotic family of proteins has no known function.
Q#15463 - 	CGI_10020811	superfamily	152088	132	212	1.77E-20	82.2507	cl13155	DUF3259 superfamily	 - 	 - 	Protein of unknown function (DUF3259); This eukaryotic family of proteins has no known function.
Q#15466 - 	CGI_10020814	superfamily	247794	6	280	1.86E-54	181.824	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#15467 - 	CGI_10020815	superfamily	248097	51	161	6.44E-23	88.8614	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15468 - 	CGI_10006595	superfamily	247807	165	182	0.00169094	36.119	cl17253	AAA_17 superfamily	C	 - 	AAA domain; AAA domain.  
Q#15471 - 	CGI_10006599	superfamily	206083	56	78	0.00198666	37.9728	cl16471	zf-C2H2_6 superfamily	 - 	 - 	C2H2-type zinc finger; C2H2-type zinc finger.  
Q#15478 - 	CGI_10002870	superfamily	221643	89	235	7.11E-21	85.5339	cl13947	DUF3752 superfamily	 - 	 - 	"Protein of unknown function (DUF3752); This domain family is found in eukaryotes, and is typically between 140 and 163 amino acids in length."
Q#15483 - 	CGI_10003964	superfamily	220389	2	160	6.67E-71	216.112	cl10747	DUF2053 superfamily	 - 	 - 	Predicted membrane protein (DUF2053); This entry is of the conserved N-terminal 150 residues of proteins conserved from plants to humans. The function is unknown although some annotation suggests it to be a transmembrane protein.
Q#15485 - 	CGI_10003250	superfamily	243074	144	189	5.85E-06	42.4937	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#15487 - 	CGI_10003252	superfamily	247792	12	64	0.000323162	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15489 - 	CGI_10003254	superfamily	247792	16	68	8.28E-07	45.8996	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15489 - 	CGI_10003254	superfamily	241563	100	141	0.00731844	34.6203	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15490 - 	CGI_10003104	superfamily	241563	88	127	6.43E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15491 - 	CGI_10003105	superfamily	241563	171	207	0.00102253	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15492 - 	CGI_10003107	superfamily	207662	103	174	7.62E-38	135.382	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#15492 - 	CGI_10003107	superfamily	245599	518	639	2.46E-34	129.265	cl11397	NR_LBD superfamily	C	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#15494 - 	CGI_10008916	superfamily	247805	39	147	2.60E-11	56.962	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15495 - 	CGI_10008917	superfamily	245847	7	147	0.0010165	38.6376	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#15496 - 	CGI_10008918	superfamily	241574	10	59	1.21E-08	49.1213	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15497 - 	CGI_10008919	superfamily	243066	41	139	2.28E-13	64.9461	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#15499 - 	CGI_10008921	superfamily	243092	160	384	0.00577263	36.9292	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15500 - 	CGI_10008922	superfamily	243092	288	431	0.00402451	38.47	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15501 - 	CGI_10008923	superfamily	217316	138	195	0.00857908	34.9096	cl03832	DUF234 superfamily	C	 - 	Archaea bacterial proteins of unknown function; Archaea bacterial proteins of unknown function.  
Q#15502 - 	CGI_10008924	superfamily	247750	135	292	1.17E-75	241.425	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#15502 - 	CGI_10008924	superfamily	247750	1	67	5.00E-35	132.413	cl17196	E1_enzyme_family superfamily	NC	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#15502 - 	CGI_10008924	superfamily	202124	40	102	1.42E-11	59.098	cl08340	UBACT superfamily	 - 	 - 	Repeat in ubiquitin-activating (UBA) protein; Repeat in ubiquitin-activating (UBA) protein.  
Q#15503 - 	CGI_10008925	superfamily	241563	62	103	0.00404099	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15504 - 	CGI_10008926	superfamily	241983	36	78	0.000219258	38.1078	cl00614	ADP_ribosyl_GH superfamily	N	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#15506 - 	CGI_10008928	superfamily	245201	17	107	1.45E-21	87.1901	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15507 - 	CGI_10008929	superfamily	245201	168	428	0	529.585	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15507 - 	CGI_10008929	superfamily	246908	52	153	5.55E-52	171.996	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15507 - 	CGI_10008929	superfamily	247683	1	44	6.17E-08	49.118	cl17036	SH3 superfamily	N	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#15509 - 	CGI_10011333	superfamily	243069	3	46	0.000104979	37.1267	cl02525	Band_7 superfamily	N	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#15510 - 	CGI_10011334	superfamily	243119	2	22	0.00148722	33.9566	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#15511 - 	CGI_10011335	superfamily	222429	38	116	8.24E-10	53.3984	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#15512 - 	CGI_10011336	superfamily	217062	208	275	5.65E-09	54.5827	cl12266	Branch superfamily	N	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#15513 - 	CGI_10011337	superfamily	221636	12	59	1.18E-18	75.6882	cl13929	MOZART1 superfamily	 - 	 - 	"Mitotic-spindle organizing gamma-tubulin ring associated; The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, this family does not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. MOZART1 is required for gamma-TuRC recruitment to centrosomes."
Q#15516 - 	CGI_10005647	superfamily	246918	118	161	1.08E-06	44.1147	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#15519 - 	CGI_10005650	superfamily	247724	29	193	1.46E-108	312.572	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15521 - 	CGI_10005652	superfamily	219565	86	400	1.21E-26	110.273	cl06690	DUF1619 superfamily	 - 	 - 	Protein of unknown function (DUF1619); This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.
Q#15525 - 	CGI_10017434	superfamily	247725	121	153	0.00935034	32.6761	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15526 - 	CGI_10017435	superfamily	217293	15	113	3.18E-05	42.6199	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15526 - 	CGI_10017435	superfamily	202474	135	197	0.0061411	35.7073	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#15527 - 	CGI_10017436	superfamily	248097	3	122	9.64E-20	79.2314	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15529 - 	CGI_10017438	superfamily	245814	351	429	0.00038592	39.4109	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15529 - 	CGI_10017438	superfamily	245814	270	321	0.00715487	35.4604	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15531 - 	CGI_10017440	superfamily	241832	191	336	5.19E-47	157.783	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15533 - 	CGI_10017442	superfamily	198738	242	325	5.72E-46	154.016	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#15533 - 	CGI_10017442	superfamily	247057	122	210	5.99E-43	146.344	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#15533 - 	CGI_10017442	superfamily	152056	1	81	3.51E-20	83.6904	cl13126	GABP-alpha superfamily	 - 	 - 	"GA-binding protein alpha chain; This family of proteins represents the transcription factor GABP alpha. This alpha domain is a five-stranded beta-sheet crossed by a distorted helix termed an OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300, a direct link between GABP and transcriptional machinery has been made."
Q#15534 - 	CGI_10004631	superfamily	248372	60	167	2.75E-18	76.8544	cl17818	Nuc_deoxyrib_tr superfamily	 - 	 - 	Nucleoside 2-deoxyribosyltransferase; Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyzes the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides.
Q#15535 - 	CGI_10004632	superfamily	243092	131	159	0.00133632	35.0204	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15536 - 	CGI_10004633	superfamily	245205	131	212	0.00110277	36.8321	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#15538 - 	CGI_10003780	superfamily	241750	226	563	1.60E-67	229.888	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#15539 - 	CGI_10004018	superfamily	247727	111	190	5.17E-06	43.5727	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#15540 - 	CGI_10004019	superfamily	245847	25	93	1.38E-05	40.6178	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#15541 - 	CGI_10004020	superfamily	218913	260	410	1.16E-06	48.8981	cl18486	Trehalose_recp superfamily	N	 - 	"Trehalose receptor; In Drosophila, taste is perceived by gustatory neurons located in sensilla distributed on several different appendages throughout the body of the animal. This family represents the taste receptor sensitive to trehalose."
Q#15542 - 	CGI_10004021	superfamily	247866	10	210	2.89E-05	43.5952	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#15544 - 	CGI_10004023	superfamily	248054	10	83	6.26E-09	51.704	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#15545 - 	CGI_10003781	superfamily	245226	7	197	2.11E-114	331.485	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#15545 - 	CGI_10003781	superfamily	207658	226	306	4.69E-16	71.1742	cl02578	HRDC superfamily	 - 	 - 	HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Q#15550 - 	CGI_10013537	superfamily	241913	33	143	3.38E-23	89.9245	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#15551 - 	CGI_10013538	superfamily	241640	214	353	1.04E-48	165.527	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#15551 - 	CGI_10013538	superfamily	241571	45	155	6.20E-33	119.439	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15551 - 	CGI_10013538	superfamily	241613	162	196	3.67E-08	49.1274	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#15552 - 	CGI_10013539	superfamily	241640	537	751	1.01E-77	251.427	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#15552 - 	CGI_10013539	superfamily	241571	405	515	7.20E-32	120.595	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15552 - 	CGI_10013539	superfamily	241571	86	199	1.13E-31	120.21	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15552 - 	CGI_10013539	superfamily	241571	270	382	1.99E-29	113.661	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15552 - 	CGI_10013539	superfamily	241913	28	77	2.55E-06	46.397	cl00509	hot_dog superfamily	N	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#15553 - 	CGI_10013540	superfamily	241640	239	474	1.11E-92	284.169	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#15553 - 	CGI_10013540	superfamily	241613	117	152	1.90E-09	53.7498	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#15553 - 	CGI_10013540	superfamily	243061	173	218	1.29E-12	64.2854	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#15553 - 	CGI_10013540	superfamily	243061	16	105	4.40E-09	54.0098	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#15554 - 	CGI_10013541	superfamily	220695	66	256	9.94E-08	52.1959	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#15555 - 	CGI_10013542	superfamily	243072	3	123	1.16E-16	75.883	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15555 - 	CGI_10013542	superfamily	243072	104	168	0.00621408	35.4371	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15557 - 	CGI_10013544	superfamily	241644	1064	1212	1.25E-34	131.941	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#15557 - 	CGI_10013544	superfamily	226749	1705	1901	1.15E-18	88.7832	cl18777	COG4299 superfamily	N	 - 	Uncharacterized protein conserved in bacteria [Function unknown]
Q#15557 - 	CGI_10013544	superfamily	226749	1549	1625	1.35E-08	57.582	cl18777	COG4299 superfamily	C	 - 	Uncharacterized protein conserved in bacteria [Function unknown]
Q#15558 - 	CGI_10013545	superfamily	245206	19	265	1.27E-110	322.999	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15559 - 	CGI_10013546	superfamily	220607	23	98	2.56E-21	81.2988	cl10858	DDDD superfamily	 - 	 - 	Putative mitochondrial precursor protein; This is a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. Members are putatively assigned to be mitochondrial precursor proteins but this could not be confirmed.
Q#15560 - 	CGI_10013547	superfamily	241631	734	919	2.86E-63	216.705	cl00136	Sec7 superfamily	 - 	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#15560 - 	CGI_10013547	superfamily	243072	1835	1962	9.29E-22	94.7578	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15560 - 	CGI_10013547	superfamily	245201	2060	2218	6.26E-14	73.0397	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15561 - 	CGI_10013548	superfamily	243062	235	334	1.90E-35	125.851	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#15564 - 	CGI_10023394	superfamily	241584	565	641	9.90E-08	51.3431	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#15564 - 	CGI_10023394	superfamily	222150	52	77	3.30E-07	48.5421	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#15564 - 	CGI_10023394	superfamily	247724	713	815	2.11E-06	49.4664	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15564 - 	CGI_10023394	superfamily	222150	136	160	3.77E-06	45.4605	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#15564 - 	CGI_10023394	superfamily	222150	108	133	2.23E-05	43.1493	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#15564 - 	CGI_10023394	superfamily	222150	83	105	2.55E-05	43.1493	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#15564 - 	CGI_10023394	superfamily	242669	457	535	0.000312143	42.8345	cl01728	DUF2232 superfamily	N	 - 	"Predicted membrane protein (DUF2232); This domain, found in various hypothetical bacterial proteins, has no known function."
Q#15565 - 	CGI_10023395	superfamily	247724	1	159	1.37E-111	322.831	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15566 - 	CGI_10023396	superfamily	222005	464	515	9.25E-07	48.8876	cl18632	AAA_19 superfamily	C	 - 	Part of AAA domain; Part of AAA domain.  
Q#15566 - 	CGI_10023396	superfamily	221913	1025	1054	0.00520866	39.0607	cl18626	AAA_12 superfamily	C	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#15568 - 	CGI_10023398	superfamily	248458	176	598	2.60E-42	156.32	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#15569 - 	CGI_10023399	superfamily	245213	253	286	1.93E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15570 - 	CGI_10023400	superfamily	216290	157	275	5.65E-08	51.135	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#15570 - 	CGI_10023400	superfamily	217685	289	435	1.28E-06	47.3288	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#15572 - 	CGI_10023402	superfamily	247725	9	105	2.53E-33	122.388	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15572 - 	CGI_10023402	superfamily	207724	176	233	2.65E-15	71.1075	cl02772	BSD superfamily	 - 	 - 	BSD domain; This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function.
Q#15572 - 	CGI_10023402	superfamily	207724	109	152	5.53E-06	44.1435	cl02772	BSD superfamily	 - 	 - 	BSD domain; This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function.
Q#15573 - 	CGI_10023403	superfamily	245213	42	72	0.0049667	35.305	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15573 - 	CGI_10023403	superfamily	248012	394	534	0.00012284	41.1548	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#15575 - 	CGI_10023405	superfamily	247792	103	143	1.08E-09	55.9148	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15575 - 	CGI_10023405	superfamily	247999	174	228	1.33E-05	44.0184	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#15576 - 	CGI_10023406	superfamily	246748	87	277	9.82E-122	361.139	cl14876	Zinc_peptidase_like superfamily	NC	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#15576 - 	CGI_10023406	superfamily	246748	272	329	1.15E-32	125.782	cl14876	Zinc_peptidase_like superfamily	N	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#15576 - 	CGI_10023406	superfamily	246748	46	90	7.73E-14	70.6981	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#15577 - 	CGI_10023407	superfamily	246748	6	461	0	871.143	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#15580 - 	CGI_10023410	superfamily	247805	58	265	1.66E-82	258.954	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15580 - 	CGI_10023410	superfamily	247905	307	408	1.83E-20	88.0636	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#15580 - 	CGI_10023410	superfamily	222474	439	501	7.03E-23	92.8713	cl16500	DUF4217 superfamily	 - 	 - 	Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many helicase proteins.
Q#15581 - 	CGI_10023411	superfamily	241563	74	113	3.54E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15581 - 	CGI_10023411	superfamily	110440	491	517	0.000407099	38.5429	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#15581 - 	CGI_10023411	superfamily	218425	348	376	0.00994621	37.2918	cl04931	eIF-3_zeta superfamily	NC	 - 	"Eukaryotic translation initiation factor 3 subunit 7 (eIF-3); This family is made up of eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is a multi-subunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. These functions and the complex nature of eIF3 suggest multiple interactions with many components of the translational machinery. The gene coding for the protein has been implicated in cancer in mammals."
Q#15583 - 	CGI_10023413	superfamily	247724	35	198	1.80E-61	192.492	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15585 - 	CGI_10023415	superfamily	110440	82	108	0.000433768	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#15585 - 	CGI_10023415	superfamily	110440	125	152	0.00156201	33.9205	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#15586 - 	CGI_10023416	superfamily	241563	83	121	6.77E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15586 - 	CGI_10023416	superfamily	243362	382	423	0.000210634	40.4863	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#15587 - 	CGI_10023417	superfamily	243061	1	102	2.36E-39	142.481	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#15587 - 	CGI_10023417	superfamily	243061	110	209	3.64E-37	136.318	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#15587 - 	CGI_10023417	superfamily	215647	638	844	4.08E-26	108.465	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#15587 - 	CGI_10023417	superfamily	243086	586	626	3.06E-15	71.6373	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#15587 - 	CGI_10023417	superfamily	221370	383	560	0.000566329	41.2029	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#15588 - 	CGI_10023418	superfamily	241739	224	413	6.07E-94	302.202	cl00268	class_II_aaRS-like_core superfamily	N	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#15588 - 	CGI_10023418	superfamily	241805	9	57	2.93E-19	83.6898	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#15588 - 	CGI_10023418	superfamily	241739	68	140	3.22E-25	106.906	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#15588 - 	CGI_10023418	superfamily	241738	541	575	9.47E-10	57.9528	cl00266	HGTP_anticodon superfamily	C	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#15588 - 	CGI_10023418	superfamily	241563	676	714	0.000204323	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15589 - 	CGI_10023419	superfamily	248438	35	141	1.01E-06	48.188	cl17884	COG1214 superfamily	C	 - 	"Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]"
Q#15591 - 	CGI_10023421	superfamily	222370	38	119	1.43E-19	82.5709	cl16386	Longin superfamily	 - 	 - 	"Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain."
Q#15591 - 	CGI_10023421	superfamily	243035	318	411	5.57E-15	71.0917	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15592 - 	CGI_10023422	superfamily	204415	13	83	6.24E-19	90.7413	cl16016	TTKRSYEDQ superfamily	N	 - 	Predicted coiled-coil domain-containing protein; This is the C-terminal 500 amino acids of a family of proteins with a predicted coiled-coil domain conserved from nematodes to humans. It carries a characteristic TTKRSYEDQ sequence-motif. The function is not known.
Q#15592 - 	CGI_10023422	superfamily	152912	527	553	0.000179164	40.9316	cl13860	DUF3697 superfamily	C	 - 	"Ubiquitin-associated protein 2; This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam00627. There are two conserved sequence motifs: AVEMPG and QFG."
Q#15593 - 	CGI_10023423	superfamily	241736	10	96	1.98E-20	84.2091	cl00263	TFold superfamily	N	 - 	"Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1),  6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and share a fold-related binding site with a glutamate or glutamine residue anchoring the substrate and a lot of conserved interactions. They also share a similar oligomerization mode: several T-folds join together to form a beta(2n)alpha(n) barrel, then two barrels join together in a head-to-head fashion to made up the native enzymes. The functional enzyme is a tetramer for UO, a hexamer for PTPS, an octamer for DHNA/DHNTPE and a decamer for GTPCH-1. The substrate is located in a deep and narrow pocket at the interface between monomers. In PTPS, the active site is located at the interface of three monomers, two from one trimer and one from the other trimer. In GTPCH-1, it is also located at the interface of three subunits, two from one pentamer and one from the other pentamer. There are four equivalent active sites in UO, six in PTPS, eight in DHNA/DHNTPE and ten in GTPCH-1.   Each globular multimeric enzyme encloses a tunnel which is lined with charged residues for DHNA and UO, and with basic residues in PTPS. The N and C-terminal ends are located on one side of the T-fold while the residues involved in the catalytic activity are located at the opposite side. In PTPS, UO and DHNA/DHNTPE, the N and C-terminal extremities of the enzyme are located on the exterior side of the functional multimeric enzyme. In GTPCH-1, the extra C-terminal helix places the extremity inside the tunnel."
Q#15594 - 	CGI_10023424	superfamily	242232	108	157	5.46E-14	62.9608	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#15596 - 	CGI_10023426	superfamily	241567	472	707	5.66E-85	270.241	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#15596 - 	CGI_10023426	superfamily	241567	62	251	1.95E-78	252.907	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#15597 - 	CGI_10023427	superfamily	241567	59	304	5.85E-105	309.146	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#15598 - 	CGI_10023428	superfamily	218556	18	509	4.01E-140	419.786	cl05076	RRN3 superfamily	 - 	 - 	RNA polymerase I specific transcription initiation factor RRN3; This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae.
Q#15600 - 	CGI_10023430	superfamily	247743	495	585	1.66E-08	54.8447	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#15601 - 	CGI_10023431	superfamily	219975	211	302	2.98E-32	116.644	cl07355	Fcf2 superfamily	 - 	 - 	Fcf2 pre-rRNA processing; This is a family of eukaryotic nucleolar proteins that are involved in pre-rRNA processing.
Q#15603 - 	CGI_10023433	superfamily	243179	186	322	1.03E-09	55.0465	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#15605 - 	CGI_10023435	superfamily	243179	214	351	6.79E-13	64.4763	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#15606 - 	CGI_10023436	superfamily	243179	135	263	6.22E-16	71.7951	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#15607 - 	CGI_10023437	superfamily	243098	567	613	2.97E-15	73.4011	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15607 - 	CGI_10023437	superfamily	243098	111	158	3.72E-14	70.3195	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15607 - 	CGI_10023437	superfamily	243098	1340	1385	9.77E-14	69.1639	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15607 - 	CGI_10023437	superfamily	243098	1840	1887	2.05E-12	65.3119	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15607 - 	CGI_10023437	superfamily	243098	762	808	2.07E-12	65.3119	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15607 - 	CGI_10023437	superfamily	243098	961	1006	2.13E-12	65.3119	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15607 - 	CGI_10023437	superfamily	243098	1145	1190	1.92E-10	59.5339	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15607 - 	CGI_10023437	superfamily	243098	1583	1629	3.93E-07	49.9039	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15608 - 	CGI_10023438	superfamily	243098	61	106	1.09E-12	63.7711	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15608 - 	CGI_10023438	superfamily	243098	630	675	7.03E-11	58.7635	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15608 - 	CGI_10023438	superfamily	243098	238	284	3.86E-08	50.6743	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15608 - 	CGI_10023438	superfamily	243098	422	466	0.000166881	40.274	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#15609 - 	CGI_10023439	superfamily	247058	1417	1619	3.61E-56	196.242	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#15609 - 	CGI_10023439	superfamily	247743	370	521	9.38E-27	109.543	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#15609 - 	CGI_10023439	superfamily	202367	1739	1917	1.54E-61	210.859	cl18226	3HCDH_N superfamily	 - 	 - 	"3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda crystallin."
Q#15609 - 	CGI_10023439	superfamily	243084	902	1013	2.03E-39	144.807	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#15609 - 	CGI_10023439	superfamily	216084	1920	2015	4.67E-28	111.53	cl08285	3HCDH superfamily	 - 	 - 	"3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; This family also includes lambda crystallin. Some proteins include two copies of this domain."
Q#15610 - 	CGI_10023440	superfamily	245210	47	465	1.41E-158	457.711	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#15611 - 	CGI_10023441	superfamily	246597	7	295	7.66E-108	318.092	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#15612 - 	CGI_10023442	superfamily	241899	516	548	0.00340215	38.217	cl00489	60KD_IMP superfamily	C	 - 	60Kd inner membrane protein; 60Kd inner membrane protein.  
Q#15613 - 	CGI_10006895	superfamily	241619	276	313	0.00124353	38.7173	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#15614 - 	CGI_10006896	superfamily	245835	187	404	9.39E-121	352.402	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#15614 - 	CGI_10006896	superfamily	243088	31	171	2.23E-79	243.495	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#15618 - 	CGI_10020689	superfamily	219562	77	343	2.84E-87	278.031	cl06685	LETM1 superfamily	 - 	 - 	LETM1-like protein; Members of this family are inner mitochondrial membrane proteins which play a role in potassium and hydrogen ion exchange. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans.
Q#15619 - 	CGI_10020690	superfamily	241629	58	172	1.13E-30	113.564	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#15620 - 	CGI_10020691	superfamily	220657	78	469	1.03E-101	318.91	cl10940	RAI16-like superfamily	 - 	 - 	Retinoic acid induced 16-like protein; This is the conserved N-terminal 450 residues of a family of proteins described as retinoic acid-induced protein 16-like proteins. The exact function is not known. The proteins are found from worms to humans.
Q#15622 - 	CGI_10020693	superfamily	243035	9	136	1.85E-19	81.8973	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15623 - 	CGI_10020694	superfamily	243035	345	469	4.11E-17	77.2749	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15623 - 	CGI_10020694	superfamily	243035	212	326	2.23E-11	60.7113	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15624 - 	CGI_10020695	superfamily	214545	420	562	7.68E-56	188.298	cl10551	CULLIN superfamily	 - 	 - 	Cullin; Cullin.  
Q#15624 - 	CGI_10020695	superfamily	245539	688	760	1.95E-24	98.0097	cl11186	Cullin_Nedd8 superfamily	 - 	 - 	"Cullin protein neddylation domain; This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue."
Q#15625 - 	CGI_10020696	superfamily	241583	103	178	1.24E-24	100.723	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#15625 - 	CGI_10020696	superfamily	241583	177	222	0.00300743	37.5507	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#15627 - 	CGI_10020698	superfamily	246908	581	691	1.22E-26	105.859	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15628 - 	CGI_10020699	superfamily	207921	1	113	5.84E-45	151.166	cl03350	Ribosomal_L28e superfamily	 - 	 - 	Ribosomal L28e protein family; Ribosomal L28e protein family.  
Q#15628 - 	CGI_10020699	superfamily	218303	131	176	2.28E-11	59.4992	cl15325	Mak16 superfamily	C	 - 	Mak16 protein C-terminal region; The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus.
Q#15629 - 	CGI_10020700	superfamily	241599	67	109	3.66E-13	63.0312	cl00084	homeodomain superfamily	C	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#15629 - 	CGI_10020700	superfamily	243061	209	307	2.94E-44	148.259	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#15631 - 	CGI_10020702	superfamily	241646	55	96	1.37E-07	43.9779	cl00156	WAP superfamily	N	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#15633 - 	CGI_10020704	superfamily	247905	262	317	4.81E-08	50.3141	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#15633 - 	CGI_10020704	superfamily	247805	57	143	2.89E-07	48.4095	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15636 - 	CGI_10020707	superfamily	217293	35	234	5.88E-36	131.986	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15636 - 	CGI_10020707	superfamily	202474	241	329	5.00E-12	63.8269	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#15638 - 	CGI_10020709	superfamily	247743	580	646	0.00010289	42.1331	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#15639 - 	CGI_10020710	superfamily	242934	13	154	1.32E-43	148.864	cl02219	Bap31 superfamily	 - 	 - 	"B-cell receptor-associated protein 31-like; Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31."
Q#15640 - 	CGI_10020711	superfamily	243072	25	144	1.69E-09	52.771	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15641 - 	CGI_10020712	superfamily	245206	3	290	3.26E-135	387.958	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15643 - 	CGI_10020714	superfamily	243092	20	255	5.63E-25	104.724	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15644 - 	CGI_10020715	superfamily	248097	49	108	1.16E-10	54.1934	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15645 - 	CGI_10020716	superfamily	241832	2	90	3.35E-38	130.166	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15645 - 	CGI_10020716	superfamily	243175	104	227	3.05E-35	123.585	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#15646 - 	CGI_10020717	superfamily	242730	73	120	0.00457812	36.4703	cl01825	Phage_Mu_Gam superfamily	C	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#15648 - 	CGI_10020719	superfamily	241640	225	329	5.35E-06	44.8709	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#15649 - 	CGI_10020720	superfamily	247684	5	424	5.13E-106	327.697	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15651 - 	CGI_10011595	superfamily	247799	1	76	3.10E-22	84.2177	cl17245	KH-I superfamily	N	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#15652 - 	CGI_10011596	superfamily	245847	15	77	0.0010524	34.0694	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#15654 - 	CGI_10011598	superfamily	245201	91	332	4.22E-97	292.887	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15657 - 	CGI_10011601	superfamily	243035	64	109	0.000566864	37.2142	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15660 - 	CGI_10015738	superfamily	247792	5194	5249	0.000692435	41.2772	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15660 - 	CGI_10015738	superfamily	201217	1087	1134	1.52E-12	66.7804	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#15660 - 	CGI_10015738	superfamily	205718	1072	1100	3.15E-07	50.9518	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#15660 - 	CGI_10015738	superfamily	205718	856	885	0.00149414	40.1662	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#15661 - 	CGI_10015739	superfamily	202715	125	223	2.61E-31	111.901	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#15662 - 	CGI_10015740	superfamily	241631	248	422	2.28E-31	118.491	cl00136	Sec7 superfamily	 - 	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#15662 - 	CGI_10015740	superfamily	202715	61	156	7.31E-29	108.82	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#15662 - 	CGI_10015740	superfamily	243074	185	226	5.53E-10	55.2053	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#15663 - 	CGI_10015741	superfamily	247725	642	741	2.86E-39	143.208	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15663 - 	CGI_10015741	superfamily	241645	1505	1581	2.29E-08	53.446	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#15663 - 	CGI_10015741	superfamily	243095	1277	1462	4.73E-57	197.916	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#15663 - 	CGI_10015741	superfamily	243047	850	978	2.15E-39	144.685	cl02464	ArfGap superfamily	 - 	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#15663 - 	CGI_10015741	superfamily	247725	1070	1178	4.03E-13	68.5374	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15663 - 	CGI_10015741	superfamily	247725	754	831	1.32E-11	63.1021	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15663 - 	CGI_10015741	superfamily	247057	8	62	3.10E-11	61.5424	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#15664 - 	CGI_10015742	superfamily	241599	237	297	7.73E-09	51.0901	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#15665 - 	CGI_10015743	superfamily	219608	8	174	5.19E-64	197.979	cl06751	DUF1649 superfamily	 - 	 - 	Protein of unknown function (DUF1649); This family is made up of sequences derived from hypothetical eukaryotic proteins of unknown function.
Q#15666 - 	CGI_10015744	superfamily	245021	29	57	0.00817743	30.3423	cl09153	PhdYeFM_antitox superfamily	C	 - 	"Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957."
Q#15667 - 	CGI_10015745	superfamily	115278	1	128	2.64E-28	102.848	cl05898	DUF1143 superfamily	 - 	 - 	Protein of unknown function (DUF1143); This family consists of several hypothetical mammalian proteins (from mouse and human). The function of this family is unknown.
Q#15668 - 	CGI_10015746	superfamily	241597	958	1029	3.85E-38	140.126	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#15668 - 	CGI_10015746	superfamily	215882	2260	2343	0.00250452	38.8011	cl09511	FERM_M superfamily	C	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#15673 - 	CGI_10015752	superfamily	243094	46	260	6.64E-107	317.829	cl02569	RasGAP superfamily	N	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#15675 - 	CGI_10015754	superfamily	248097	9	125	1.31E-16	70.757	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15676 - 	CGI_10015755	superfamily	248097	45	153	2.49E-20	81.5426	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15677 - 	CGI_10015756	superfamily	241571	190	295	1.07E-22	90.5494	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15677 - 	CGI_10015756	superfamily	241571	41	156	1.43E-10	57.037	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15678 - 	CGI_10015757	superfamily	150144	27	170	1.58E-22	92.5362	cl09624	Tex_N superfamily	N	 - 	Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Bordetella pertussis tex. This protein defines a novel family of prokaryotic transcriptional accessory factors.
Q#15679 - 	CGI_10015758	superfamily	241574	49	104	2.33E-07	46.0398	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15679 - 	CGI_10015758	superfamily	242611	12	52	0.00309615	34.1361	cl01629	TPP_enzymes superfamily	NC	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#15680 - 	CGI_10008573	superfamily	248264	55	212	3.07E-42	141.991	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#15681 - 	CGI_10008574	superfamily	241552	35	112	3.99E-14	63.5464	cl00017	Cyt_c_Oxidase_VIa superfamily	 - 	 - 	"Cytochrome c oxidase subunit VIa.   Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome.  Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform.  Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip in CcO, depending on the presence of cardiolipin and palmitate."
Q#15682 - 	CGI_10008575	superfamily	243051	797	908	1.69E-22	95.9077	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#15682 - 	CGI_10008575	superfamily	243051	651	732	9.35E-17	78.9589	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#15682 - 	CGI_10008575	superfamily	241563	68	109	5.44E-07	47.8592	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15682 - 	CGI_10008575	superfamily	241563	15	58	0.00673359	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15684 - 	CGI_10006230	superfamily	243077	173	208	8.65E-09	51.3772	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#15685 - 	CGI_10006231	superfamily	247740	387	454	0.00257756	38.0307	cl17186	TIM_phosphate_binding superfamily	NC	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#15686 - 	CGI_10006232	superfamily	222005	289	353	1.20E-05	43.88	cl18632	AAA_19 superfamily	C	 - 	Part of AAA domain; Part of AAA domain.  
Q#15686 - 	CGI_10006232	superfamily	221913	702	749	1.87E-05	44.8387	cl18626	AAA_12 superfamily	C	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#15690 - 	CGI_10006236	superfamily	243065	243	378	3.80E-18	80.5237	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#15692 - 	CGI_10006238	superfamily	220131	597	727	1.03E-29	122.385	cl11721	DUF1943 superfamily	C	 - 	"Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined."
Q#15692 - 	CGI_10006238	superfamily	243065	2376	2512	3.66E-18	85.1461	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#15694 - 	CGI_10006240	superfamily	247786	95	183	2.57E-07	47.5881	cl17232	F420_oxidored superfamily	 - 	 - 	NADP oxidoreductase coenzyme F420-dependent; NADP oxidoreductase coenzyme F420-dependent.  
Q#15695 - 	CGI_10003288	superfamily	241578	69	226	2.87E-33	122.785	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15695 - 	CGI_10003288	superfamily	241578	253	373	3.17E-26	102.755	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15695 - 	CGI_10003288	superfamily	241578	21	57	0.00670508	36.2093	cl00057	vWFA superfamily	NC	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15696 - 	CGI_10003289	superfamily	241578	26	205	1.19E-36	132.352	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15696 - 	CGI_10003289	superfamily	241578	241	405	1.17E-30	115.847	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15697 - 	CGI_10003290	superfamily	243146	16	66	2.23E-08	46.7827	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15697 - 	CGI_10003290	superfamily	243146	55	109	0.00242251	33.1906	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15698 - 	CGI_10003291	superfamily	243146	12	47	1.78E-06	41.3899	cl02701	Kelch_3 superfamily	N	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15698 - 	CGI_10003291	superfamily	243146	36	90	0.000450612	34.7314	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15700 - 	CGI_10003293	superfamily	222090	331	516	2.72E-14	71.535	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#15702 - 	CGI_10000838	superfamily	245814	327	394	0.00071344	37.4687	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15703 - 	CGI_10013895	superfamily	245206	1	260	1.04E-92	279.109	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15704 - 	CGI_10013896	superfamily	218375	23	283	2.33E-63	203.87	cl09349	IFRD superfamily	 - 	 - 	"Interferon-related developmental regulator (IFRD); Interferon-related developmental regulator (IFRD1) is the human homologue of the rat early response protein PC4 and its murine homologue TIS7. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary to muscle differentiation and that it might have a role in signal transduction. This family also contains IFRD2 and its murine equivalent SKMc15 which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis."
Q#15709 - 	CGI_10013901	superfamily	243072	31	147	1.02E-19	87.0538	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15709 - 	CGI_10013901	superfamily	243072	298	421	2.81E-15	73.957	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15709 - 	CGI_10013901	superfamily	243072	96	243	1.37E-14	72.031	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15709 - 	CGI_10013901	superfamily	243072	395	453	1.99E-08	53.5414	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	955	1074	2.07E-25	104.388	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	892	1010	3.46E-24	100.921	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	1588	1703	1.87E-23	98.995	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	1361	1475	1.08E-22	96.6838	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	1024	1140	2.62E-22	95.5282	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	1123	1236	8.99E-22	93.9874	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	1525	1639	3.53E-21	92.4466	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	1185	1295	6.05E-20	88.5946	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15710 - 	CGI_10013902	superfamily	243072	833	945	6.19E-19	85.8982	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15712 - 	CGI_10013904	superfamily	192997	298	443	1.72E-37	138.869	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#15713 - 	CGI_10013905	superfamily	245210	5	252	1.07E-117	346.468	cl09938	cond_enzymes superfamily	C	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#15714 - 	CGI_10001123	superfamily	246664	287	673	1.05E-173	504.416	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#15714 - 	CGI_10001123	superfamily	243092	76	169	5.17E-17	80.842	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15714 - 	CGI_10001123	superfamily	246664	183	225	0.00782974	37.675	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#15715 - 	CGI_10005302	superfamily	214531	40	83	0.00300797	31.4181	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#15716 - 	CGI_10005303	superfamily	149010	39	111	1.49E-31	121.634	cl06656	DUF1604 superfamily	 - 	 - 	Protein of unknown function (DUF1604); This family is found at the N-terminus of several eukaryotic RNA processing proteins.
Q#15716 - 	CGI_10005303	superfamily	248289	1762	1819	9.13E-08	51.6559	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#15716 - 	CGI_10005303	superfamily	214531	1049	1081	1.10E-07	51.0633	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#15716 - 	CGI_10005303	superfamily	111397	1859	1936	5.79E-07	49.6471	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#15716 - 	CGI_10005303	superfamily	243107	150	167	1.37E-05	45.2286	cl02611	G-patch superfamily	C	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#15716 - 	CGI_10005303	superfamily	214531	1083	1124	9.22E-05	42.5889	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#15716 - 	CGI_10005303	superfamily	214531	1358	1400	0.00284964	38.3517	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#15716 - 	CGI_10005303	superfamily	214531	1304	1358	0.00376331	37.9665	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#15719 - 	CGI_10004614	superfamily	247085	161	234	6.64E-12	59.8266	cl15820	RICIN superfamily	N	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#15719 - 	CGI_10004614	superfamily	245596	18	148	2.75E-77	237.873	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#15723 - 	CGI_10004618	superfamily	246680	1	66	0.00942431	32.944	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#15724 - 	CGI_10004619	superfamily	201362	4	75	0.000887223	35.4188	cl08277	Motile_Sperm superfamily	C	 - 	MSP (Major sperm protein) domain; Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
Q#15725 - 	CGI_10004620	superfamily	219425	30	148	3.04E-17	72.9594	cl06494	Hydrolase_2 superfamily	 - 	 - 	"Cell Wall Hydrolase; These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance B. subtilis sleB is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex. A similar role is carried out by the partially redundant B. subtilis cwlJ. It is not clear whether these enzymes are amidases or peptidases."
Q#15726 - 	CGI_10004621	superfamily	247057	424	464	0.00105183	37.1304	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#15727 - 	CGI_10000506	superfamily	241568	8	49	2.32E-05	40.1388	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#15727 - 	CGI_10000506	superfamily	241568	53	108	0.000242349	37.1696	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#15731 - 	CGI_10004922	superfamily	191444	53	128	0.000525737	35.3777	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#15732 - 	CGI_10004923	superfamily	247727	330	421	8.01E-13	64.7586	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#15732 - 	CGI_10004923	superfamily	247727	278	368	0.0020735	38.6116	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#15738 - 	CGI_10010262	superfamily	248097	9	125	2.46E-16	69.9866	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15740 - 	CGI_10010264	superfamily	247769	252	380	8.75E-08	50.8009	cl17215	HDc superfamily	C	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#15741 - 	CGI_10010265	superfamily	247792	57	103	0.000725457	38.1956	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15741 - 	CGI_10010265	superfamily	110440	595	620	1.33E-05	43.1653	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#15741 - 	CGI_10010265	superfamily	241563	209	238	0.000248092	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15741 - 	CGI_10010265	superfamily	110440	424	447	0.00306406	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#15743 - 	CGI_10010267	superfamily	243056	38	237	1.62E-21	93.1925	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#15743 - 	CGI_10010267	superfamily	241626	313	364	0.00875114	35.1728	cl00125	RHOD superfamily	C	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#15744 - 	CGI_10010268	superfamily	246908	241	335	4.68E-62	198.429	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15744 - 	CGI_10010268	superfamily	247792	366	408	7.90E-10	54.7592	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15744 - 	CGI_10010268	superfamily	111184	32	161	1.56E-74	232.078	cl03506	Cbl_N superfamily	 - 	 - 	"CBL proto-oncogene N-terminal domain 1; Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. Cbl_N is comprised of 3 structural domains of which this is the first - a four helix bundle."
Q#15744 - 	CGI_10010268	superfamily	202379	164	247	1.65E-44	151.899	cl03701	Cbl_N2 superfamily	 - 	 - 	"CBL proto-oncogene N-terminus, EF hand-like domain; Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the central EF hand domain."
Q#15745 - 	CGI_10010269	superfamily	241563	96	131	0.00080667	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15749 - 	CGI_10007771	superfamily	202224	463	579	5.82E-49	172.095	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#15749 - 	CGI_10007771	superfamily	243120	79	164	7.47E-31	119.221	cl02633	ARID superfamily	 - 	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#15749 - 	CGI_10007771	superfamily	217292	669	722	2.02E-25	102.346	cl03786	zf-C5HC2 superfamily	 - 	 - 	C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.
Q#15749 - 	CGI_10007771	superfamily	210240	13	54	1.22E-17	79.6142	cl15840	JmjN superfamily	 - 	 - 	jmjN domain; jmjN domain.  
Q#15749 - 	CGI_10007771	superfamily	247999	289	337	4.04E-15	72.5231	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#15749 - 	CGI_10007771	superfamily	247999	1622	1665	9.54E-08	51.0586	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#15749 - 	CGI_10007771	superfamily	247999	1151	1189	1.04E-05	45.2806	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#15750 - 	CGI_10007772	superfamily	218657	6	140	8.87E-29	105.465	cl09577	THOC7 superfamily	 - 	 - 	Tho complex subunit 7; The Tho complex is involved in transcription elongation and mRNA export from the nucleus.
Q#15751 - 	CGI_10007773	superfamily	149388	342	396	3.22E-17	78.1875	cl07068	SCA7 superfamily	 - 	 - 	"SCA7, zinc-binding domain; This domain is found in the protein Sgf73/Sca7 which is a component of the multihistone acetyltransferase complexes SAGA and SILK. This domain is also found in Ataxin-7, a human protein which in its polyglutamine expanded pathological form, is responsible for the neurodegenerative disease spinocerebellar ataxia 7 (SCA7). Ataxin-7 is an integral component of the mammalian SAGA-like complexes, the TATA-binding protein-free TAF-containing complex (TFTC) and the SPT3/TAF9/GCN5 acetyltransferase complex (STAGA). This domain is a minimal domain in ataxin-7-like proteins that is required for interaction with TFTC/STAGA subunits and is conserved highly through evolution. The domain contains a conserved Cys(3)His motif that binds zinc, thus indicating this to be a new zinc-binding domain."
Q#15752 - 	CGI_10007774	superfamily	247750	103	345	3.43E-133	393.557	cl17196	E1_enzyme_family superfamily	 - 	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#15752 - 	CGI_10007774	superfamily	245106	505	591	2.40E-45	157.036	cl09615	UBA_e1_C superfamily	C	 - 	Ubiquitin-activating enzyme e1 C-terminal domain; This presumed domain found at the C-terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterized.
Q#15752 - 	CGI_10007774	superfamily	247750	441	483	5.89E-20	89.6341	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#15754 - 	CGI_10007776	superfamily	245206	165	303	1.00E-29	114.486	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15759 - 	CGI_10002620	superfamily	220788	517	577	2.02E-09	55.2317	cl11144	MCC-bdg_PDZ superfamily	 - 	 - 	PDZ domain of MCC-2 bdg protein for Usher syndrome; The protein has a high homology to the tumour suppressor MCC (mutated in colon cancer; or MCC1 hereafter) and was named MCC2. MCC2 protein binds the first PDZ domain of AIE-75 with its C-terminal amino acids -DTFL. A possible role of MCC2 as a tumor suppressor has been put forward. The carboxyl terminus of the predicted protein was DTFL which matched the consensus motif X-S/T-X-phi (phi: hydrophobic amino acid residue) for binding to the PDZ domain of AIE-75.
Q#15759 - 	CGI_10002620	superfamily	220788	811	853	0.00574385	35.9718	cl11144	MCC-bdg_PDZ superfamily	C	 - 	PDZ domain of MCC-2 bdg protein for Usher syndrome; The protein has a high homology to the tumour suppressor MCC (mutated in colon cancer; or MCC1 hereafter) and was named MCC2. MCC2 protein binds the first PDZ domain of AIE-75 with its C-terminal amino acids -DTFL. A possible role of MCC2 as a tumor suppressor has been put forward. The carboxyl terminus of the predicted protein was DTFL which matched the consensus motif X-S/T-X-phi (phi: hydrophobic amino acid residue) for binding to the PDZ domain of AIE-75.
Q#15761 - 	CGI_10011689	superfamily	243035	34	81	9.74E-09	51.4466	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15763 - 	CGI_10011691	superfamily	241647	92	119	0.000831616	37.8926	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#15763 - 	CGI_10011691	superfamily	221479	461	636	8.89E-83	261.5	cl13646	PCIF1_WW superfamily	 - 	 - 	"Phosphorylated CTD interacting factor 1 WW domain; This domain family is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. This domain is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity."
Q#15764 - 	CGI_10011692	superfamily	247692	16	487	0	525.268	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#15768 - 	CGI_10011696	superfamily	246925	318	476	4.07E-09	57.7506	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15768 - 	CGI_10011696	superfamily	246925	95	208	3.83E-08	54.669	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15768 - 	CGI_10011696	superfamily	214507	597	646	3.29E-05	42.8024	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#15768 - 	CGI_10011696	superfamily	246925	397	573	0.000638539	41.5722	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15769 - 	CGI_10011697	superfamily	198738	1	31	2.15E-09	48.4183	cl02599	Ets superfamily	N	 - 	Ets-domain; Ets-domain.  
Q#15771 - 	CGI_10011699	superfamily	198738	2	49	1.95E-16	67.293	cl02599	Ets superfamily	N	 - 	Ets-domain; Ets-domain.  
Q#15773 - 	CGI_10011701	superfamily	245814	164	216	6.71E-09	52.1063	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15773 - 	CGI_10011701	superfamily	245814	51	130	2.03E-09	53.9303	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15773 - 	CGI_10011701	superfamily	245814	245	326	4.30E-09	52.8929	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15774 - 	CGI_10011702	superfamily	243250	415	841	3.47E-136	430.917	cl02959	Glyco_hydro_9 superfamily	 - 	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#15774 - 	CGI_10011702	superfamily	243250	1140	1566	7.09E-135	427.45	cl02959	Glyco_hydro_9 superfamily	 - 	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#15775 - 	CGI_10011703	superfamily	246925	187	501	7.32E-24	102.049	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15776 - 	CGI_10012360	superfamily	241752	15	135	5.30E-45	144.77	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#15777 - 	CGI_10012361	superfamily	247097	47	83	9.66E-06	40.8974	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#15779 - 	CGI_10012363	superfamily	247097	94	130	0.000121744	36.6602	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#15780 - 	CGI_10012364	superfamily	247097	91	126	6.51E-05	37.0454	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#15781 - 	CGI_10012365	superfamily	244895	41	520	0	547.145	cl08294	Peptidase_M17 superfamily	 - 	 - 	"Cytosol aminopeptidase family, N-terminal and catalytic domains.  Family M17 contains zinc- and manganese-dependent exopeptidases ( EC  3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants."
Q#15782 - 	CGI_10012366	superfamily	241594	453	810	1.92E-122	374.979	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#15785 - 	CGI_10012370	superfamily	243072	197	323	5.07E-33	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15785 - 	CGI_10012370	superfamily	245201	532	783	1.46E-118	361.283	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15785 - 	CGI_10012370	superfamily	246908	338	425	5.89E-19	83.2402	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15785 - 	CGI_10012370	superfamily	246908	54	139	1.08E-18	82.2767	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#15786 - 	CGI_10012371	superfamily	247792	54	128	2.42E-28	100.58	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15787 - 	CGI_10012372	superfamily	241592	23	117	4.03E-43	139.778	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#15788 - 	CGI_10012373	superfamily	192151	244	383	9.36E-60	194.479	cl07405	DP superfamily	 - 	 - 	Transcription factor DP; DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer and negatively regulates the G1-S transition.
Q#15788 - 	CGI_10012373	superfamily	202203	160	224	6.97E-12	61.0449	cl03534	E2F_TDP superfamily	C	 - 	"E2F/DP family winged-helix DNA-binding domain; This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins."
Q#15790 - 	CGI_10012375	superfamily	248458	53	227	3.07E-12	66.9537	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#15791 - 	CGI_10006857	superfamily	247684	24	450	2.45E-107	331.549	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15792 - 	CGI_10006858	superfamily	245206	71	247	1.70E-48	163.549	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15792 - 	CGI_10006858	superfamily	245206	44	90	0.000173379	40.6481	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15793 - 	CGI_10006859	superfamily	243093	111	202	0.00954782	34.3681	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#15794 - 	CGI_10006860	superfamily	245206	20	339	1.21E-161	465.234	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#15794 - 	CGI_10006860	superfamily	176932	366	455	1.22E-31	117.271	cl03838	FAR_C superfamily	 - 	 - 	"C-terminal domain of fatty acyl CoA reductases; C-terminal domain of fatty acyl CoA reductases, a family of SDR-like proteins. SDRs or short-chain dehydrogenases/reductases are Rossmann-fold NAD(P)H-binding proteins. Many proteins in this FAR_C family may function as fatty acyl-CoA reductases (FARs), acting on medium and long chain fatty acids, and have been reported to be involved in diverse processes such as the biosynthesis of insect pheromones, plant cuticular wax production, and mammalian wax biosynthesis. In Arabidopsis thaliana, proteins with this particular architecture have also been identified as the MALE STERILITY 2 (MS2) gene product, which is implicated in male gametogenesis. Mutations in MS2 inhibit the synthesis of exine (sporopollenin), rendering plants unable to reduce pollen wall fatty acids to corresponding alcohols. The function of this C-terminal domain is unclear."
Q#15796 - 	CGI_10006862	superfamily	216363	9	80	6.17E-10	50.9318	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#15797 - 	CGI_10006863	superfamily	243119	644	692	0.000114303	40.4949	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#15799 - 	CGI_10001894	superfamily	244895	1	267	1.53E-122	360.708	cl08294	Peptidase_M17 superfamily	N	 - 	"Cytosol aminopeptidase family, N-terminal and catalytic domains.  Family M17 contains zinc- and manganese-dependent exopeptidases ( EC  3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants."
Q#15800 - 	CGI_10001897	superfamily	215733	1	102	1.16E-23	97.6358	cl02811	E1-E2_ATPase superfamily	N	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#15800 - 	CGI_10001897	superfamily	226572	262	374	1.47E-08	52.5612	cl18761	COG4087 superfamily	N	 - 	Soluble P-type ATPase [General function prediction only]
Q#15801 - 	CGI_10001899	superfamily	241857	16	142	1.25E-06	44.5769	cl00427	TM_PBP2 superfamily	N	 - 	"Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. For these transporters the ABCs and TMs are on independent polypeptide chains. These systems transport a diverse range of substrates. Most are specific for a single substrate or a group of related substrates; however some transporters are more promiscuous, transporting structurally diverse substrates such as the histidine/lysine and arginine transporter in Enterobacteriaceae. In the latter case, this is achieved through binding different PBPs with different specificities to the TMs. For other promiscuous transporters such as the multiple-sugar transporter Msm of Streptococcus mutans, the PBP has a wide substrate specificity. These transporters include the maltose-maltodextrin, phosphate and sulfate transporters, among others."
Q#15802 - 	CGI_10001900	superfamily	247986	42	263	1.58E-38	137.89	cl17432	PBPb superfamily	 - 	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#15803 - 	CGI_10001908	superfamily	241825	17	101	5.08E-18	73.3431	cl00379	Ribosomal_L18_L5e superfamily	 - 	 - 	"Ribosomal L18/L5e:  L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified."
Q#15804 - 	CGI_10001909	superfamily	215872	25	99	2.52E-19	76.4634	cl08261	Ribosomal_L6 superfamily	 - 	 - 	Ribosomal protein L6; Ribosomal protein L6.  
Q#15806 - 	CGI_10006664	superfamily	247792	195	233	0.000937357	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15808 - 	CGI_10006666	superfamily	247684	38	241	2.68E-26	108.204	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15809 - 	CGI_10006667	superfamily	241596	278	335	4.05E-13	64.1575	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#15812 - 	CGI_10006670	superfamily	241580	686	760	1.96E-12	64.4974	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#15813 - 	CGI_10006671	superfamily	241810	231	287	1.55E-21	88.0134	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#15813 - 	CGI_10006671	superfamily	241810	434	485	9.08E-14	66.0364	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#15813 - 	CGI_10006671	superfamily	243107	131	208	7.44E-23	92.4382	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#15814 - 	CGI_10006672	superfamily	241900	36	196	1.67E-65	210.558	cl00490	EEP superfamily	C	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#15814 - 	CGI_10006672	superfamily	241900	200	372	3.20E-62	202.083	cl00490	EEP superfamily	N	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#15815 - 	CGI_10006673	superfamily	241600	64	248	5.88E-71	219.419	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#15816 - 	CGI_10006674	superfamily	241600	51	220	6.62E-67	207.478	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#15817 - 	CGI_10006675	superfamily	241600	1	168	7.56E-71	215.567	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#15818 - 	CGI_10003205	superfamily	241563	68	109	1.92E-07	48.2444	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15818 - 	CGI_10003205	superfamily	241563	28	59	0.00135158	37.0736	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15822 - 	CGI_10007566	superfamily	243310	287	524	3.19E-93	286.827	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#15823 - 	CGI_10007567	superfamily	241574	219	439	2.09E-64	211.29	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15823 - 	CGI_10007567	superfamily	241574	1	156	8.25E-59	196.268	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#15826 - 	CGI_10007570	superfamily	245230	26	456	0	952.12	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#15827 - 	CGI_10007571	superfamily	245230	9	81	8.53E-43	144.741	cl10017	Tubulin_FtsZ superfamily	NC	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#15828 - 	CGI_10007572	superfamily	247905	307	439	1.19E-22	93.8416	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#15828 - 	CGI_10007572	superfamily	247805	76	149	9.45E-06	44.2504	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15829 - 	CGI_10000647	superfamily	221377	3	91	0.000191806	38.2187	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#15834 - 	CGI_10003440	superfamily	243035	403	513	2.53E-12	63.7929	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15837 - 	CGI_10002327	superfamily	192107	63	137	5.15E-18	78.0277	cl07312	Med14 superfamily	NC	 - 	"Mediator complex subunit MED14; Saccharomyces cerevisiae RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes and sporulation, required for glucose repression, HO repression, RME1 repression and sporulation. This subunit is also found in higher eukaryotes and Med14 is the agreed unified nomenclature for this subunit. Med14 is found in the tail region of Mediator."
Q#15841 - 	CGI_10017082	superfamily	246925	23	321	3.57E-23	98.1965	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15843 - 	CGI_10017084	superfamily	219285	178	427	3.44E-90	278.823	cl06207	D123 superfamily	 - 	 - 	"D123; This family contains a number of eukaryotic D123 proteins approximately 330 residues long. It has been shown that mutated variants of D123 exhibit temperature-dependent differences in their degradation rate. D123 proteins are regulators of eIF2, the central regulator of translational initiation."
Q#15846 - 	CGI_10017087	superfamily	243119	8	54	6.69E-05	40.4949	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#15846 - 	CGI_10017087	superfamily	243119	99	152	0.000804671	37.0382	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#15847 - 	CGI_10017088	superfamily	248100	26	78	2.90E-09	52.5416	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#15847 - 	CGI_10017088	superfamily	248100	143	192	0.00226457	35.5928	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#15848 - 	CGI_10017089	superfamily	216897	97	181	7.13E-18	74.6401	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#15849 - 	CGI_10017090	superfamily	151051	63	276	7.75E-107	320.728	cl11131	Nrf1_DNA-bind superfamily	 - 	 - 	"NLS-binding and DNA-binding and dimerisation domains of Nrf1; In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity."
Q#15851 - 	CGI_10017092	superfamily	241764	280	351	5.05E-23	95.1048	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#15851 - 	CGI_10017092	superfamily	245201	880	1040	1.80E-65	220.879	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15851 - 	CGI_10017092	superfamily	243088	17	89	4.44E-24	99.3168	cl02563	PX_domain superfamily	C	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#15851 - 	CGI_10017092	superfamily	245201	391	470	8.17E-24	101.852	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15852 - 	CGI_10017093	superfamily	247724	3	175	1.98E-120	340.842	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15853 - 	CGI_10017094	superfamily	245201	831	1118	0	589.031	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15853 - 	CGI_10017094	superfamily	247723	274	364	1.49E-37	138.162	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15853 - 	CGI_10017094	superfamily	247723	377	449	1.28E-31	120.344	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15853 - 	CGI_10017094	superfamily	241620	461	491	1.69E-11	61.5171	cl00113	CRIB superfamily	C	 - 	"PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules."
Q#15854 - 	CGI_10017095	superfamily	248013	699	738	0.000504793	39.9399	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#15854 - 	CGI_10017095	superfamily	243120	308	392	2.49E-26	105.739	cl02633	ARID superfamily	 - 	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#15854 - 	CGI_10017095	superfamily	149305	184	277	1.49E-09	57.0733	cl06977	RBB1NT superfamily	 - 	 - 	RBB1NT (NUC162) domain; This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family.
Q#15855 - 	CGI_10017096	superfamily	215754	102	193	3.13E-16	71.9008	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#15855 - 	CGI_10017096	superfamily	215754	221	296	5.78E-14	65.7376	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#15855 - 	CGI_10017096	superfamily	215754	21	93	7.40E-08	48.7888	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#15856 - 	CGI_10017097	superfamily	242896	21	311	1.03E-109	323.889	cl02127	RNA_pol_Rpc34 superfamily	 - 	 - 	"RNA polymerase Rpc34 subunit; Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is therefore participates in Pol III recruitment."
Q#15857 - 	CGI_10017098	superfamily	248013	26	76	0.000209268	39.1695	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#15859 - 	CGI_10017100	superfamily	242162	22	61	1.48E-20	77.8953	cl00876	Ribosomal_S27 superfamily	 - 	 - 	Ribosomal protein S27a; This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins.
Q#15860 - 	CGI_10017101	superfamily	243034	683	769	2.02E-11	61.6272	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#15860 - 	CGI_10017101	superfamily	243034	644	710	3.01E-06	46.2192	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#15860 - 	CGI_10017101	superfamily	243034	343	457	2.04E-05	43.5228	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#15860 - 	CGI_10017101	superfamily	243034	441	525	0.000518964	39.2856	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#15862 - 	CGI_10017103	superfamily	247905	967	1091	2.01E-27	110.02	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#15862 - 	CGI_10017103	superfamily	247805	434	579	2.10E-21	92.7856	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15862 - 	CGI_10017103	superfamily	206063	242	362	9.56E-38	140.092	cl16460	DBINO superfamily	 - 	 - 	DNA-binding domain; DBINO is a DNA-binding domain found on global transcription activator SNF2L1 proteins and chromatin re-modelling proteins.
Q#15863 - 	CGI_10017104	superfamily	241565	20	89	2.47E-10	53.8647	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#15864 - 	CGI_10017105	superfamily	247804	375	429	4.93E-05	41.407	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#15864 - 	CGI_10017105	superfamily	247804	326	368	0.000293843	39.0958	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#15865 - 	CGI_10017106	superfamily	245814	45	133	0.00099114	34.3871	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15867 - 	CGI_10017108	superfamily	217685	288	434	4.69E-26	104.338	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#15867 - 	CGI_10017108	superfamily	216290	152	273	3.53E-21	89.6549	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#15868 - 	CGI_10017109	superfamily	245814	168	236	9.92E-05	39.7799	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15868 - 	CGI_10017109	superfamily	245814	82	135	0.00384262	35.0633	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15871 - 	CGI_10017112	superfamily	247684	56	163	4.72E-14	69.9251	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15872 - 	CGI_10006447	superfamily	241864	25	187	9.63E-43	141.065	cl00439	UPF0047 superfamily	 - 	 - 	Uncharacterized protein family UPF0047; This family has no known function. The alignment contains a conserved aspartate and histidine that may be functionally important.
Q#15873 - 	CGI_10006448	superfamily	243072	35	154	3.97E-24	94.7578	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15873 - 	CGI_10006448	superfamily	243072	128	197	4.08E-06	43.9115	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15873 - 	CGI_10006448	superfamily	243073	221	260	5.84E-06	42.4573	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#15875 - 	CGI_10006451	superfamily	243161	14	68	8.14E-07	42.4222	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#15877 - 	CGI_10006453	superfamily	245226	277	448	1.25E-19	87.7412	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#15879 - 	CGI_10006455	superfamily	247743	335	368	1.66E-05	45.2147	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#15879 - 	CGI_10006455	superfamily	243092	888	1222	1.55E-17	84.3088	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15880 - 	CGI_10006456	superfamily	217410	30	71	0.000464934	37.3336	cl18409	DDE_1 superfamily	NC	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere."
Q#15882 - 	CGI_10021302	superfamily	238012	126	174	2.32E-08	50.0454	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#15882 - 	CGI_10021302	superfamily	238012	176	218	5.68E-07	45.8082	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#15882 - 	CGI_10021302	superfamily	238012	226	264	1.39E-06	44.6526	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#15882 - 	CGI_10021302	superfamily	238012	73	119	5.77E-05	40.0302	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#15883 - 	CGI_10021303	superfamily	241563	68	109	1.17E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15883 - 	CGI_10021303	superfamily	241563	28	59	0.00120833	37.0736	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15885 - 	CGI_10021305	superfamily	245602	663	968	8.04E-70	235.573	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#15885 - 	CGI_10021305	superfamily	245602	898	1051	1.06E-26	113.491	cl11402	GH31 superfamily	N	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#15891 - 	CGI_10021311	superfamily	247745	5	283	2.77E-95	285.379	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#15892 - 	CGI_10021312	superfamily	241832	277	333	0.000771864	38.3712	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#15893 - 	CGI_10021313	superfamily	241563	105	143	5.64E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15894 - 	CGI_10021314	superfamily	243091	104	204	4.54E-14	65.206	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#15895 - 	CGI_10021315	superfamily	241563	62	100	7.25E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15895 - 	CGI_10021315	superfamily	243092	306	434	0.00220636	38.8552	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15895 - 	CGI_10021315	superfamily	217020	100	199	0.00371837	36.0334	cl03574	Seryl_tRNA_N superfamily	 - 	 - 	Seryl-tRNA synthetase N-terminal domain; This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Q#15896 - 	CGI_10021316	superfamily	241817	1	110	4.86E-41	138.479	cl00365	F1-ATPase_gamma superfamily	N	 - 	"mitochondrial ATP synthase gamma subunit; The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain of F-ATPases is composed of alpha, beta, gamma, delta, and epsilon (not present in bacteria) subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain."
Q#15897 - 	CGI_10021317	superfamily	216363	66	118	2.11E-13	62.4878	cl08312	UPF0029 superfamily	NC	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#15898 - 	CGI_10021318	superfamily	247905	403	519	1.54E-26	106.168	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#15898 - 	CGI_10021318	superfamily	192726	189	338	6.43E-53	181.111	cl12779	Med25 superfamily	 - 	 - 	"Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear."
Q#15901 - 	CGI_10021321	superfamily	245814	81	162	0.000176508	39.4109	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15901 - 	CGI_10021321	superfamily	246918	222	245	0.000506741	37.9515	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#15902 - 	CGI_10021322	superfamily	241645	7	120	1.92E-53	165.486	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#15903 - 	CGI_10021323	superfamily	217293	1	194	4.02E-38	137.764	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#15906 - 	CGI_10021326	superfamily	244859	244	471	6.31E-17	79.9229	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#15907 - 	CGI_10021327	superfamily	243179	89	200	5.65E-11	57.1575	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#15908 - 	CGI_10021328	superfamily	243035	132	262	6.34E-12	60.4802	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15909 - 	CGI_10021329	superfamily	243035	128	252	3.32E-06	44.1478	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#15910 - 	CGI_10021330	superfamily	234583	6	422	6.90E-165	483.896	cl18873	PRK00029 superfamily	C	 - 	hypothetical protein; Validated
Q#15910 - 	CGI_10021330	superfamily	234583	508	585	5.36E-18	85.9852	cl18873	PRK00029 superfamily	N	 - 	hypothetical protein; Validated
Q#15911 - 	CGI_10021331	superfamily	243212	103	223	5.08E-16	71.6061	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#15911 - 	CGI_10021331	superfamily	215866	10	78	6.78E-09	51.9424	cl18349	Arrestin_N superfamily	N	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#15913 - 	CGI_10021333	superfamily	205121	23	47	3.44E-05	40.5652	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#15914 - 	CGI_10021334	superfamily	198913	1628	1756	6.98E-55	189.491	cl07883	CAMSAP_CKK superfamily	 - 	 - 	"Microtubule-binding calmodulin-regulated spectrin-associated; This is the C-terminal domain of a family of eumetazoan proteins collectively defined as calmodulin-regulated spectrin-associated, or CAMSAP, proteins. CAMSAP proteins carry an N-terminal region that includes the CH domain, a central region including a predicted coiled-coil and this C-terminal, or CKK, domain - defined as being present in CAMSAP, KIAA1078 and KIAA1543, The C-terminal domain is the part of the CAMSAP proteins that binds to microtubules. The domain appears to act by producing inhibition of neurite extension, probably by blocking microtubule function. CKK represents a domain that has evolved with the metazoa. The structure of a murine hypothetical protein from RIKEN cDNA has shown the domain to adopt a mainly beta barrel structure with an associated alpha-helical hairpin."
Q#15914 - 	CGI_10021334	superfamily	241559	221	304	6.16E-21	90.4228	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#15915 - 	CGI_10021335	superfamily	203690	439	494	6.34E-13	64.4912	cl06576	UnbV_ASPIC superfamily	C	 - 	ASPIC and UnbV; This conserved sequence is found associated with pfam00515 in several paralogous proteins in Rhodopirellula baltica. It is also found associated with pfam01839 in several eukaryotic integrin-like proteins (e.g. human ASPIC) and in several other bacterial proteins.
Q#15916 - 	CGI_10021336	superfamily	216292	3	208	1.74E-37	131.403	cl03091	Clathrin_lg_ch superfamily	 - 	 - 	Clathrin light chain; Clathrin light chain.  
Q#15917 - 	CGI_10021337	superfamily	245205	5	110	3.27E-23	88.0889	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#15918 - 	CGI_10021338	superfamily	148567	31	101	1.06E-16	69.9143	cl06182	Rab5ip superfamily	 - 	 - 	Rab5-interacting protein (Rab5ip); This family consists of several Rab5-interacting protein (RIP5 or Rab5ip) sequences. The ras-related GTPase rab5 is rate-limiting for homotypic early endosome fusion. Rab5ip represents a novel rab5 interacting protein that may function on endocytic vesicles as a receptor for rab5-GDP and participate in the activation of rab5.
Q#15920 - 	CGI_10006624	superfamily	218118	63	133	7.03E-16	68.7948	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#15923 - 	CGI_10006627	superfamily	218118	163	240	2.27E-12	60.3205	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#15923 - 	CGI_10006627	superfamily	218118	27	93	8.80E-12	58.7797	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#15927 - 	CGI_10011136	superfamily	244859	8	115	1.27E-08	51.0081	cl08171	HtrL_YibB superfamily	N	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#15928 - 	CGI_10011137	superfamily	248097	101	226	4.32E-07	46.5265	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#15928 - 	CGI_10011137	superfamily	245674	17	77	0.00388719	34.187	cl11531	DUF904 superfamily	 - 	 - 	Protein of unknown function (DUF904); This family consists of several bacterial and archaeal hypothetical proteins of unknown function.
Q#15934 - 	CGI_10011143	superfamily	241754	208	429	7.28E-115	356.685	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#15934 - 	CGI_10011143	superfamily	241754	16	138	2.40E-46	169.478	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#15934 - 	CGI_10011143	superfamily	245835	495	618	0.00762155	37.456	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#15935 - 	CGI_10011144	superfamily	241571	366	489	2.46E-14	69.3634	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#15935 - 	CGI_10011144	superfamily	241583	171	361	5.69E-41	145.792	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#15937 - 	CGI_10011146	superfamily	216254	21	62	8.89E-09	51.4798	cl08303	Recep_L_domain superfamily	C	 - 	Receptor L domain; The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
Q#15942 - 	CGI_10003675	superfamily	247805	35	149	8.31E-14	64.666	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#15943 - 	CGI_10003676	superfamily	243072	21	122	3.68E-07	46.6078	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15943 - 	CGI_10003676	superfamily	243072	94	197	0.000430162	37.7483	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15946 - 	CGI_10023339	superfamily	221808	105	193	0.00826726	36.1718	cl15119	Tet_JBP superfamily	C	 - 	"Oxygenase domain of the 2OGFeDO superfamily; A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in various eukaryotes, bacteria and bacteriophages. Members of this family catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids, and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (hmC), or further oxidation to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Metazoan TET proteins contain a cysteine-rich region inserted into the core of the DSBH fold. Vertebrate TET proteins are oncogenes that are mutated in various myeloid cancers. Fungal and algal versions of this family are linked to a predicted transposase and show lineage-specific expansions."
Q#15946 - 	CGI_10023339	superfamily	241563	70	105	0.00971585	34.6203	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#15948 - 	CGI_10023341	superfamily	245882	21	116	1.13E-34	123.555	cl12119	Alpha_L_fucos superfamily	C	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#15949 - 	CGI_10023342	superfamily	245882	25	400	1.23E-166	477.553	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#15950 - 	CGI_10023343	superfamily	243146	161	206	3.98E-08	49.197	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15950 - 	CGI_10023343	superfamily	243146	17	62	7.08E-08	48.4266	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15950 - 	CGI_10023343	superfamily	243146	113	162	1.57E-07	47.4429	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15950 - 	CGI_10023343	superfamily	243146	65	111	3.43E-05	40.7226	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15950 - 	CGI_10023343	superfamily	243146	260	306	0.000105957	39.1818	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#15953 - 	CGI_10023346	superfamily	218165	30	103	8.37E-10	53.7763	cl04619	Ribophorin_I superfamily	C	 - 	"Ribophorin I; Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as Dolichyl-diphosphooligosaccharide--protein glycosyltransferase, (EC:2.4.1.119). OST catalyzes the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum. Ribophorin I and OST48 are though to be responsible for OST catalytic activity. Both yeast and mammalian proteins are glycosylated but the sites are not conserved. Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function Most family members are predicted to have a transmembrane helix at the C terminus of this region."
Q#15954 - 	CGI_10023347	superfamily	218165	32	452	5.92E-169	490.978	cl04619	Ribophorin_I superfamily	 - 	 - 	"Ribophorin I; Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as Dolichyl-diphosphooligosaccharide--protein glycosyltransferase, (EC:2.4.1.119). OST catalyzes the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum. Ribophorin I and OST48 are though to be responsible for OST catalytic activity. Both yeast and mammalian proteins are glycosylated but the sites are not conserved. Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function Most family members are predicted to have a transmembrane helix at the C terminus of this region."
Q#15956 - 	CGI_10023349	superfamily	243056	174	420	8.58E-42	148.661	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#15958 - 	CGI_10023351	superfamily	247724	37	362	0	575.63	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#15958 - 	CGI_10023351	superfamily	246925	601	741	0.000246629	42.7278	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#15959 - 	CGI_10023352	superfamily	238012	15705	15739	0.00683274	39.645	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#15959 - 	CGI_10023352	superfamily	238012	14247	14295	0.00798614	39.645	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#15959 - 	CGI_10023352	superfamily	245847	156	283	6.28E-10	62.3697	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#15959 - 	CGI_10023352	superfamily	243065	15195	15347	1.09E-08	58.6073	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#15959 - 	CGI_10023352	superfamily	219677	13695	13726	8.82E-05	45.1212	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#15959 - 	CGI_10023352	superfamily	219677	12780	12813	0.000141245	44.3508	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#15959 - 	CGI_10023352	superfamily	241611	14787	14946	0.000198994	45.072	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#15959 - 	CGI_10023352	superfamily	219677	13433	13464	0.00087752	42.0396	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#15959 - 	CGI_10023352	superfamily	219677	13305	13336	0.000945954	42.0396	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#15959 - 	CGI_10023352	superfamily	219677	12751	12775	0.00961244	38.958	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#15961 - 	CGI_10023354	superfamily	219677	2	33	0.00260467	36.6468	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#15962 - 	CGI_10023355	superfamily	243134	30	160	1.25E-33	120.832	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#15962 - 	CGI_10023355	superfamily	243134	175	307	1.58E-25	98.8755	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#15963 - 	CGI_10023356	superfamily	243056	200	422	1.37E-43	159.009	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#15964 - 	CGI_10023357	superfamily	247792	654	697	0.000159624	40.892	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#15965 - 	CGI_10023358	superfamily	247829	10	412	0	647.411	cl17275	PRTase_typeII superfamily	 - 	 - 	"Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate phosphoribosyltransferase (NAPRTase), to be used in the synthesis of NAD. QAPRTase catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide, an important step in the de novo synthesis of NAD. NAPRTase catalyses a similar reaction leading to NAMN and pyrophosphate, using nicotinic acid an PPRP as substrates, used in the NAD salvage pathway."
Q#15966 - 	CGI_10023359	superfamily	241584	625	715	8.04E-11	60.5879	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#15966 - 	CGI_10023359	superfamily	245814	60	134	7.38E-08	51.3359	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15966 - 	CGI_10023359	superfamily	241584	944	1036	2.76E-07	50.1875	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#15966 - 	CGI_10023359	superfamily	245814	547	618	3.01E-06	46.7135	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15966 - 	CGI_10023359	superfamily	222432	1175	1258	1.78E-19	86.593	cl16451	Bravo_FIGEY superfamily	N	 - 	C-terminal domain of Fibronectin type III; This is the very C-terminal region of neural adhesion molecule L1 proteins that are also known as Bravo or NrCAM. It lies upstream of the IG and Fn3 domains and has the highly conserved motif FIGEY. The function is not known.
Q#15966 - 	CGI_10023359	superfamily	245814	356	429	1.32E-15	73.973	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15966 - 	CGI_10023359	superfamily	245814	440	517	2.00E-11	62.1376	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15966 - 	CGI_10023359	superfamily	245814	277	325	3.02E-08	52.4091	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15966 - 	CGI_10023359	superfamily	245814	158	239	6.51E-07	49.0908	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#15967 - 	CGI_10023360	superfamily	215754	102	197	5.03E-28	104.643	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#15967 - 	CGI_10023360	superfamily	215754	201	290	2.78E-25	97.324	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#15967 - 	CGI_10023360	superfamily	215754	2	99	1.94E-18	78.064	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#15968 - 	CGI_10023361	superfamily	243082	749	894	1.03E-53	187.11	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#15968 - 	CGI_10023361	superfamily	243082	255	439	2.74E-22	98.2136	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#15968 - 	CGI_10023361	superfamily	245879	19	116	2.78E-16	75.8577	cl12116	DUSP superfamily	 - 	 - 	DUSP domain; The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Q#15969 - 	CGI_10023362	superfamily	247723	251	329	7.55E-42	148.703	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15969 - 	CGI_10023362	superfamily	247723	336	407	6.39E-33	123.085	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15969 - 	CGI_10023362	superfamily	247723	79	157	7.30E-28	108.887	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#15969 - 	CGI_10023362	superfamily	243072	545	660	1.01E-25	104.388	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15969 - 	CGI_10023362	superfamily	243072	800	915	1.01E-25	104.388	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#15969 - 	CGI_10023362	superfamily	243073	990	1027	1.05E-07	50.2221	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#15970 - 	CGI_10023363	superfamily	244089	1	168	1.10E-102	294.941	cl05433	ARPC4 superfamily	 - 	 - 	ARP2/3 complex 20 kDa subunit (ARPC4); This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion.
Q#15971 - 	CGI_10023364	superfamily	111626	44	244	1.05E-125	361.902	cl17929	Synapsin_C superfamily	 - 	 - 	"Synapsin, ATP binding domain; Ca dependent ATP binding in this ATP grasp fold. Function unknown."
Q#15971 - 	CGI_10023364	superfamily	111020	8	42	8.13E-11	57.9236	cl03435	Synapsin superfamily	N	 - 	"Synapsin, N-terminal domain; Synapsin, N-terminal domain.  "
Q#15972 - 	CGI_10023365	superfamily	243064	20	186	5.09E-20	84.0042	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#15973 - 	CGI_10023366	superfamily	150823	28	182	3.59E-48	156.079	cl10897	Armet superfamily	 - 	 - 	"Degradation arginine-rich protein for mis-folding; This is a family of small proteins of approximately 170 residues which contain four di-sulfide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress."
Q#15974 - 	CGI_10023367	superfamily	247684	2	358	2.07E-146	425.259	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#15975 - 	CGI_10023368	superfamily	241705	91	203	7.02E-29	106.903	cl00228	HIT_like superfamily	 - 	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#15975 - 	CGI_10023368	superfamily	218677	2	63	9.72E-16	69.9749	cl12312	DcpS superfamily	N	 - 	Scavenger mRNA decapping enzyme (DcpS) N-terminal; This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the N-terminal domain of these proteins. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway.
Q#15975 - 	CGI_10023368	superfamily	243836	197	236	0.00267467	35.7343	cl04661	Polysacc_synt_4 superfamily	NC	 - 	Polysaccharide biosynthesis; This family of proteins plays a role in xylan biosynthesis in plant cell walls. Its precise role in xylan biosynthesis is unknown. Its function in other organisms is unknown.
Q#15977 - 	CGI_10023370	superfamily	245213	84	121	0.000766461	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15977 - 	CGI_10023370	superfamily	245213	123	164	0.000828818	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15977 - 	CGI_10023370	superfamily	243119	496	533	0.000893112	37.7985	cl02629	CBM_14 superfamily	C	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#15981 - 	CGI_10023374	superfamily	241900	2	312	1.30E-127	377.813	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#15981 - 	CGI_10023374	superfamily	219199	474	523	2.82E-10	56.2344	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#15982 - 	CGI_10023375	superfamily	243125	12	28	0.00380983	32.6613	cl02649	LEM superfamily	N	 - 	"LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins; The family corresponds to a group of inner nuclear membrane proteins containing LEM domain. Emerin occurs in four phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy. Emerin interacts with A-type and B-type lamins. Man1, also termed LEM domain-containing protein 3 (LEMD3) is an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and post-mitotic reassembly. Some LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are non-membrane nuclear polypeptides. This family also contains LEM domain-containing protein LEMP-1 and LEM2. LEMP-1, also termed cancer/testis antigen 50 (CT50), is encoded by LEMD1, a novel testis-specific gene expressed in colorectal cancers. LEMP-1 may function as a cancer-testis antigen for immunotherapy of colorectal carcinoma (CRC). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization while its binding to lamin C plays an important role in the organization of lamin A/C complexes. Some uncharacterized LEM domain-containing proteins are also included in this family. Unlike other family members, these harbor an ankyrin repeat region that may mediate protein-protein interactions."
Q#15984 - 	CGI_10023377	superfamily	241665	275	662	9.80E-89	284.255	cl00183	AGE superfamily	 - 	 - 	"AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is structurally and mechanistically distinct from the other four types of epimerases. The AGE domain monomer is composed of an alpha(6)/alpha(6)-barrel, the structure of which is also found in glucoamylase and cellulase. The active form is a homodimer. The alignment also contains subtype III mannose 6-phosphate isomerases."
Q#15985 - 	CGI_10023378	superfamily	217473	231	374	6.85E-15	73.1681	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#15986 - 	CGI_10023379	superfamily	241617	186	251	3.85E-19	83.5761	cl00110	MBD superfamily	 - 	 - 	"MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin.  MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family."
Q#15986 - 	CGI_10023379	superfamily	246713	707	807	3.52E-05	43.1142	cl14786	ENDO3c superfamily	C	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#15987 - 	CGI_10023380	superfamily	243092	24	296	4.89E-33	128.607	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#15988 - 	CGI_10023381	superfamily	244913	1	441	2.53E-157	458.204	cl08327	Glyco_hydro_47 superfamily	 - 	 - 	"Glycosyl hydrolase family 47; Members of this family are alpha-mannosidases that catalyze the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2)."
Q#15989 - 	CGI_10023382	superfamily	247068	69	130	3.90E-05	43.8414	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#15989 - 	CGI_10023382	superfamily	245847	1368	1511	3.01E-06	47.7321	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#15990 - 	CGI_10023383	superfamily	245201	375	636	5.83E-122	366.798	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#15990 - 	CGI_10023383	superfamily	247038	48	155	3.08E-18	81.3093	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15991 - 	CGI_10023384	superfamily	247042	41	488	2.13E-57	199.094	cl15693	Sema superfamily	 - 	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#15991 - 	CGI_10023384	superfamily	247038	542	586	2.56E-11	60.3157	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#15991 - 	CGI_10023384	superfamily	243104	491	535	3.03E-09	53.7029	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#15992 - 	CGI_10023385	superfamily	247939	125	278	6.61E-05	40.8132	cl17385	DUF442 superfamily	C	 - 	Putative phosphatase (DUF442); Although this domain is uncharacterized it seems likely that it performs a phosphatase function.
Q#15993 - 	CGI_10023386	superfamily	243096	450	634	9.35E-21	91.2052	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#15993 - 	CGI_10023386	superfamily	247725	632	813	3.30E-29	115.738	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#15994 - 	CGI_10023387	superfamily	241578	598	785	1.37E-58	201.854	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#15994 - 	CGI_10023387	superfamily	219821	476	586	7.02E-31	119.783	cl07136	VWA_N superfamily	 - 	 - 	"VWA N-terminal; This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits."
Q#15994 - 	CGI_10023387	superfamily	217211	866	924	6.66E-10	57.6793	cl03691	Cache_1 superfamily	N	 - 	Cache domain; Cache domain.  
Q#15994 - 	CGI_10023387	superfamily	117050	937	1007	3.60E-09	55.8842	cl07190	VGCC_alpha2 superfamily	C	 - 	"Neuronal voltage-dependent calcium channel alpha 2acd; This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2 delta subunits to the N-terminus of a Cache domain (pfam02743)."
Q#15995 - 	CGI_10023388	superfamily	248275	167	190	0.00175764	36.0188	cl17721	zf-C2H2_jaz superfamily	 - 	 - 	"Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation."
Q#15996 - 	CGI_10023389	superfamily	241884	8	220	6.16E-149	418.279	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#15998 - 	CGI_10023391	superfamily	245847	1506	1629	7.20E-10	58.9029	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#15999 - 	CGI_10023392	superfamily	245213	9	44	1.13E-10	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#15999 - 	CGI_10023392	superfamily	245847	48	194	9.78E-15	67.5817	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#16000 - 	CGI_10023393	superfamily	248247	130	290	1.66E-23	101.527	cl17693	Integrin_beta superfamily	N	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#16000 - 	CGI_10023393	superfamily	248247	18	132	2.51E-10	61.081	cl17693	Integrin_beta superfamily	C	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#16000 - 	CGI_10023393	superfamily	219677	300	327	0.00925446	34.3356	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#16001 - 	CGI_10004341	superfamily	247792	18	68	1.26E-06	46.2848	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16001 - 	CGI_10004341	superfamily	220605	252	306	0.00951008	37.3403	cl10853	Med17 superfamily	NC	 - 	Subunit 17 of Mediator complex; This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures.
Q#16004 - 	CGI_10004344	superfamily	246954	34	578	1.20E-105	331.513	cl15415	Sec1 superfamily	 - 	 - 	Sec1 family; Sec1 family.  
Q#16005 - 	CGI_10004345	superfamily	243103	15	56	0.00226873	35.9248	cl02600	HTH_MerR-SF superfamily	N	 - 	"Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates."
Q#16006 - 	CGI_10004346	superfamily	243176	7	552	0	893.959	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#16008 - 	CGI_10009050	superfamily	243034	32	59	0.00799382	31.2628	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#16009 - 	CGI_10009051	superfamily	247724	183	388	1.30E-56	186.546	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16009 - 	CGI_10009051	superfamily	204472	8	88	9.10E-33	120.195	cl11057	TrmE_N superfamily	N	 - 	"GTP-binding protein TrmE N-terminus; This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein."
Q#16009 - 	CGI_10009051	superfamily	204989	396	464	4.27E-15	70.2405	cl14994	GTPase_Cys_C superfamily	 - 	 - 	"Catalytic cysteine-containing C-terminus of GTPase, MnmE; This short C-terminal region contains the only cysteine present in these proteins. It is proposed that MnmE is a tRNA-modifying enzyme and that Cys-451 functions as a catalytic residue in the modification reaction."
Q#16010 - 	CGI_10009052	superfamily	241563	58	98	5.29E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16011 - 	CGI_10009053	superfamily	246910	10	85	7.98E-46	150.846	cl15257	GIY-YIG_SF superfamily	 - 	 - 	"GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions."
Q#16012 - 	CGI_10009054	superfamily	215866	17	156	9.75E-41	142.464	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#16012 - 	CGI_10009054	superfamily	243212	178	305	7.92E-27	103.963	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#16013 - 	CGI_10009055	superfamily	242889	309	410	5.44E-24	95.3625	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#16014 - 	CGI_10009056	superfamily	220612	33	96	2.01E-28	99.5222	cl10867	DDA1 superfamily	 - 	 - 	"Det1 complexing ubiquitin ligase; DDA1 (De-etiolated 1, Damaged DNA binding protein 1 associated 1) protein binds strongly with DDB1 and Det1 forming a DDD complex which is part of the ubiquitin conjugation system."
Q#16015 - 	CGI_10009057	superfamily	177822	2	213	2.04E-12	63.7857	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#16017 - 	CGI_10009059	superfamily	241547	96	323	4.98E-96	286.486	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#16018 - 	CGI_10009060	superfamily	241547	89	317	1.02E-89	270.308	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#16021 - 	CGI_10000541	superfamily	241750	5	183	3.01E-125	365.537	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#16023 - 	CGI_10000738	superfamily	248009	15	112	9.67E-27	106.915	cl17455	UPF0027 superfamily	N	 - 	Uncharacterized protein family UPF0027; Uncharacterized protein family UPF0027.  
Q#16024 - 	CGI_10000640	superfamily	248054	36	88	1.76E-09	52.8596	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#16025 - 	CGI_10000754	superfamily	245205	42	123	5.56E-08	47.6177	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#16026 - 	CGI_10004553	superfamily	220627	13	43	4.90E-07	44.1382	cl10886	Telomere_reg-2 superfamily	N	 - 	Telomere length regulation protein; This family is the central conserved 110 amino acid region of a group of proteins called telomere-length regulation or clock abnormal protein-2 which are conserved from plants to humans. The full-length protein regulates telomere length and contributes to silencing of sub-telomeric regions. In vitro the protein binds to telomeric DNA repeats.
Q#16027 - 	CGI_10004554	superfamily	242184	1	27	5.54E-07	42.8861	cl00909	Ribosomal_L24e_L24 superfamily	N	 - 	"Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site.  L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination.  L24 may be an important protein in eukaryotic reproduction:  in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identified in bacteria, but a functionally equivalent protein may exist.  Bacterial L19 forms an interprotein beta sheet with L14 that is similar to the L24e/L14 interprotein beta sheet observed in the archaeal L24e structures. Some eukaryotic L24 proteins were initially identified as L30, and this alignment model contains several sequences called L30."
Q#16030 - 	CGI_10004557	superfamily	221130	1	93	4.09E-17	71.1527	cl13043	ARL2_Bind_BART superfamily	C	 - 	The ARF-like 2 binding protein BART; BART binds specifically to ARL2.GTP with a high affinity however it does not bind to ARL2.GDP. It is thought that this specific interaction is due to BART being the first identified ARL2-specific effector. The function is not completely characterized. BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1.
Q#16031 - 	CGI_10001008	superfamily	241619	34	80	2.13E-05	39.1025	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#16035 - 	CGI_10010119	superfamily	246713	11	32	0.000806372	32.7612	cl14786	ENDO3c superfamily	N	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#16036 - 	CGI_10010120	superfamily	241750	19	261	2.21E-19	83.871	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#16038 - 	CGI_10010122	superfamily	241600	17	97	1.17E-26	98.4666	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16040 - 	CGI_10001477	superfamily	241568	147	172	0.00292366	35.1312	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#16040 - 	CGI_10001477	superfamily	245847	184	329	1.55E-21	88.7677	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#16040 - 	CGI_10001477	superfamily	241619	16	83	0.00280458	35.2505	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#16041 - 	CGI_10001121	superfamily	217293	26	224	1.00E-38	139.305	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16041 - 	CGI_10001121	superfamily	202474	231	304	0.00269032	37.6333	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16042 - 	CGI_10001122	superfamily	248012	101	236	7.91E-27	101.631	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#16043 - 	CGI_10001523	superfamily	247999	667	717	1.12E-06	46.4362	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#16049 - 	CGI_10001980	superfamily	245213	154	189	2.02E-09	51.8686	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16049 - 	CGI_10001980	superfamily	245213	116	151	1.83E-08	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16049 - 	CGI_10001980	superfamily	245847	195	261	1.31E-13	65.6557	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#16051 - 	CGI_10001987	superfamily	247724	13	77	2.05E-30	109.127	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16051 - 	CGI_10001987	superfamily	247724	73	106	2.72E-11	57.1246	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16056 - 	CGI_10002166	superfamily	243134	27	149	1.72E-36	128.151	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#16056 - 	CGI_10002166	superfamily	243134	163	285	3.25E-36	127.38	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#16057 - 	CGI_10002167	superfamily	248312	35	128	0.000984737	36.5625	cl17758	PMP22_Claudin superfamily	C	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#16058 - 	CGI_10002807	superfamily	247792	314	367	4.39E-05	40.892	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16060 - 	CGI_10026085	superfamily	247743	53	178	0.00154039	37.9496	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16062 - 	CGI_10026087	superfamily	247792	94	139	3.55E-10	52.0628	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16064 - 	CGI_10026089	superfamily	241976	1	110	3.19E-28	101.065	cl00606	Archease superfamily	N	 - 	"Archease protein family (MTH1598/TM1083); This archease family of proteins, has two SHS2 domains, with one inserted into another. It is predicted to be an enzyme. It is predicted to act as a chaperone in DNA/RNA metabolism."
Q#16066 - 	CGI_10026091	superfamily	247725	48	131	5.89E-34	128.174	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16066 - 	CGI_10026091	superfamily	247725	180	229	7.27E-10	58.0234	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16067 - 	CGI_10026092	superfamily	246680	35	120	1.27E-19	83.142	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#16067 - 	CGI_10026092	superfamily	248012	179	312	7.86E-12	62.3408	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#16072 - 	CGI_10026097	superfamily	248458	67	451	2.48E-40	149.001	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16073 - 	CGI_10026098	superfamily	241874	29	589	0	577.208	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#16074 - 	CGI_10026099	superfamily	246680	24	107	4.19E-18	77.7492	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#16074 - 	CGI_10026099	superfamily	248012	172	282	9.78E-11	58.4888	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#16075 - 	CGI_10026100	superfamily	246680	24	105	2.23E-14	63.882	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#16076 - 	CGI_10026101	superfamily	248012	22	132	2.25E-10	55.022	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#16077 - 	CGI_10026102	superfamily	245847	29	99	0.000948741	38.6918	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#16079 - 	CGI_10026105	superfamily	247905	223	362	1.78E-19	84.2116	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#16079 - 	CGI_10026105	superfamily	247805	37	192	1.12E-15	73.9108	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16080 - 	CGI_10026106	superfamily	245226	319	421	3.81E-11	61.5477	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#16080 - 	CGI_10026106	superfamily	248264	585	626	9.66E-05	41.839	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#16082 - 	CGI_10026108	superfamily	242406	1	62	0.00106883	35.6449	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#16083 - 	CGI_10026109	superfamily	218200	114	343	5.25E-73	235.339	cl04660	Glyco_transf_54 superfamily	 - 	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#16088 - 	CGI_10026114	superfamily	246675	147	435	1.33E-132	390.93	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#16088 - 	CGI_10026114	superfamily	246669	461	587	6.67E-46	158.474	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#16088 - 	CGI_10026114	superfamily	247856	3	57	6.96E-05	40.9941	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16088 - 	CGI_10026114	superfamily	150071	66	147	5.68E-17	76.4582	cl08538	efhand_like superfamily	 - 	 - 	"Phosphoinositide-specific phospholipase C, efhand-like; Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme."
Q#16089 - 	CGI_10026115	superfamily	247725	41	135	1.86E-15	68.1097	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16090 - 	CGI_10026116	superfamily	247725	789	923	3.60E-60	205.576	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16090 - 	CGI_10026116	superfamily	247725	1837	1933	5.15E-49	172.096	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16090 - 	CGI_10026116	superfamily	241566	1734	1783	1.50E-16	76.7619	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#16090 - 	CGI_10026116	superfamily	221536	416	667	8.35E-104	333.222	cl13732	SBF2 superfamily	 - 	 - 	"Myotubularin protein; This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with pfam02141, pfam03456, pfam03455. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease."
Q#16090 - 	CGI_10026116	superfamily	245670	2	164	2.42E-56	195.854	cl11519	DENN superfamily	 - 	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#16090 - 	CGI_10026116	superfamily	206020	1399	1453	1.65E-27	108.364	cl18286	Y_phosphatase_m superfamily	 - 	 - 	"Myotubularin Y_phosphatase-like; This short region is highly conserved and seems to be common to many myotubularin proteins with protein tyrosine pyrophosphate activity. As the family has a number of highly conserved residues such as histidine, cysteine, glutamine and aspartate, it is possible that this represents a catalytic core of the active enzymatic part of the proteins."
Q#16090 - 	CGI_10026116	superfamily	219103	1069	1125	1.73E-14	72.7891	cl05893	Myotub-related superfamily	C	 - 	"Myotubularin-related; This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease."
Q#16090 - 	CGI_10026116	superfamily	208095	240	308	5.84E-14	69.6262	cl04084	dDENN superfamily	 - 	 - 	dDENN domain; This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
Q#16091 - 	CGI_10026117	superfamily	243066	23	122	1.65E-14	70.7241	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#16092 - 	CGI_10026118	superfamily	243066	23	117	3.33E-12	64.1757	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#16092 - 	CGI_10026118	superfamily	243066	405	475	6.82E-07	48.3825	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#16092 - 	CGI_10026118	superfamily	221377	748	881	0.000481807	40.5299	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#16093 - 	CGI_10026119	superfamily	220692	203	289	2.42E-06	47.1989	cl18570	7TM_GPCR_Srw superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#16095 - 	CGI_10026121	superfamily	245206	99	377	2.30E-95	289.178	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16096 - 	CGI_10026122	superfamily	147120	79	208	1.98E-31	113.623	cl04763	Cor1 superfamily	 - 	 - 	"Cor1/Xlr/Xmr conserved region; Cor1 is a component of the chromosome core in the meiotic prophase chromosomes. Xlr is a lymphoid cell specific protein. Xlm is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner. The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes."
Q#16097 - 	CGI_10026123	superfamily	241692	14	213	2.40E-72	220.996	cl00214	Aldolase_II superfamily	 - 	 - 	"Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and  include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations."
Q#16099 - 	CGI_10026125	superfamily	241578	16	141	0.00800869	35.8932	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16100 - 	CGI_10026126	superfamily	222340	533	757	3.42E-91	289.756	cl18665	GNAT_acetyltr_2 superfamily	 - 	 - 	GNAT acetyltransferase 2; This domain has N-acetyltransferase activity. It has a GCN5-related N-acetyltransferase (GNAT) fold.
Q#16100 - 	CGI_10026126	superfamily	218449	293	492	2.48E-61	206.273	cl18457	Helicase_RecD superfamily	 - 	 - 	"Helicase; This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases."
Q#16100 - 	CGI_10026126	superfamily	149420	107	201	2.34E-43	153.45	cl07096	DUF1726 superfamily	 - 	 - 	"Domain of unknown function (DUF1726); This domain of unknown function is often found at the N-terminus of proteins containing pfam05127. Its fold resembles that of pfam05127, but it does not appear to bind ATP."
Q#16100 - 	CGI_10026126	superfamily	222344	780	897	1.09E-27	109.292	cl16364	tRNA_bind_2 superfamily	 - 	 - 	"Possible tRNA binding domain; This domain, found at the C-terminus of tRNA(Met) cytidine acetyltransferase, may be involved in tRNA-binding."
Q#16101 - 	CGI_10026127	superfamily	247743	748	907	1.74E-06	48.6815	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16101 - 	CGI_10026127	superfamily	243092	1299	1648	4.87E-13	70.4416	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16101 - 	CGI_10026127	superfamily	243092	1834	2022	4.73E-07	52.3372	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16103 - 	CGI_10026129	superfamily	247723	10	82	5.35E-16	69.6632	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16104 - 	CGI_10026130	superfamily	217293	62	263	5.38E-48	165.113	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16104 - 	CGI_10026130	superfamily	202474	270	330	1.84E-21	91.5612	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16105 - 	CGI_10026131	superfamily	241641	143	213	6.46E-07	44.7621	cl00150	TY superfamily	 - 	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#16106 - 	CGI_10026132	superfamily	245864	46	182	0.00013193	40.7246	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#16107 - 	CGI_10026133	superfamily	245864	3	291	9.16E-52	177.856	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#16108 - 	CGI_10026134	superfamily	245864	243	452	1.40E-48	174.004	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#16108 - 	CGI_10026134	superfamily	245864	27	181	8.95E-11	62.2958	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#16110 - 	CGI_10026136	superfamily	177822	54	230	1.67E-09	56.0817	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#16111 - 	CGI_10026137	superfamily	246748	267	598	4.02E-145	428.046	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#16111 - 	CGI_10026137	superfamily	245213	79	110	5.57E-07	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16111 - 	CGI_10026137	superfamily	245213	40	72	5.43E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16111 - 	CGI_10026137	superfamily	245213	116	145	0.000667157	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16113 - 	CGI_10026139	superfamily	247792	11	56	1.79E-08	47.4404	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16114 - 	CGI_10026140	superfamily	245202	33	109	4.10E-45	145.744	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#16117 - 	CGI_10026143	superfamily	246671	88	231	1.07E-23	93.6416	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#16118 - 	CGI_10026144	superfamily	245596	178	478	1.91E-177	508.283	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16118 - 	CGI_10026144	superfamily	247085	491	608	9.58E-21	88.7166	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#16119 - 	CGI_10026145	superfamily	247723	19	99	4.45E-41	143.241	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16119 - 	CGI_10026145	superfamily	247723	117	186	9.33E-31	114.804	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16119 - 	CGI_10026145	superfamily	247723	478	545	1.17E-28	108.937	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16119 - 	CGI_10026145	superfamily	247723	312	380	6.25E-21	87.3816	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16121 - 	CGI_10002480	superfamily	241599	191	247	8.63E-21	84.2172	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#16122 - 	CGI_10006332	superfamily	243035	126	173	0.000137743	38.3698	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#16123 - 	CGI_10006333	superfamily	247941	175	316	1.89E-11	60.8124	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#16124 - 	CGI_10006334	superfamily	247684	1153	1572	4.64E-108	351.194	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16126 - 	CGI_10001975	superfamily	243152	204	332	4.15E-42	144.354	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#16127 - 	CGI_10001976	superfamily	241638	49	145	0.00206491	35.0365	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#16130 - 	CGI_10003122	superfamily	241600	61	191	3.84E-65	209.789	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16130 - 	CGI_10003122	superfamily	241600	289	423	9.63E-64	206.323	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16131 - 	CGI_10003123	superfamily	241600	7	187	1.28E-89	264.102	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16133 - 	CGI_10016789	superfamily	243064	37	108	0.00597916	33.8679	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#16134 - 	CGI_10016790	superfamily	243064	11	104	0.0061653	33.4863	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#16137 - 	CGI_10016794	superfamily	247684	11	68	2.11E-13	62.7951	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16138 - 	CGI_10016795	superfamily	241889	110	258	1.24E-45	152.399	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#16139 - 	CGI_10016796	superfamily	241600	2	176	1.79E-73	223.271	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16140 - 	CGI_10016797	superfamily	241600	581	789	2.42E-84	269.495	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16140 - 	CGI_10016797	superfamily	245205	397	464	1.24E-07	49.9289	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#16143 - 	CGI_10016800	superfamily	243092	16	294	8.93E-86	261.501	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16144 - 	CGI_10016801	superfamily	222150	189	214	3.19E-06	43.1493	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16144 - 	CGI_10016801	superfamily	243091	41	136	1.38E-05	42.4792	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#16146 - 	CGI_10016803	superfamily	245201	1488	1732	7.67E-47	169.725	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16146 - 	CGI_10016803	superfamily	241584	1380	1469	1.96E-18	83.6999	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16146 - 	CGI_10016803	superfamily	245814	505	569	1.33E-11	63.2771	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16146 - 	CGI_10016803	superfamily	245814	265	334	8.71E-11	60.5807	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16146 - 	CGI_10016803	superfamily	245814	166	235	3.05E-08	53.2619	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16146 - 	CGI_10016803	superfamily	245814	1169	1227	6.05E-08	52.4915	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16146 - 	CGI_10016803	superfamily	245814	1877	1950	1.07E-06	48.6395	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16146 - 	CGI_10016803	superfamily	245814	368	431	1.76E-06	47.8691	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16146 - 	CGI_10016803	superfamily	245814	1299	1373	2.69E-11	62.2132	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16146 - 	CGI_10016803	superfamily	245814	59	133	1.33E-06	48.6557	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16147 - 	CGI_10016804	superfamily	241584	44	136	4.08E-18	79.0775	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	245201	12218	12464	1.45E-56	200.926	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16149 - 	CGI_10016806	superfamily	241584	8357	8451	2.44E-20	91.7891	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11688	11774	1.95E-19	89.0927	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11094	11187	2.67E-19	88.7075	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7548	7639	2.75E-19	88.7075	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10891	10985	1.49E-18	86.3963	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11196	11285	1.77E-18	86.3963	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7453	7536	2.80E-18	85.6259	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10283	10372	4.81E-18	85.2407	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7852	7945	2.03E-17	83.3147	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7143	7236	2.21E-17	83.3147	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8156	8249	2.37E-17	82.9295	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7245	7336	2.48E-17	82.9295	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7954	8044	3.46E-17	82.5443	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9067	9156	3.53E-17	82.5443	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9978	10067	4.13E-17	82.5443	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10486	10574	8.11E-17	81.3887	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10789	10878	1.18E-16	81.0035	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7347	7438	1.28E-16	81.0035	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8664	8755	1.36E-16	81.0035	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8462	8552	1.73E-16	80.6183	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9675	9764	3.26E-16	79.8479	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8763	8856	3.42E-16	79.8479	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8965	9053	3.70E-16	79.4627	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11586	11679	3.89E-16	79.4627	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8868	8957	4.37E-16	79.4627	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9370	9459	5.37E-16	79.0775	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10993	11077	5.39E-16	79.0775	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11788	11879	8.20E-16	78.6923	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9270	9362	1.24E-15	77.9219	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10588	10675	1.99E-15	77.5367	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9878	9970	2.53E-15	77.1515	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11405	11492	2.86E-15	77.1515	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10188	10269	3.05E-15	76.7663	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9580	9661	4.03E-15	76.3811	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7759	7840	6.61E-15	75.9959	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11297	11384	7.22E-15	75.9959	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8055	8144	1.48E-14	74.8403	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10080	10170	1.09E-13	72.5291	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	7650	7734	1.67E-13	71.7587	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10689	10781	5.48E-13	70.2179	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	11498	11578	1.08E-12	69.4475	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	8257	8348	3.62E-12	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	12084	12173	9.10E-12	66.7511	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	245814	12959	13026	1.66E-11	65.5883	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	13637	13704	6.33E-11	63.6623	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	241584	8561	8644	7.09E-11	64.0547	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	10385	10475	2.42E-10	62.5139	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	245814	4118	4189	4.02E-10	61.3511	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	241584	9472	9562	3.62E-09	59.0471	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	245814	13063	13133	3.88E-09	58.6547	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	12826	12897	8.92E-09	57.4991	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	4430	4498	1.62E-08	56.7287	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	4339	4403	1.95E-08	56.3435	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	2543	2616	8.14E-08	54.8027	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	13397	13466	1.49E-07	54.0323	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	4016	4082	1.57E-07	53.6471	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	3809	3879	3.40E-06	49.7951	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	4626	4697	6.87E-06	49.0247	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	12736	12788	1.69E-05	47.8691	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	5669	5724	9.18E-05	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	241584	9777	9869	0.000170699	44.7947	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	241584	9169	9261	0.000170699	44.7947	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16149 - 	CGI_10016806	superfamily	245814	6976	7031	0.00226403	41.3207	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	5043	5107	0.00338166	40.5503	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	12007	12080	9.77E-15	74.9248	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	11899	11982	9.60E-14	72.1528	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	4715	4797	1.04E-13	72.1528	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	2429	2512	3.11E-13	70.612	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	3892	3975	2.44E-11	65.2192	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	3610	3692	2.08E-10	62.5228	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	4532	4602	4.43E-10	61.0576	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	4209	4292	5.40E-10	61.3672	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	13187	13270	5.40E-10	61.3672	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	2679	2762	7.25E-10	60.982	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	7066	7139	1.89E-09	59.5168	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	5390	5467	1.41E-07	54.0485	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	5569	5632	4.06E-07	52.8929	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	12555	12670	1.50E-06	50.9669	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	3706	3787	1.84E-06	50.5817	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	2910	2980	2.29E-06	50.1885	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	13529	13604	2.90E-06	50.1965	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	5484	5557	1.47E-05	47.8853	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	5223	5288	0.000448756	43.2629	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	5122	5199	0.000880507	42.4925	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16149 - 	CGI_10016806	superfamily	245814	2	55	0.00517876	40.1813	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	6576	6647	1.38E-13	71.3663	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	3432	3503	2.68E-13	70.5959	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	5793	5861	5.49E-13	69.4403	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	243054	1921	2131	7.68E-12	68.6263	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	245814	5683	5752	1.52E-11	65.2031	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	10748	10817	2.50E-11	64.8179	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	6855	6924	3.38E-11	64.4327	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	3904	3973	8.14E-11	63.2771	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	8049	8115	8.86E-11	62.8919	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	2384	2453	1.21E-10	62.5067	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	2825	2893	2.02E-10	62.1215	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	3014	3083	2.89E-10	61.7363	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	6284	6352	1.24E-09	59.8103	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	6717	6785	1.26E-09	59.8103	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	243054	588	792	2.17E-09	60.5372	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	243054	2030	2241	2.18E-09	60.5372	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	245814	2286	2354	4.72E-09	57.8843	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	6163	6232	6.77E-09	57.4991	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	2592	2658	9.05E-09	57.1139	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	243054	1363	1544	1.24E-08	58.226	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	245814	5581	5650	1.69E-08	56.3435	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	3672	3740	3.95E-08	55.1879	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	5220	5291	3.47E-07	52.4915	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	243054	818	1029	7.61E-07	52.8332	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	243054	1552	1715	8.52E-07	52.8332	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	245814	3303	3372	2.45E-06	49.7951	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	243054	1128	1287	8.75E-06	49.7516	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	245814	8755	8824	1.69E-05	47.4839	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	5893	5975	4.40E-17	81.7828	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	6027	6104	8.17E-15	75.2344	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	3794	3878	1.13E-12	68.686	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	3100	3182	1.53E-12	68.3008	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	2691	2770	5.67E-12	66.76	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	245814	2469	2551	7.95E-11	63.2932	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	247069	356	459	1.42E-10	63.9018	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#16151 - 	CGI_10016808	superfamily	245814	5363	5430	1.67E-07	53.6633	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16151 - 	CGI_10016808	superfamily	243054	468	691	2.47E-05	48.596	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#16151 - 	CGI_10016808	superfamily	245814	10539	10621	0.000428054	43.2629	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16153 - 	CGI_10016810	superfamily	241578	8	89	3.45E-09	52.2938	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16155 - 	CGI_10003058	superfamily	241631	666	850	5.30E-83	272.174	cl00136	Sec7 superfamily	 - 	 - 	Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Q#16155 - 	CGI_10003058	superfamily	204198	1182	1267	8.32E-34	127.321	cl07820	DUF1981 superfamily	 - 	 - 	Domain of unknown function (DUF1981); Members of this family of functionally uncharacterized domains are found in various plant and yeast protein transport proteins.
Q#16156 - 	CGI_10003059	superfamily	246598	41	311	5.70E-142	405.483	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#16161 - 	CGI_10012682	superfamily	247724	5	179	6.99E-92	268.913	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16162 - 	CGI_10012683	superfamily	247724	5	169	1.30E-88	260.053	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16163 - 	CGI_10012684	superfamily	247724	5	179	8.48E-134	380.621	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16163 - 	CGI_10012684	superfamily	247724	180	307	9.88E-94	278.543	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16164 - 	CGI_10012685	superfamily	243092	728	1002	1.31E-31	126.296	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16164 - 	CGI_10012685	superfamily	241563	87	125	6.33E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16165 - 	CGI_10012686	superfamily	238076	7	135	1.95E-64	203.805	cl18938	PAX superfamily	 - 	 - 	Paired Box domain
Q#16166 - 	CGI_10012687	superfamily	216290	157	266	7.75E-16	71.1654	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#16167 - 	CGI_10012688	superfamily	221377	257	300	7.31E-05	41.6855	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#16171 - 	CGI_10012692	superfamily	241675	66	297	1.80E-100	305.71	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#16172 - 	CGI_10012694	superfamily	152787	88	153	1.30E-11	56.8373	cl18053	V-SNARE_C superfamily	 - 	 - 	Snare region anchored in the vesicle membrane C-terminus; Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle pfam05008.
Q#16173 - 	CGI_10012695	superfamily	248318	481	533	1.53E-13	66.3053	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#16173 - 	CGI_10012695	superfamily	248318	596	645	5.56E-13	64.7645	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#16173 - 	CGI_10012695	superfamily	247724	61	290	1.38E-30	119.735	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16174 - 	CGI_10012696	superfamily	200724	308	395	5.05E-29	111.975	cl02186	Plus-3 superfamily	 - 	 - 	"Plus-3 domain; This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor."
Q#16175 - 	CGI_10012697	superfamily	221913	91	252	2.05E-63	200.459	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#16176 - 	CGI_10012698	superfamily	222005	244	296	3.85E-08	49.658	cl18632	AAA_19 superfamily	 - 	 - 	Part of AAA domain; Part of AAA domain.  
Q#16177 - 	CGI_10014735	superfamily	241600	61	273	4.10E-73	225.582	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16179 - 	CGI_10014737	superfamily	241594	239	305	9.73E-06	44.9888	cl00077	HECTc superfamily	N	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#16180 - 	CGI_10014738	superfamily	246675	1	274	1.81E-68	217.109	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#16181 - 	CGI_10014739	superfamily	219541	1	112	1.29E-20	83.6719	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#16182 - 	CGI_10014740	superfamily	219541	245	390	2.28E-19	85.2127	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#16182 - 	CGI_10014740	superfamily	215896	49	120	2.85E-07	49.2156	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#16182 - 	CGI_10014740	superfamily	219542	483	568	3.71E-05	42.614	cl18517	Cu-oxidase_3 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#16184 - 	CGI_10014742	superfamily	241570	271	388	3.44E-31	115.501	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#16184 - 	CGI_10014742	superfamily	241570	159	262	4.29E-21	87.3813	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#16184 - 	CGI_10014742	superfamily	213107	5	43	2.53E-15	69.5819	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#16185 - 	CGI_10014743	superfamily	110440	366	392	0.00343429	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16187 - 	CGI_10014745	superfamily	241659	153	230	1.69E-17	74.4787	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#16188 - 	CGI_10014746	superfamily	247727	500	554	0.000960461	38.1799	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#16188 - 	CGI_10014746	superfamily	218498	533	683	3.78E-09	56.5548	cl18459	TRM13 superfamily	N	 - 	Methyltransferase TRM13; This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4. TRM13 shows no sequence similarity to other known methyltransferases.
Q#16188 - 	CGI_10014746	superfamily	243175	322	374	0.000739344	38.4252	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#16189 - 	CGI_10014747	superfamily	241577	252	452	1.14E-159	452.797	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#16189 - 	CGI_10014747	superfamily	241576	10	133	3.25E-79	243.949	cl00055	MH1 superfamily	 - 	 - 	"N-terminal Mad Homology 1 (MH1) domain; The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure.  It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. Receptor-regulated SMAD proteins (R-SMADs, including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by phosphorylation by transforming growth factor (TGF)-beta type I receptors. The active R-SMAD associates with a common mediator SMAD (Co-SMAD or SMAD4) and other cofactors, which together translocate to the nucleus to regulate gene expression. The inhibitory or antagonistic SMADs (I-SMADs, including SMAD6 and SMAD7) negatively regulate TGF-beta signaling by competing with R-SMADs for type I receptor or Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a nuclear localization signal as well as DNA-binding activity. The activated R-SMAD/SMAD4 complex then binds with very low affinity to a DNA sequence CAGAC called SMAD-binding element (SBE) via the MH1 domain."
Q#16190 - 	CGI_10014748	superfamily	243066	37	145	1.31E-26	103.081	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#16190 - 	CGI_10014748	superfamily	198867	155	259	1.12E-10	58.5068	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#16191 - 	CGI_10014749	superfamily	247684	15	180	6.88E-43	158.609	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16194 - 	CGI_10014752	superfamily	241589	11	132	9.12E-33	121.587	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#16194 - 	CGI_10014752	superfamily	241589	428	538	2.95E-32	120.431	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#16194 - 	CGI_10014752	superfamily	241589	150	278	5.14E-32	119.661	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#16194 - 	CGI_10014752	superfamily	241589	287	416	1.60E-21	90.7711	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#16196 - 	CGI_10003275	superfamily	222429	51	100	0.000455397	37.6053	cl18676	Myb_DNA-bind_5 superfamily	N	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#16197 - 	CGI_10003276	superfamily	203031	96	154	6.97E-09	51.1748	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#16198 - 	CGI_10012924	superfamily	241691	224	268	2.31E-05	43.5414	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#16199 - 	CGI_10012925	superfamily	241568	378	426	0.00617086	34.8584	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#16200 - 	CGI_10012926	superfamily	192357	3	235	3.53E-92	279.499	cl10725	DUF2045 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2045); This entry is the conserved 250 residues of proteins of approximately 450 amino acids. It contains several highly conserved motifs including a CVxLxxxD motif.The function is unknown.
Q#16202 - 	CGI_10012929	superfamily	241610	3	55	8.60E-21	82.683	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#16203 - 	CGI_10012930	superfamily	247683	220	257	9.71E-16	69.2786	cl17036	SH3 superfamily	C	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#16204 - 	CGI_10012931	superfamily	247683	44	69	7.29E-10	49.6334	cl17036	SH3 superfamily	N	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#16206 - 	CGI_10012933	superfamily	245598	90	201	6.18E-26	99.6611	cl11396	Patatin_and_cPLA2 superfamily	C	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#16207 - 	CGI_10012934	superfamily	245598	1	82	7.89E-35	122.773	cl11396	Patatin_and_cPLA2 superfamily	N	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#16208 - 	CGI_10012935	superfamily	242406	16	112	1.22E-12	61.0681	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#16209 - 	CGI_10012936	superfamily	245213	257	293	0.000400593	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16209 - 	CGI_10012936	superfamily	243061	99	198	5.31E-38	131.695	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#16209 - 	CGI_10012936	superfamily	243061	51	97	4.24E-06	43.8698	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#16211 - 	CGI_10007716	superfamily	243098	100	148	4.97E-08	48.7483	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#16212 - 	CGI_10007717	superfamily	247799	42	116	4.57E-09	50.2511	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#16212 - 	CGI_10007717	superfamily	247799	128	187	2.29E-05	40.2359	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#16213 - 	CGI_10007718	superfamily	247724	2492	2654	5.26E-47	169.439	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16213 - 	CGI_10007718	superfamily	243109	1493	1628	2.04E-24	104.298	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#16213 - 	CGI_10007718	superfamily	243109	697	830	5.13E-11	63.4497	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#16217 - 	CGI_10006243	superfamily	245213	415	442	0.000149601	40.3126	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16219 - 	CGI_10002292	superfamily	241584	2	37	0.00529396	33.2387	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16221 - 	CGI_10004705	superfamily	241563	61	96	0.00035992	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16223 - 	CGI_10003450	superfamily	218758	77	246	1.00E-27	106.477	cl05400	Noggin superfamily	N	 - 	"Noggin; This family consists of the eukaryotic Noggin proteins. Noggin is a glycoprotein that binds bone morphogenetic proteins (BMPs) selectively and, when added to osteoblasts, it opposes the effects of BMPs. It has been found that noggin arrests the differentiation of stromal cells, preventing cellular maturation."
Q#16225 - 	CGI_10003452	superfamily	218758	52	246	2.72E-55	178.895	cl05400	Noggin superfamily	 - 	 - 	"Noggin; This family consists of the eukaryotic Noggin proteins. Noggin is a glycoprotein that binds bone morphogenetic proteins (BMPs) selectively and, when added to osteoblasts, it opposes the effects of BMPs. It has been found that noggin arrests the differentiation of stromal cells, preventing cellular maturation."
Q#16226 - 	CGI_10003453	superfamily	245814	29	129	1.64E-10	53.6633	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16228 - 	CGI_10017993	superfamily	245226	19	182	4.39E-45	150.513	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#16229 - 	CGI_10017994	superfamily	247907	1620	1782	4.00E-36	136.394	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#16229 - 	CGI_10017994	superfamily	247907	1401	1552	8.83E-31	120.986	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#16229 - 	CGI_10017994	superfamily	247907	1131	1278	1.73E-25	105.578	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#16229 - 	CGI_10017994	superfamily	238012	797	837	3.34E-08	52.3566	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#16229 - 	CGI_10017994	superfamily	241607	110	150	2.84E-07	49.5758	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	311	344	1.95E-06	47.2646	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	956	989	1.27E-05	44.5682	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	232	272	2.53E-05	43.7978	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	676	708	3.05E-05	43.7978	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	175	211	0.000281677	40.7162	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	453	493	0.00317818	37.6346	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	276	330	0.000155764	42.0802	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	238012	851	886	0.0020224	38.4894	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#16229 - 	CGI_10017994	superfamily	241607	578	621	0.00774717	36.5034	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16229 - 	CGI_10017994	superfamily	241607	512	552	0.00943032	36.1182	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16230 - 	CGI_10017995	superfamily	111984	1	114	2.13E-22	86.3013	cl03912	NtA superfamily	 - 	 - 	"Agrin NtA domain; Agrin is a multidomain heparan sulphate proteoglycan, that is a key organiser for the induction of postsynaptic specialisations at the neuromuscular junction. Binding of agrin to basement membranes requires the amino terminal (NtA) domain. This region mediates high affinity interaction with the coiled-coil domain of laminins. The binding of agrin to laminins via the NtA domain is subject to tissue-specific regulation. The NtA domain-containing form of agrin is expressed in non-neuronal cells or in neurons that project to non-neuronal cell such as motor neurons. The structure of this domain is an OB-fold."
Q#16231 - 	CGI_10017996	superfamily	219431	383	431	4.66E-10	56.6704	cl06504	zf-CW superfamily	 - 	 - 	"CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found."
Q#16231 - 	CGI_10017996	superfamily	243083	441	467	0.00725729	35.825	cl02554	PWWP superfamily	C	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#16232 - 	CGI_10017997	superfamily	247727	48	103	4.11E-06	43.5727	cl17173	AdoMet_MTases superfamily	N	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#16233 - 	CGI_10017998	superfamily	243035	40	169	2.60E-24	97.3053	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#16233 - 	CGI_10017998	superfamily	243035	319	447	4.82E-23	93.8385	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#16234 - 	CGI_10017999	superfamily	247755	411	648	3.36E-142	433.889	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#16234 - 	CGI_10017999	superfamily	247755	1054	1292	2.17E-132	407.696	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#16234 - 	CGI_10017999	superfamily	216049	734	1009	1.71E-48	175.552	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#16234 - 	CGI_10017999	superfamily	216049	116	364	1.70E-45	167.078	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#16238 - 	CGI_10018003	superfamily	217859	57	268	1.32E-120	347.726	cl04376	P34-Arc superfamily	 - 	 - 	"Arp2/3 complex, 34 kD subunit p34-Arc; Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. This family represents the p34-Arc subunit."
Q#16239 - 	CGI_10018004	superfamily	241601	759	843	0.00271963	38.1956	cl00086	HPT superfamily	 - 	 - 	"Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is modulated by phosphorylation and dephosphorylation of a conserved aspartic acid residue; two-component proteins are abundant in most eubacteria; In E. coli there are 62 two-component proteins involved in a variety of processes such as chemotaxis, osmoregulation, metabolism and transport 1; also present in both Gram positive and Gram negative pathogenic bacteria where they regulate basic housekeeping functions and control expression of toxins and other proteins important for pathogenesis; in archaea and eukaryotes, two-component pathways constitute a very small number of all signaling systems; in fungi they mediate environmental stress responses and, in pathogenic yeast, hyphal development. In Dictyostelium and in plants, they are involved in important processes such as osmoregulation, cell growth, and differentiation; to date two-component proteins have not been identified in animals; in most prokaryotic systems, the output response is effected directly by the RR, which functions as a transcription factor while in eukaryotic systems, two-component proteins are found at the beginning of signaling pathways where they interface with more conventional eukaryotic signaling strategies such as MAP kinase and cyclic nucleotide cascades"
Q#16241 - 	CGI_10018006	superfamily	247675	425	794	0	710.268	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#16242 - 	CGI_10018007	superfamily	241574	767	998	1.46E-102	322.613	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#16243 - 	CGI_10018008	superfamily	245213	430	458	0.000278727	39.157	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16243 - 	CGI_10018008	superfamily	241583	124	219	1.44E-18	83.7746	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#16243 - 	CGI_10018008	superfamily	241571	304	421	0.000214696	40.0883	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#16244 - 	CGI_10018009	superfamily	241563	61	96	0.000763068	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16248 - 	CGI_10009121	superfamily	245206	44	283	4.02E-99	294.15	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16249 - 	CGI_10009122	superfamily	218540	130	428	0	510.666	cl05044	Bystin superfamily	 - 	 - 	"Bystin; Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy. This family also includes the yeast protein ENP1. ENP1 is an essential protein in Saccharomyces cerevisiae and is localised in the nucleus. It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective yeast cannot synthesise 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits."
Q#16250 - 	CGI_10009123	superfamily	241583	202	411	6.79E-23	96.5305	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#16251 - 	CGI_10009124	superfamily	243744	155	254	2.15E-10	57.7586	cl04410	DFP superfamily	N	 - 	"DNA / pantothenate metabolism flavoprotein; The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism."
Q#16251 - 	CGI_10009124	superfamily	243744	36	70	0.00262464	37.2742	cl04410	DFP superfamily	C	 - 	"DNA / pantothenate metabolism flavoprotein; The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism."
Q#16252 - 	CGI_10009125	superfamily	246597	145	226	3.70E-32	120.097	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#16252 - 	CGI_10009125	superfamily	246597	9	74	2.47E-24	98.5253	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#16252 - 	CGI_10009125	superfamily	218208	305	401	3.05E-28	108.616	cl18447	CwfJ_C_1 superfamily	 - 	 - 	Protein similar to CwfJ C-terminus 1; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.
Q#16252 - 	CGI_10009125	superfamily	218207	411	500	4.28E-27	104.664	cl04666	CwfJ_C_2 superfamily	 - 	 - 	Protein similar to CwfJ C-terminus 2; This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing.
Q#16254 - 	CGI_10009127	superfamily	248136	102	208	9.37E-53	168.265	cl17582	Sybindin superfamily	 - 	 - 	"Sybindin-like family; Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses."
Q#16254 - 	CGI_10009127	superfamily	248136	3	48	0.00776808	34.2157	cl17582	Sybindin superfamily	C	 - 	"Sybindin-like family; Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses."
Q#16255 - 	CGI_10009128	superfamily	247792	62	104	0.000142562	35.8844	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16256 - 	CGI_10009129	superfamily	241622	111	190	1.76E-15	72.2142	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#16256 - 	CGI_10009129	superfamily	241622	206	286	2.38E-14	68.7474	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#16256 - 	CGI_10009129	superfamily	241622	326	413	1.76E-12	63.3546	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#16256 - 	CGI_10009129	superfamily	241622	442	526	2.37E-11	60.273	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#16256 - 	CGI_10009129	superfamily	190233	24	78	4.75E-08	50.1454	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#16258 - 	CGI_10009131	superfamily	247856	12	65	1.01E-09	50.2389	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16259 - 	CGI_10009132	superfamily	247724	527	691	8.39E-72	232.346	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16260 - 	CGI_10009133	superfamily	190261	189	208	2.79E-06	46.0026	cl03504	RFX_DNA_binding superfamily	N	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#16261 - 	CGI_10009134	superfamily	247723	29	119	2.74E-41	138.879	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16262 - 	CGI_10009135	superfamily	246669	261	380	2.17E-43	149.75	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#16263 - 	CGI_10003932	superfamily	220695	73	198	0.00502757	37.1731	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#16264 - 	CGI_10003933	superfamily	247769	569	744	1.38E-10	60.0457	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#16264 - 	CGI_10003933	superfamily	248010	111	270	4.89E-24	99.7631	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#16264 - 	CGI_10003933	superfamily	248010	295	471	1.84E-11	62.784	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#16265 - 	CGI_10003934	superfamily	248097	75	197	4.62E-24	92.7134	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16268 - 	CGI_10003656	superfamily	243035	92	208	3.37E-12	59.9409	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#16269 - 	CGI_10003657	superfamily	243038	800	882	1.49E-31	119.358	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#16269 - 	CGI_10003657	superfamily	245014	31	350	6.35E-21	93.8969	cl09117	Mem_trans superfamily	 - 	 - 	Membrane transport protein; This family includes auxin efflux carrier proteins and other transporter proteins from all domains of life.
Q#16270 - 	CGI_10003658	superfamily	247905	482	585	7.69E-29	113.872	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#16270 - 	CGI_10003658	superfamily	247805	285	424	6.13E-17	79.6888	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16270 - 	CGI_10003658	superfamily	245114	687	775	4.18E-14	69.8118	cl09632	RQC superfamily	 - 	 - 	"RQC domain; This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain."
Q#16270 - 	CGI_10003658	superfamily	207658	856	921	1.25E-12	64.8782	cl02578	HRDC superfamily	 - 	 - 	HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Q#16270 - 	CGI_10003658	superfamily	247805	264	297	0.000138668	41.4334	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16270 - 	CGI_10003658	superfamily	247811	947	995	0.00262773	37.4422	cl17257	Sigma70_r4 superfamily	 - 	 - 	"Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA.  Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis.   Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT).  Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP)."
Q#16273 - 	CGI_10004328	superfamily	243083	6	90	3.39E-36	131.254	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#16273 - 	CGI_10004328	superfamily	151906	554	662	8.15E-15	71.2381	cl12990	LEDGF superfamily	 - 	 - 	Lens epithelium-derived growth factor (LEDGF); LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure.
Q#16274 - 	CGI_10004329	superfamily	222047	13	134	2.85E-24	93.5564	cl18633	HD_4 superfamily	 - 	 - 	HD domain; HD domains are metal dependent phosphohydrolases.
Q#16275 - 	CGI_10004330	superfamily	209366	384	407	8.50E-09	52.1944	cl11604	zf-A20 superfamily	 - 	 - 	A20-like zinc finger; The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation.
Q#16275 - 	CGI_10004330	superfamily	207411	540	570	8.34E-07	46.6137	cl01438	zf-AN1 superfamily	 - 	 - 	"AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues."
Q#16276 - 	CGI_10004331	superfamily	219574	370	561	1.12E-49	174.007	cl06698	DC_STAMP superfamily	 - 	 - 	"DC-STAMP-like protein; This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family."
Q#16277 - 	CGI_10004332	superfamily	248028	126	359	3.39E-33	124.923	cl17474	Steroid_dh superfamily	 - 	 - 	"3-oxo-5-alpha-steroid 4-dehydrogenase; This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development."
Q#16277 - 	CGI_10004332	superfamily	247684	1	87	2.96E-06	47.272	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16278 - 	CGI_10001478	superfamily	247692	84	646	0	700.07	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#16279 - 	CGI_10002644	superfamily	241563	75	112	0.00325809	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16280 - 	CGI_10002645	superfamily	243095	76	110	5.37E-07	48.9707	cl02570	RhoGAP superfamily	N	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#16283 - 	CGI_10006272	superfamily	245206	20	333	5.24E-115	342.327	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16284 - 	CGI_10006273	superfamily	247799	255	300	1.62E-07	47.5547	cl17245	KH-I superfamily	C	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#16284 - 	CGI_10006273	superfamily	247799	192	252	0.000542286	37.5396	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#16286 - 	CGI_10006275	superfamily	217473	57	335	1.73E-29	117.851	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#16287 - 	CGI_10006276	superfamily	243092	56	353	4.10E-30	117.051	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16288 - 	CGI_10006277	superfamily	217473	55	333	1.02E-26	110.532	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#16289 - 	CGI_10006278	superfamily	243353	1196	1236	1.11E-10	58.98	cl03225	GRIP superfamily	 - 	 - 	"GRIP domain; The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures in."
Q#16290 - 	CGI_10003160	superfamily	247725	892	1035	1.59E-38	140.531	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16290 - 	CGI_10003160	superfamily	241622	34	148	4.66E-13	66.4362	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#16291 - 	CGI_10009075	superfamily	189857	2	121	5.80E-43	140.078	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#16292 - 	CGI_10009076	superfamily	241584	1376	1468	2.05E-15	74.4551	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	1275	1368	1.76E-13	68.6771	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	1177	1269	2.06E-13	68.6771	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	876	966	3.40E-13	67.9067	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	575	670	1.16E-11	63.2843	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	1476	1567	1.30E-11	63.2843	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	781	864	6.22E-11	61.3583	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	978	1069	6.63E-11	61.3583	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	678	776	8.02E-10	57.8915	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	1074	1166	1.03E-08	54.8099	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	241584	461	563	1.13E-06	48.6467	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	245814	312	384	0.000216993	41.3207	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16292 - 	CGI_10009076	superfamily	241584	1572	1605	0.00377412	37.4759	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16292 - 	CGI_10009076	superfamily	248097	91	195	1.12E-23	99.2618	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16292 - 	CGI_10009076	superfamily	245814	243	285	3.54E-05	43.7643	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#16294 - 	CGI_10009078	superfamily	216653	100	233	6.40E-34	124.632	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#16295 - 	CGI_10009079	superfamily	216653	1	112	2.10E-13	62.2295	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#16296 - 	CGI_10021368	superfamily	247724	9	170	8.32E-131	366.115	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16303 - 	CGI_10021375	superfamily	243072	765	890	1.04E-34	130.581	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16303 - 	CGI_10021375	superfamily	243072	831	956	1.81E-34	129.811	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16303 - 	CGI_10021375	superfamily	243072	666	791	3.03E-34	129.041	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16303 - 	CGI_10021375	superfamily	243072	1029	1153	3.12E-30	117.87	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16303 - 	CGI_10021375	superfamily	243072	897	1022	8.06E-29	113.633	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16303 - 	CGI_10021375	superfamily	243072	591	725	1.86E-23	98.2246	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16307 - 	CGI_10021379	superfamily	221550	163	268	0.00743396	36.9827	cl13761	Casc1 superfamily	C	 - 	"Cancer susceptibility candidate 1; This domain family is found in eukaryotes, and is typically between 216 and 263 amino acids in length. Casc1 has many SNPs associated with cancer susceptibility."
Q#16310 - 	CGI_10021382	superfamily	216152	90	358	5.91E-54	183.284	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#16312 - 	CGI_10021384	superfamily	246940	68	268	2.19E-19	84.6925	cl15377	Radical_SAM superfamily	 - 	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#16312 - 	CGI_10021384	superfamily	115139	238	364	4.00E-48	161.239	cl05790	Mob_synth_C superfamily	 - 	 - 	Molybdenum Cofactor Synthesis C; This region contains two iron-sulphur (3Fe-4S) binding sites. Mutations in this region of human MOCS1 cause MOCOD (Molybdenum Co-Factor Deficiency) type A.
Q#16313 - 	CGI_10021385	superfamily	110440	80	106	0.000251694	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16316 - 	CGI_10021388	superfamily	247941	144	278	5.47E-09	53.4937	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#16317 - 	CGI_10021389	superfamily	247941	318	452	3.01E-08	51.9529	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#16318 - 	CGI_10021390	superfamily	245206	3	174	1.11E-63	199.776	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16319 - 	CGI_10021391	superfamily	246921	284	336	6.03E-11	59.6965	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#16319 - 	CGI_10021391	superfamily	246921	212	274	0.00101618	38.5105	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#16321 - 	CGI_10021393	superfamily	243033	55	181	1.44E-13	63.8765	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#16322 - 	CGI_10021394	superfamily	243859	78	171	1.82E-20	81.9926	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#16322 - 	CGI_10021394	superfamily	243859	4	92	1.38E-10	54.6434	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#16323 - 	CGI_10021395	superfamily	243859	4	75	1.49E-09	49.6358	cl04722	PLAC8 superfamily	C	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#16324 - 	CGI_10021396	superfamily	243859	4	74	2.05E-09	49.2506	cl04722	PLAC8 superfamily	C	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#16325 - 	CGI_10021397	superfamily	241674	140	220	1.50E-35	122.32	cl00194	EF1B superfamily	 - 	 - 	"Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction."
Q#16325 - 	CGI_10021397	superfamily	243175	3	62	4.72E-23	89.4052	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#16326 - 	CGI_10021398	superfamily	245203	255	636	0	623.903	cl09928	Molybdopterin-Binding superfamily	 - 	 - 	"Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a  large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is the eukaryotic/eubacterial protein domain family of the 75-kDa subunit/Nad11/NuoG (second domain) of respiratory complex 1/NADH-quinone oxidoreductase which is postulated to have lost an ancestral formate dehydrogenase activity and only vestigial sequence evidence remains of a molybdopterin binding site."
Q#16326 - 	CGI_10021398	superfamily	241649	33	105	2.05E-09	55.4788	cl00159	fer2 superfamily	 - 	 - 	"2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin."
Q#16326 - 	CGI_10021398	superfamily	245548	115	155	8.89E-17	75.6072	cl11210	NADH-G_4Fe-4S_3 superfamily	 - 	 - 	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; NADH-ubiquinone oxidoreductase-G iron-sulfur binding region.  
Q#16326 - 	CGI_10021398	superfamily	204199	663	716	1.08E-11	61.1338	cl08544	DUF1982 superfamily	 - 	 - 	Domain of unknown function (DUF1982); Members of this family of functionally uncharacterized domains are found in the C-terminal region of various prokaryotic NADH dehydrogenases.
Q#16327 - 	CGI_10021399	superfamily	100116	68	114	5.22E-07	46.1844	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#16327 - 	CGI_10021399	superfamily	241762	200	273	1.19E-28	106.673	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#16328 - 	CGI_10021400	superfamily	100116	723	771	5.85E-13	65.4444	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#16328 - 	CGI_10021400	superfamily	100116	843	895	5.88E-11	59.2812	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#16328 - 	CGI_10021400	superfamily	100116	781	824	1.06E-09	55.8144	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#16328 - 	CGI_10021400	superfamily	100116	905	932	5.74E-09	53.8884	cl10082	NF-X1-zinc-finger superfamily	C	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#16329 - 	CGI_10021401	superfamily	220630	20	138	8.61E-48	152.062	cl10898	DUF2340 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2340); This is a family of small proteins of approximately 150 amino acids of unknown function.
Q#16330 - 	CGI_10021402	superfamily	243082	39	381	9.12E-93	302.254	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#16331 - 	CGI_10021403	superfamily	247085	511	628	2.60E-16	76.005	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#16331 - 	CGI_10021403	superfamily	245596	294	491	1.00E-110	337.639	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16331 - 	CGI_10021403	superfamily	245596	124	293	9.64E-82	262.14	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16333 - 	CGI_10021405	superfamily	248097	24	146	3.03E-13	66.1717	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16335 - 	CGI_10021407	superfamily	218118	100	165	4.54E-07	44.1421	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#16338 - 	CGI_10021410	superfamily	241754	7	315	0	579.238	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#16341 - 	CGI_10003021	superfamily	247799	178	252	5.88E-08	49.4807	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#16341 - 	CGI_10003021	superfamily	247799	108	174	0.00345806	35.2302	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#16342 - 	CGI_10006932	superfamily	247861	1329	1472	6.92E-28	111.835	cl17307	SpoU_methylase superfamily	 - 	 - 	SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
Q#16344 - 	CGI_10006934	superfamily	199166	110	219	0.000211842	40.0032	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#16345 - 	CGI_10006935	superfamily	214642	331	362	0.00479354	35.6026	cl02592	HAT superfamily	 - 	 - 	HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Q#16347 - 	CGI_10006937	superfamily	243045	154	250	3.17E-15	72.6659	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#16347 - 	CGI_10006937	superfamily	243045	5	57	7.63E-08	51.0947	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#16349 - 	CGI_10006939	superfamily	247743	141	308	1.00E-24	98.3723	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16350 - 	CGI_10006940	superfamily	244880	97	268	1.70E-117	344.203	cl08263	TBP_TLF superfamily	 - 	 - 	"TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many equivalent positions, suggesting similar structure. However, TLFs contain distinct, conserved amino acids at several positions that distinguish them from TBP."
Q#16350 - 	CGI_10006940	superfamily	241574	259	385	3.06E-32	119.636	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#16351 - 	CGI_10006941	superfamily	241772	37	112	0.00780207	35.0661	cl00311	UbiD superfamily	NC	 - 	3-octaprenyl-4-hydroxybenzoate carboxy-lyase; This family has been characterized as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes. This enzyme catalyzes the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+.
Q#16352 - 	CGI_10006942	superfamily	247804	379	421	2.62E-05	42.1774	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#16352 - 	CGI_10006942	superfamily	212559	156	200	4.29E-13	64.9431	cl18297	SANT_MTA3_like superfamily	 - 	 - 	"Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle.  MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis."
Q#16352 - 	CGI_10006942	superfamily	216509	71	122	1.00E-12	63.797	cl03218	ELM2 superfamily	 - 	 - 	"ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a member from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain."
Q#16352 - 	CGI_10006942	superfamily	241648	249	291	6.75E-05	41.2042	cl00158	ZnF_GATA superfamily	 - 	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#16353 - 	CGI_10006943	superfamily	241578	357	512	1.09E-13	70.2874	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16353 - 	CGI_10006943	superfamily	246918	692	748	1.56E-16	75.7011	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16353 - 	CGI_10006943	superfamily	246918	524	575	1.41E-13	67.2267	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16353 - 	CGI_10006943	superfamily	246918	634	687	4.21E-09	54.5151	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16354 - 	CGI_10006944	superfamily	247739	14	207	1.03E-66	209.787	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#16355 - 	CGI_10006945	superfamily	215577	8	243	2.10E-49	168.308	cl14728	PLN03103 superfamily	C	 - 	GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional
Q#16359 - 	CGI_10016293	superfamily	246925	3	111	0.0095108	34.2534	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#16362 - 	CGI_10016296	superfamily	241600	22	231	1.02E-97	286.444	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16363 - 	CGI_10016297	superfamily	245206	15	245	1.34E-76	235.967	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16364 - 	CGI_10016298	superfamily	241563	89	126	1.06E-06	46.1263	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16365 - 	CGI_10016299	superfamily	243092	4	217	9.17E-17	81.2272	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16365 - 	CGI_10016299	superfamily	243092	850	907	2.92E-05	45.7888	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16366 - 	CGI_10016301	superfamily	241596	60	118	3.34E-11	58.7647	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#16368 - 	CGI_10016303	superfamily	245864	1	201	1.85E-75	236.406	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#16369 - 	CGI_10016304	superfamily	244657	40	98	1.08E-22	85.8652	cl07247	CDC37_C superfamily	C	 - 	Cdc37 C terminal domain; Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the C terminal domain whose function is unclear. It is found C terminal to the Hsp90 chaperone (Heat shocked protein 90) binding domain pfam08565 and the N terminal kinase binding domain of Cdc37 pfam03234.
Q#16369 - 	CGI_10016304	superfamily	244658	1	27	0.00167605	35.1158	cl07248	CDC37_M superfamily	N	 - 	"Cdc37 Hsp90 binding domain; Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the Hsp90 chaperone (Heat shocked protein 90) binding domain of Cdc37. It is found between the N terminal Cdc37 domain pfam03234, which is predominantly involved in kinase binding, and the C terminal domain of Cdc37 pfam08564 whose function is unclear."
Q#16370 - 	CGI_10016305	superfamily	247724	7	168	4.76E-60	188.255	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16372 - 	CGI_10016307	superfamily	242385	125	430	0	608.291	cl01244	arom_aa_hydroxylase superfamily	 - 	 - 	"Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers."
Q#16372 - 	CGI_10016307	superfamily	245020	39	112	4.29E-26	100.711	cl09141	ACT superfamily	 - 	 - 	"ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but  the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times."
Q#16374 - 	CGI_10016309	superfamily	248097	1	127	1.06E-25	95.0246	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16375 - 	CGI_10016310	superfamily	246597	25	311	5.22E-131	385.743	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#16375 - 	CGI_10016310	superfamily	217260	347	509	1.83E-45	157.416	cl03752	5_nucleotid_C superfamily	 - 	 - 	"5'-nucleotidase, C-terminal domain; 5'-nucleotidase, C-terminal domain.  "
Q#16377 - 	CGI_10016312	superfamily	243092	100	412	6.91E-39	148.252	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16377 - 	CGI_10016312	superfamily	241607	1218	1243	4.64E-06	45.7238	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	578	612	4.85E-05	42.6422	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	1047	1081	6.65E-05	42.257	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	921	955	0.000120189	41.4866	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	878	912	0.000637876	39.1754	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	708	742	0.00110708	38.405	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	1132	1157	0.00169407	38.0198	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	663	687	0.00247034	37.6346	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	544	572	0.00278991	37.2494	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	750	774	0.00532181	36.479	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	243092	10	173	2.62E-20	92.398	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16377 - 	CGI_10016312	superfamily	241607	839	874	1.69E-07	49.975	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	1008	1043	2.88E-07	49.2046	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	1083	1106	9.77E-05	41.5765	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	1173	1193	0.000278398	40.3451	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	791	816	0.000468884	39.5747	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	963	984	0.000560517	39.5747	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16377 - 	CGI_10016312	superfamily	241607	616	640	0.000997441	38.8043	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16382 - 	CGI_10016317	superfamily	241737	129	258	8.18E-72	219.722	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#16382 - 	CGI_10016317	superfamily	241737	11	130	7.03E-66	204.7	cl00264	Ferritin_like superfamily	C	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#16383 - 	CGI_10012322	superfamily	247792	251	290	0.00015154	39.7364	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16383 - 	CGI_10012322	superfamily	148004	186	223	0.000139844	40.3857	cl05589	Ifi-6-16 superfamily	N	 - 	Interferon-induced 6-16 family; Interferon-induced 6-16 family.  
Q#16384 - 	CGI_10012323	superfamily	247792	438	477	0.000159314	39.3512	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16385 - 	CGI_10012324	superfamily	247792	297	336	4.31E-05	40.5068	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16385 - 	CGI_10012324	superfamily	148004	120	183	4.05E-12	61.1865	cl05589	Ifi-6-16 superfamily	N	 - 	Interferon-induced 6-16 family; Interferon-induced 6-16 family.  
Q#16386 - 	CGI_10012325	superfamily	241822	143	187	2.94E-08	47.8544	cl00373	Ribosomal_S18 superfamily	 - 	 - 	Ribosomal protein S18; Ribosomal protein S18.  
Q#16390 - 	CGI_10012329	superfamily	245235	864	1265	0	687.39	cl10023	POLBc superfamily	 - 	 - 	"DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y).  Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis."
Q#16390 - 	CGI_10012329	superfamily	245226	558	794	1.45E-97	313.78	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#16390 - 	CGI_10012329	superfamily	220087	1286	1477	1.97E-51	181.307	cl18544	zf-DNA_Pol superfamily	 - 	 - 	"DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain."
Q#16390 - 	CGI_10012329	superfamily	221491	42	105	1.85E-14	70.7749	cl13661	DNA_pol_alpha_N superfamily	 - 	 - 	"DNA polymerase alpha subunit p180 N terminal; This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00136, pfam08996, pfam03104. This family is the N terminal of DNA polymerase alpha subunit p180 protein. The N terminal contains the catalytic region of the alpha subunit."
Q#16391 - 	CGI_10012330	superfamily	245230	2	426	0	950.949	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#16392 - 	CGI_10012331	superfamily	242109	3	140	2.36E-34	122.484	cl00809	RbsD_FucU superfamily	 - 	 - 	"RbsD / FucU transport protein family; The Escherichia coli high-affinity ribose-transport system consists of six proteins encoded by the rbs operon (rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). Of the six components, RbsD is the only one whose function is unknown although it is thought that it somehow plays a critical role in PtsG-mediated ribose transport. This family also includes FucU a protein from the fucose biosynthesis operon that is presumably also involved in fucose transport by similarity to RbsD."
Q#16392 - 	CGI_10012331	superfamily	242232	203	252	1.23E-12	60.6496	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#16393 - 	CGI_10012332	superfamily	220783	2	92	6.32E-15	68.2271	cl11136	Syntaxin-18_N superfamily	 - 	 - 	"SNARE-complex protein Syntaxin-18 N-terminus; This is the conserved N-terminal of Syntaxin-18. Syntaxin-18 is found in the SNARE complex of the endoplasmic reticulum and functions in the trafficking between the ER intermediate compartment and the cis-Golgi vesicle. In particular, the N-terminal region is important for the formation of ER aggregates. More specifically, syntaxin-18 is involved in endoplasmic reticulum-mediated phagocytosis, presumably by regulating the specific and direct fusion of the ER with the plasma or phagosomal membranes."
Q#16394 - 	CGI_10012333	superfamily	247684	13	187	4.79E-17	77.6291	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16396 - 	CGI_10012335	superfamily	241638	35	112	2.27E-05	42.7405	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#16398 - 	CGI_10012337	superfamily	241638	150	259	0.00330163	35.8069	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#16399 - 	CGI_10012338	superfamily	198867	747	844	4.09E-30	116.874	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#16399 - 	CGI_10012338	superfamily	243066	646	742	1.73E-25	103.54	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#16399 - 	CGI_10012338	superfamily	243146	992	1035	3.47E-10	57.6714	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16399 - 	CGI_10012338	superfamily	243146	1086	1141	2.62E-08	52.2786	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16399 - 	CGI_10012338	superfamily	243146	1038	1083	9.92E-08	50.7378	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16399 - 	CGI_10012338	superfamily	243146	946	1002	0.00127251	38.6935	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16400 - 	CGI_10012339	superfamily	207712	75	180	3.21E-38	137.828	cl02728	DUF1126 superfamily	 - 	 - 	Repeat of unknown function (DUF1126); This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.
Q#16400 - 	CGI_10012339	superfamily	207712	407	514	1.48E-32	122.035	cl02728	DUF1126 superfamily	 - 	 - 	Repeat of unknown function (DUF1126); This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.
Q#16400 - 	CGI_10012339	superfamily	207712	226	345	1.41E-30	116.643	cl02728	DUF1126 superfamily	 - 	 - 	Repeat of unknown function (DUF1126); This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.
Q#16401 - 	CGI_10012340	superfamily	246679	178	395	3.90E-65	208.562	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#16401 - 	CGI_10012340	superfamily	246679	6	161	3.57E-13	66.0142	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#16402 - 	CGI_10012341	superfamily	246918	27	50	4.24E-05	39.1071	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16402 - 	CGI_10012341	superfamily	246918	90	133	0.00189857	34.4847	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16403 - 	CGI_10012342	superfamily	248458	862	1150	1.56E-16	81.9765	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16403 - 	CGI_10012342	superfamily	248458	1219	1471	6.52E-13	71.1909	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16403 - 	CGI_10012342	superfamily	248458	512	800	2.40E-11	66.1833	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16403 - 	CGI_10012342	superfamily	248458	37	206	2.06E-06	50.7753	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16404 - 	CGI_10012343	superfamily	241599	108	166	1.34E-23	91.1508	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#16404 - 	CGI_10012343	superfamily	146451	253	271	8.31E-05	38.8795	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#16406 - 	CGI_10023267	superfamily	216101	1	463	8.58E-180	521.468	cl08288	Carn_acyltransf superfamily	N	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#16407 - 	CGI_10023268	superfamily	241563	56	92	0.00240893	35.918	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16408 - 	CGI_10023269	superfamily	201678	134	163	5.44E-08	48.2652	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#16408 - 	CGI_10023269	superfamily	201678	104	129	9.81E-05	39.0204	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#16408 - 	CGI_10023269	superfamily	201678	65	88	0.000228952	38.25	cl03138	PPTA superfamily	C	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#16408 - 	CGI_10023269	superfamily	201678	207	236	0.000820444	36.324	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#16408 - 	CGI_10023269	superfamily	201678	168	196	0.00421634	34.398	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#16409 - 	CGI_10023270	superfamily	246918	15	67	2.76E-12	56.4411	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16410 - 	CGI_10023271	superfamily	246918	32	53	0.000431081	33.7143	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16411 - 	CGI_10023272	superfamily	248288	19	99	0.00014941	35.8422	cl17734	DAN superfamily	 - 	 - 	"DAN domain; This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family after the first member to be reported. This family includes DAN, Cerberus and Gremlin. The gremlin protein is an antagonist of bone morphogenetic protein signaling. It is postulated that all members of this family antagonise different TGF beta pfam00019 ligands. Recent work shows that the DAN protein is not an efficient antagonist of BMP-2/4 class signals, we found that DAN was able to interact with GDF-5 in a frog embryo assay, suggesting that DAN may regulate signaling by the GDF-5/6/7 class of BMPs in vivo."
Q#16412 - 	CGI_10023273	superfamily	246598	24	306	1.29E-165	465.189	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#16415 - 	CGI_10023276	superfamily	247743	42	145	5.17E-06	43.2887	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16416 - 	CGI_10023277	superfamily	247941	100	248	4.50E-13	64.2792	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#16417 - 	CGI_10023278	superfamily	247941	209	351	1.26E-16	75.8352	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#16418 - 	CGI_10023280	superfamily	216301	42	223	8.02E-32	115.824	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#16419 - 	CGI_10023281	superfamily	241565	8	84	0.000140868	43.0791	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#16419 - 	CGI_10023281	superfamily	242919	2844	3087	2.82E-91	301.122	cl02173	Tfb4 superfamily	 - 	 - 	Transcription factor Tfb4; This family appears to be distantly related to the VWA domain.
Q#16419 - 	CGI_10023281	superfamily	241752	269	567	2.29E-30	126.231	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#16419 - 	CGI_10023281	superfamily	241578	868	1031	7.15E-24	102.678	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16419 - 	CGI_10023281	superfamily	207701	625	733	2.86E-23	99.3547	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#16419 - 	CGI_10023281	superfamily	241645	1280	1348	5.22E-08	53.3354	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16423 - 	CGI_10023285	superfamily	243077	3	62	5.42E-14	65.2593	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#16423 - 	CGI_10023285	superfamily	242914	100	132	0.000472862	37.208	cl02163	zf-CSL superfamily	C	 - 	CSL zinc finger; This is a zinc binding motif which contains four cysteine residues which chelate zinc. This domain is often found associated with a pfam00226 domain. This domain is named after the conserved motif of the final cysteine.
Q#16424 - 	CGI_10023286	superfamily	218655	45	161	1.72E-66	202.082	cl05269	DUF778 superfamily	 - 	 - 	Protein of unknown function (DUF778); This family consists of several eukaryotic proteins of unknown function.
Q#16426 - 	CGI_10023288	superfamily	242849	7	60	2.08E-09	51.4357	cl02041	Cyt-b5 superfamily	C	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#16428 - 	CGI_10023290	superfamily	246671	29	131	3.54E-20	85.1672	cl14606	Reeler_cohesin_like superfamily	N	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#16429 - 	CGI_10023291	superfamily	246671	35	174	1.01E-18	79.7744	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#16430 - 	CGI_10023292	superfamily	245201	701	968	0	534.611	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16430 - 	CGI_10023292	superfamily	247057	1003	1063	2.59E-24	98.4563	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#16430 - 	CGI_10023292	superfamily	241584	408	492	1.64E-14	70.9883	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16430 - 	CGI_10023292	superfamily	241584	512	601	5.99E-06	45.5651	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16430 - 	CGI_10023292	superfamily	243148	130	280	8.95E-48	169.506	cl02704	EphR_LBD superfamily	 - 	 - 	"Ligand Binding Domain of Ephrin Receptors; Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). They are subdivided into 2 groups, A and B type receptors, depending on their ligand ephrin-A or ephrin-B, respectively. In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. One exception is EphB2, which also interacts with ephrin A5. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis."
Q#16430 - 	CGI_10023292	superfamily	219467	354	393	0.0069368	36.1572	cl08456	NCD3G superfamily	 - 	 - 	"Nine Cysteines Domain of family 3 GPCR; This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins."
Q#16432 - 	CGI_10023294	superfamily	192535	34	183	5.09E-06	45.2794	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#16433 - 	CGI_10023295	superfamily	247870	70	244	0.00541927	37.6498	cl17316	Trp_Tyr_perm superfamily	C	 - 	Tryptophan/tyrosine permease family; Tryptophan/tyrosine permease family.  
Q#16435 - 	CGI_10023297	superfamily	247856	97	151	1.12E-10	54.0909	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16435 - 	CGI_10023297	superfamily	247856	29	88	4.16E-10	52.5501	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16435 - 	CGI_10023297	superfamily	247856	134	185	0.00319683	33.6753	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16438 - 	CGI_10023300	superfamily	241743	744	842	0.00197456	37.7413	cl00274	ML superfamily	N	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#16439 - 	CGI_10023301	superfamily	241743	102	204	0.00562356	35.4301	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#16442 - 	CGI_10023304	superfamily	245595	398	681	1.70E-153	454.358	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#16442 - 	CGI_10023304	superfamily	245595	5	271	6.68E-146	434.713	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#16442 - 	CGI_10023304	superfamily	248053	277	326	4.29E-12	63.312	cl17499	Peptidase_M14NE-CP-C_like superfamily	C	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#16442 - 	CGI_10023304	superfamily	248053	687	736	2.82E-11	60.6156	cl17499	Peptidase_M14NE-CP-C_like superfamily	C	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#16443 - 	CGI_10023305	superfamily	245201	45	416	0	740.405	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16444 - 	CGI_10023306	superfamily	219316	305	489	1.34E-53	187.043	cl06268	B9-C2 superfamily	 - 	 - 	"Ciliary basal body-associated, B9 protein; The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains. There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease. All the three distinct types of B9-C2 proteins cooperatively localise to the basal body or centrosome of cilia."
Q#16445 - 	CGI_10023307	superfamily	241565	537	607	1.60E-07	49.2423	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#16445 - 	CGI_10023307	superfamily	241565	303	370	2.99E-05	42.3087	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#16445 - 	CGI_10023307	superfamily	202000	1	148	1.51E-50	173.044	cl03375	XRCC1_N superfamily	 - 	 - 	XRCC1 N terminal domain; XRCC1 N terminal domain.  
Q#16446 - 	CGI_10023308	superfamily	241600	19	217	8.05E-84	250.62	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#16447 - 	CGI_10023309	superfamily	243092	212	506	1.62E-52	180.994	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16447 - 	CGI_10023309	superfamily	203998	66	135	3.53E-36	128.901	cl07284	Prp19 superfamily	 - 	 - 	Prp19/Pso4-like; This regions is found specifically in PRP19-like protein. The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly.
Q#16447 - 	CGI_10023309	superfamily	248098	2	68	1.17E-19	83.0533	cl17544	U-box superfamily	 - 	 - 	U-box domain; This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
Q#16448 - 	CGI_10003719	superfamily	247941	186	325	1.11E-12	64.2792	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#16449 - 	CGI_10003720	superfamily	243146	257	298	1.91E-07	47.6562	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16449 - 	CGI_10003720	superfamily	243146	151	191	0.00132674	36.4855	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16449 - 	CGI_10003720	superfamily	243146	34	94	0.00227777	35.7151	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16450 - 	CGI_10003721	superfamily	247743	337	482	0.0018217	38.6663	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16450 - 	CGI_10003721	superfamily	144608	699	757	5.96E-05	44.0429	cl18013	Mg_chelatase superfamily	NC	 - 	"Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa."
Q#16451 - 	CGI_10003722	superfamily	245244	197	262	1.90E-21	86.1726	cl10045	tRNA_int_endo superfamily	C	 - 	"tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9."
Q#16461 - 	CGI_10008371	superfamily	217658	23	70	2.97E-17	71.3901	cl04196	UPF0041 superfamily	C	 - 	Uncharacterized protein family (UPF0041); Uncharacterized protein family (UPF0041).  
Q#16462 - 	CGI_10008372	superfamily	247724	17	180	3.77E-64	209.942	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16463 - 	CGI_10008373	superfamily	207690	553	575	2.26E-06	45.0013	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#16464 - 	CGI_10008374	superfamily	217658	64	154	9.92E-26	96.0428	cl04196	UPF0041 superfamily	 - 	 - 	Uncharacterized protein family (UPF0041); Uncharacterized protein family (UPF0041).  
Q#16465 - 	CGI_10008375	superfamily	243072	563	659	1.14E-10	60.0898	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16465 - 	CGI_10008375	superfamily	243072	630	809	7.03E-05	41.9855	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16468 - 	CGI_10008378	superfamily	241832	76	262	6.91E-47	155.751	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16469 - 	CGI_10008379	superfamily	248097	136	239	2.94E-09	52.6526	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16470 - 	CGI_10008380	superfamily	248097	156	263	4.46E-09	52.6526	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16471 - 	CGI_10008381	superfamily	247727	781	878	5.82E-09	54.7434	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#16471 - 	CGI_10008381	superfamily	247727	114	209	7.19E-09	54.3583	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#16471 - 	CGI_10008381	superfamily	247727	558	654	7.28E-08	51.6619	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#16471 - 	CGI_10008381	superfamily	247727	334	429	2.82E-07	49.7359	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#16474 - 	CGI_10008384	superfamily	199166	69	272	7.92E-19	84.6864	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#16474 - 	CGI_10008384	superfamily	199166	348	434	6.94E-12	63.8856	cl15308	AMN1 superfamily	NC	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#16475 - 	CGI_10008385	superfamily	247724	11	172	9.04E-111	316.859	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16476 - 	CGI_10008386	superfamily	243056	298	533	2.06E-52	180.58	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#16476 - 	CGI_10008386	superfamily	192931	7	197	9.56E-48	167.259	cl13498	DUF3548 superfamily	 - 	 - 	Domain of unknown function (DUF3548); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 184 to 216 amino acids in length. This domain is found associated with pfam00566. This domain is found at the N-terminus of GYP7 proteins.
Q#16477 - 	CGI_10008387	superfamily	247723	44	118	8.45E-29	104.6	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16478 - 	CGI_10011371	superfamily	247058	15	178	9.15E-49	160.804	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#16479 - 	CGI_10011372	superfamily	220672	448	564	5.66E-13	68.0422	cl10957	Frag1 superfamily	N	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#16479 - 	CGI_10011372	superfamily	220672	596	708	1.09E-12	66.8866	cl10957	Frag1 superfamily	N	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#16479 - 	CGI_10011372	superfamily	220672	248	341	3.75E-09	56.101	cl10957	Frag1 superfamily	C	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#16480 - 	CGI_10011373	superfamily	186602	50	328	4.46E-125	365.876	cl03849	PSS superfamily	 - 	 - 	Phosphatidyl serine synthase; Phosphatidyl serine synthase is also known as serine exchange enzyme. This family represents eukaryotic PSS I and II which are membrane bound proteins which catalyzes the replacement of the head group of a phospholipid (phosphotidylcholine or phosphotidylethanolamine) by L-serine.
Q#16481 - 	CGI_10011374	superfamily	241644	32	163	1.21E-37	128.474	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#16482 - 	CGI_10011375	superfamily	241659	82	159	1.47E-30	107.991	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#16483 - 	CGI_10011376	superfamily	241659	68	143	1.60E-26	97.2054	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#16484 - 	CGI_10011377	superfamily	245206	53	296	1.45E-111	326.892	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16485 - 	CGI_10011378	superfamily	241546	252	366	1.48E-39	139.612	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16485 - 	CGI_10011378	superfamily	241546	380	461	4.69E-38	135.375	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16485 - 	CGI_10011378	superfamily	241546	118	244	8.02E-29	109.567	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	716	841	1.46E-51	178.903	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	868	987	3.44E-51	178.132	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	1152	1273	3.15E-47	166.576	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	999	1125	3.16E-46	163.88	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	434	541	1.18E-45	162.339	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	305	423	4.99E-42	151.939	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	179	294	6.39E-37	137.301	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	48	165	7.24E-36	134.22	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	1311	1428	1.41E-31	121.893	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	563	602	2.85E-13	68.7356	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	3	38	1.76E-07	51.0164	cl00011	PLAT superfamily	N	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16487 - 	CGI_10011380	superfamily	241546	668	702	0.000332085	41.0012	cl00011	PLAT superfamily	N	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#16488 - 	CGI_10011381	superfamily	243065	309	462	1.41E-10	60.5333	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#16492 - 	CGI_10011385	superfamily	248097	59	97	5.04E-09	49.571	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16493 - 	CGI_10011386	superfamily	248097	9	103	5.57E-13	60.7418	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16494 - 	CGI_10011387	superfamily	248097	9	125	6.07E-18	74.609	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16495 - 	CGI_10017902	superfamily	243058	670	768	3.85E-05	44.2276	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#16495 - 	CGI_10017902	superfamily	245201	10	283	9.49E-49	176.556	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16495 - 	CGI_10017902	superfamily	243093	1581	1659	3.00E-20	88.3561	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#16495 - 	CGI_10017902	superfamily	243093	1393	1471	3.46E-19	85.2745	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#16495 - 	CGI_10017902	superfamily	243093	1487	1565	2.02E-18	82.9633	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#16495 - 	CGI_10017902	superfamily	243093	1684	1796	2.01E-11	62.5478	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#16495 - 	CGI_10017902	superfamily	243093	1813	1855	1.98E-05	44.8286	cl02568	WSC superfamily	C	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#16496 - 	CGI_10017903	superfamily	246683	66	373	2.23E-162	461.205	cl14648	Aldose_epim superfamily	 - 	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#16497 - 	CGI_10017904	superfamily	222150	247	272	0.00543566	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16497 - 	CGI_10017904	superfamily	246975	233	256	0.00935045	33.7655	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#16498 - 	CGI_10017905	superfamily	246680	115	177	6.34E-05	41.5522	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#16501 - 	CGI_10017908	superfamily	203495	42	92	1.34E-06	42.9954	cl10663	Cep57_MT_bd superfamily	N	 - 	"Centrosome microtubule-binding domain of Cep57; This C-terminal region of Cep57 binds, nucleates and bundles microtubules. The N-terminal part, family Cep57_CLD, pfam14073, is the centrosome localisation domain Cep57."
Q#16509 - 	CGI_10017916	superfamily	247805	71	209	4.76E-19	84.6964	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16509 - 	CGI_10017916	superfamily	243778	496	587	3.30E-34	125.799	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#16509 - 	CGI_10017916	superfamily	247905	347	400	1.41E-08	52.5237	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#16511 - 	CGI_10017918	superfamily	220692	46	340	6.42E-06	46.4285	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#16513 - 	CGI_10017920	superfamily	219532	1	78	1.74E-30	106.63	cl06657	OB_NTP_bind superfamily	N	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#16514 - 	CGI_10017921	superfamily	193256	2969	3231	4.91E-69	237.538	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#16514 - 	CGI_10017921	superfamily	193257	3609	3839	1.99E-54	193.663	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#16514 - 	CGI_10017921	superfamily	193251	2565	2829	1.02E-44	167.035	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#16514 - 	CGI_10017921	superfamily	193253	3342	3589	2.72E-25	110.897	cl15084	MT superfamily	N	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#16514 - 	CGI_10017921	superfamily	247743	2258	2393	1.36E-06	49.9864	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16516 - 	CGI_10017923	superfamily	242169	10	100	1.73E-23	87.2894	cl00886	Robl_LC7 superfamily	 - 	 - 	"Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role."
Q#16517 - 	CGI_10017924	superfamily	243158	87	122	5.66E-06	40.62	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#16518 - 	CGI_10017925	superfamily	241733	5	83	3.71E-50	158.098	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#16519 - 	CGI_10017926	superfamily	243066	38	131	2.94E-17	74.1265	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#16520 - 	CGI_10017927	superfamily	217311	4	378	1.55E-107	330.453	cl18402	DUF229 superfamily	N	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#16522 - 	CGI_10005801	superfamily	110998	27	248	1.33E-91	281.449	cl03422	Glyco_hydro_30 superfamily	C	 - 	O-Glycosyl hydrolase family 30; O-Glycosyl hydrolase family 30.  
Q#16523 - 	CGI_10005802	superfamily	241592	37	97	2.46E-15	65.7109	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#16524 - 	CGI_10005803	superfamily	128778	110	218	0.00111167	38.0147	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#16526 - 	CGI_10005805	superfamily	241832	22	118	9.57E-44	145.215	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16527 - 	CGI_10005806	superfamily	243074	28	62	0.00385049	34.7897	cl02535	F-box-like superfamily	C	 - 	F-box-like; This is an F-box-like family.
Q#16529 - 	CGI_10005808	superfamily	241979	7	127	3.59E-68	204.11	cl00610	Ribosomal_S17e superfamily	 - 	 - 	Ribosomal S17; Ribosomal S17.  
Q#16530 - 	CGI_10005809	superfamily	243072	82	194	3.23E-31	112.092	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16530 - 	CGI_10005809	superfamily	247683	25	72	1.07E-25	95.4445	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#16532 - 	CGI_10005811	superfamily	148167	71	142	3.38E-35	119.157	cl05742	GFRP superfamily	 - 	 - 	"GTP cyclohydrolase I feedback regulatory protein (GFRP); Tetrahydrobiopterin, the cofactor required for hydroxylation of aromatic amino acids regulates its own synthesis in via feedback inhibition of GTP cyclohydrolase I. This mechanism is mediated by the regulatory subunit called GTP cyclohydrolase I feedback regulatory protein (GFRP)."
Q#16534 - 	CGI_10005813	superfamily	247724	60	300	9.66E-156	447.491	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16534 - 	CGI_10005813	superfamily	247856	449	514	2.39E-21	88.0454	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16535 - 	CGI_10005814	superfamily	217436	1	109	9.68E-56	171.23	cl03943	Yippee superfamily	 - 	 - 	Yippee putative zinc-binding protein; Yippee putative zinc-binding protein.  
Q#16536 - 	CGI_10005955	superfamily	245847	8	75	0.000838677	34.8398	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#16539 - 	CGI_10005958	superfamily	241599	131	185	2.07E-17	73.4316	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#16540 - 	CGI_10005959	superfamily	241659	103	180	2.00E-25	95.2794	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#16541 - 	CGI_10005960	superfamily	241659	13	90	7.13E-27	96.0498	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#16542 - 	CGI_10005961	superfamily	242898	11	122	8.11E-18	75.2086	cl02130	Got1 superfamily	 - 	 - 	"Got1/Sft2-like family; Traffic through the yeast Golgi complex depends on a member of the syntaxin family of SNARE proteins, Sed5, present in early Golgi cisternae. Got1 is thought to facilitate Sed5-dependent fusion events. This is a family of sequences derived from eukaryotic proteins. They are similar to a region of a SNARE-like protein required for traffic through the Golgi complex, SFT2 protein. This is a conserved protein with four putative transmembrane helices, thought to be involved in vesicular transport in later Golgi compartments."
Q#16546 - 	CGI_10024878	superfamily	248097	87	193	6.40E-16	74.2238	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16546 - 	CGI_10024878	superfamily	245852	296	475	1.67E-08	55.0506	cl12050	TraB superfamily	NC	 - 	"TraB family; pAD1 is a hemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans, suggesting that members of the TraB family have some more general function. This family also includes the bacterial GumN protein. The family has a conserved GXXH motif close to the N-terminus, a conserved glutamate and a conserved arginine that may be catalytic. The family also includes a second conserved GXXH motif near the C-terminus."
Q#16547 - 	CGI_10024879	superfamily	248097	11	124	1.43E-13	64.979	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16548 - 	CGI_10024880	superfamily	241646	478	525	6.35E-08	49.7559	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#16548 - 	CGI_10024880	superfamily	241646	25	66	1.46E-05	42.823	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#16550 - 	CGI_10024882	superfamily	243035	727	827	1.02E-15	74.9637	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#16550 - 	CGI_10024882	superfamily	241874	22	520	0	768.392	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#16550 - 	CGI_10024882	superfamily	243035	886	986	5.57E-15	73.1077	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#16551 - 	CGI_10024883	superfamily	241874	24	567	0	811.92	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#16552 - 	CGI_10024884	superfamily	243050	13	40	8.37E-06	37.9433	cl02475	LIM superfamily	NC	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#16553 - 	CGI_10024885	superfamily	245201	328	528	1.86E-50	176.658	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16553 - 	CGI_10024885	superfamily	243050	55	108	1.73E-28	109.377	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#16553 - 	CGI_10024885	superfamily	241622	185	223	1.24E-06	47.1763	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#16553 - 	CGI_10024885	superfamily	243050	22	48	4.20E-09	54.0323	cl02475	LIM superfamily	N	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#16555 - 	CGI_10024887	superfamily	247044	7	135	1.68E-42	155.793	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#16555 - 	CGI_10024887	superfamily	193256	3008	3276	6.84E-81	271.821	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#16555 - 	CGI_10024887	superfamily	193251	2661	2929	1.57E-60	213.259	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#16555 - 	CGI_10024887	superfamily	193257	3643	3873	3.96E-41	155.529	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#16555 - 	CGI_10024887	superfamily	193253	3288	3624	2.07E-33	135.935	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#16555 - 	CGI_10024887	superfamily	248019	4758	4859	1.39E-10	66.4471	cl17465	DAGK_cat superfamily	NC	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#16555 - 	CGI_10024887	superfamily	247743	2351	2486	8.06E-06	47.6752	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16556 - 	CGI_10024888	superfamily	248374	14	171	1.19E-27	103.233	cl17820	Asp_Arg_Hydrox superfamily	 - 	 - 	"Aspartyl/Asparaginyl beta-hydroxylase; Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyze oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalyzing oxidation of a free alpha-amino acid. The structure of proline 3-hydroxylase contains the conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. This family represent the arginine, asparagine and proline hydroxylases. The aspartyl/asparaginyl beta-hydroxylase (EC:1.14.11.16) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins."
Q#16557 - 	CGI_10024889	superfamily	248019	76	169	1.56E-12	69.5287	cl17465	DAGK_cat superfamily	NC	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#16559 - 	CGI_10024891	superfamily	244083	136	229	1.35E-45	150.53	cl05417	PLA2_like superfamily	 - 	 - 	"PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers."
Q#16560 - 	CGI_10024892	superfamily	243078	31	143	1.95E-27	109.231	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#16560 - 	CGI_10024892	superfamily	201885	834	1027	1.86E-77	252.929	cl12249	I_LWEQ superfamily	 - 	 - 	"I/LWEQ domain; I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin and yeast Sla2p interact with F-actin. I/LWEQ domains can be placed into four major groups based on sequence similarity: (1) Metazoan talin; (2) Dictyostelium TalA/TalB and SLA110; (3) metazoan Hip1p; and (4) yeast Sla2p. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks."
Q#16560 - 	CGI_10024892	superfamily	242926	476	623	0.00630527	38.1925	cl02193	PRK13874 superfamily	C	 - 	conjugal transfer protein TrbJ; Provisional
Q#16563 - 	CGI_10024895	superfamily	217293	19	210	8.22E-37	134.297	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16563 - 	CGI_10024895	superfamily	202474	236	312	0.00648574	36.4777	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16564 - 	CGI_10024896	superfamily	217293	8	111	1.16E-20	87.3031	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16564 - 	CGI_10024896	superfamily	202474	162	213	8.07E-06	44.9521	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16565 - 	CGI_10024897	superfamily	241578	335	492	1.38E-40	148.594	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16565 - 	CGI_10024897	superfamily	241578	692	851	1.77E-38	142.431	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16565 - 	CGI_10024897	superfamily	247856	150	210	2.57E-05	43.6905	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16565 - 	CGI_10024897	superfamily	245598	12	46	7.13E-07	49.5852	cl11396	Patatin_and_cPLA2 superfamily	N	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#16565 - 	CGI_10024897	superfamily	247097	520	555	0.00571658	36.275	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#16565 - 	CGI_10024897	superfamily	247097	965	998	0.00772745	35.8181	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#16568 - 	CGI_10024900	superfamily	217293	28	228	1.78E-35	130.445	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16568 - 	CGI_10024900	superfamily	202474	232	286	2.85E-06	46.8781	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16569 - 	CGI_10024901	superfamily	217293	36	233	4.02E-38	138.149	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16569 - 	CGI_10024901	superfamily	202474	240	330	1.81E-13	68.0641	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16570 - 	CGI_10024902	superfamily	217293	30	227	7.99E-41	145.083	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16570 - 	CGI_10024902	superfamily	202474	254	330	4.80E-10	58.0489	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16571 - 	CGI_10024903	superfamily	217293	30	227	8.64E-42	147.779	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16571 - 	CGI_10024903	superfamily	202474	255	325	5.75E-10	57.6637	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16574 - 	CGI_10024906	superfamily	219525	88	136	0.000232545	38.5542	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#16574 - 	CGI_10024906	superfamily	219525	129	170	0.00190201	35.8578	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#16574 - 	CGI_10024906	superfamily	219525	26	68	0.00774738	33.9318	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#16575 - 	CGI_10024907	superfamily	247905	375	480	8.28E-15	72.2704	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#16575 - 	CGI_10024907	superfamily	204947	631	679	5.00E-14	67.9324	cl13893	SUV3_C superfamily	 - 	 - 	"Mitochondrial degradasome RNA helicase subunit C terminal; This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00271. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes."
Q#16575 - 	CGI_10024907	superfamily	247805	211	315	0.00021053	40.7836	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16577 - 	CGI_10024909	superfamily	222150	99	122	0.00839212	32.749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16578 - 	CGI_10024910	superfamily	247684	4	192	1.44E-29	116.608	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16579 - 	CGI_10024911	superfamily	247684	10	113	1.99E-27	104.667	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16579 - 	CGI_10024911	superfamily	247684	108	136	0.00242982	35.7304	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#16580 - 	CGI_10024912	superfamily	247723	39	114	3.32E-16	70.7941	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16580 - 	CGI_10024912	superfamily	247723	130	185	1.32E-08	50.3785	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16581 - 	CGI_10024913	superfamily	242406	1	61	0.00467274	33.506	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#16582 - 	CGI_10024914	superfamily	216363	26	108	1.15E-14	65.5694	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#16587 - 	CGI_10024919	superfamily	193251	3016	3291	2.02E-26	113.492	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#16587 - 	CGI_10024919	superfamily	193256	3378	3613	1.24E-22	101.948	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#16587 - 	CGI_10024919	superfamily	193257	4218	4404	1.32E-09	60.7695	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#16588 - 	CGI_10024920	superfamily	241563	73	112	3.77E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16589 - 	CGI_10024921	superfamily	245604	777	839	3.37E-10	57.8112	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#16589 - 	CGI_10024921	superfamily	247809	285	512	8.27E-58	197.909	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#16589 - 	CGI_10024921	superfamily	201133	161	279	1.67E-33	126.058	cl02837	CPSase_L_chain superfamily	 - 	 - 	"Carbamoyl-phosphate synthase L chain, N-terminal domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117."
Q#16589 - 	CGI_10024921	superfamily	244920	550	656	4.15E-30	115.973	cl08365	Biotin_carb_C superfamily	 - 	 - 	"Biotin carboxylase C-terminal domain; Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyzes the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain."
Q#16589 - 	CGI_10024921	superfamily	219797	840	928	1.39E-19	92.7637	cl09596	ACC_central superfamily	C	 - 	"Acetyl-CoA carboxylase, central region; The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyzes the rate-limiting step in this process."
Q#16590 - 	CGI_10024922	superfamily	247792	221	263	5.64E-13	64.004	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16592 - 	CGI_10024924	superfamily	241596	99	159	1.21E-13	63.0019	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#16593 - 	CGI_10024925	superfamily	247723	498	567	1.78E-09	55.3889	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16593 - 	CGI_10024925	superfamily	247723	245	317	2.10E-08	52.3073	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16593 - 	CGI_10024925	superfamily	243098	727	766	7.53E-06	44.5111	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#16593 - 	CGI_10024925	superfamily	246749	20	96	3.39E-07	49.0328	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#16593 - 	CGI_10024925	superfamily	247723	149	194	0.000311039	39.838	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16594 - 	CGI_10024926	superfamily	242253	382	494	4.27E-42	147.092	cl01020	ASCH superfamily	 - 	 - 	"ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery."
Q#16594 - 	CGI_10024926	superfamily	218944	143	195	7.32E-21	86.224	cl05634	zf-C2HC5 superfamily	 - 	 - 	"Putative zinc finger motif, C2HC5-type; This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4."
Q#16596 - 	CGI_10004570	superfamily	243072	549	665	9.56E-29	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16596 - 	CGI_10004570	superfamily	243072	213	331	5.64E-17	81.2758	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16596 - 	CGI_10004570	superfamily	243072	1348	1488	4.64E-08	54.697	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16596 - 	CGI_10004570	superfamily	243072	2177	2259	2.71E-06	48.919	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16596 - 	CGI_10004570	superfamily	243072	1286	1403	6.96E-06	47.7634	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16596 - 	CGI_10004570	superfamily	243072	366	464	0.000120644	43.9115	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16597 - 	CGI_10004571	superfamily	111929	117	175	1.42E-05	42.0026	cl03885	Str_synth superfamily	N	 - 	Strictosidine synthase; Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyzes the condensation of tryptamine with secologanin to form strictosidine.
Q#16598 - 	CGI_10004572	superfamily	245239	38	162	1.27E-30	109.138	cl10033	F1-ATPase_delta superfamily	 - 	 - 	"mitochondrial ATP synthase delta subunit; The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta, and epsilon subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain. In bacteria, which is lacking a eukaryotic epsilon subunit homolog, this subunit is called the epsilon subunit."
Q#16599 - 	CGI_10004573	superfamily	247912	37	383	7.65E-41	148.804	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16600 - 	CGI_10004574	superfamily	247905	763	892	2.69E-27	109.635	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#16600 - 	CGI_10004574	superfamily	247805	463	611	3.34E-18	83.5408	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16601 - 	CGI_10004575	superfamily	151909	6	71	2.94E-25	99.9871	cl12992	TUG superfamily	 - 	 - 	GLUT4 regulating protein TUG; TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site.
Q#16601 - 	CGI_10004575	superfamily	241645	467	537	0.000197336	40.3324	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16603 - 	CGI_10004577	superfamily	246669	284	377	0.00884092	35.1558	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#16604 - 	CGI_10011753	superfamily	241739	543	739	8.53E-50	173.213	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#16604 - 	CGI_10011753	superfamily	202662	268	427	1.43E-20	89.5385	cl18231	B3_4 superfamily	 - 	 - 	B3/4 domain; This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.
Q#16604 - 	CGI_10011753	superfamily	208909	458	525	1.53E-07	49.4157	cl08394	B5 superfamily	 - 	 - 	tRNA synthetase B5 domain; This domain is found in phenylalanine-tRNA synthetase beta subunits.
Q#16605 - 	CGI_10011754	superfamily	245601	332	407	5.19E-12	64.3176	cl11399	HP superfamily	N	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#16605 - 	CGI_10011754	superfamily	245601	128	199	3.08E-07	50.0652	cl11399	HP superfamily	C	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#16610 - 	CGI_10011759	superfamily	243082	40	328	7.30E-11	63.271	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#16611 - 	CGI_10011760	superfamily	241874	20	548	0	567.495	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#16612 - 	CGI_10011761	superfamily	248312	1	102	7.38E-12	60.0683	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#16613 - 	CGI_10006180	superfamily	217473	140	371	8.02E-24	101.673	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#16615 - 	CGI_10006182	superfamily	241832	79	169	1.67E-05	41.9608	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16616 - 	CGI_10006183	superfamily	191582	71	146	1.98E-15	68.7953	cl05954	DUF1180 superfamily	N	 - 	Protein of unknown function (DUF1180); This family consists of several hypothetical mammalian proteins of around 190 residues in length. The function of this family is unknown.
Q#16618 - 	CGI_10006185	superfamily	245201	25	220	2.75E-47	165.488	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16619 - 	CGI_10006186	superfamily	245201	18	213	5.84E-51	177.044	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16620 - 	CGI_10006187	superfamily	242323	125	231	3.79E-23	93.3419	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#16621 - 	CGI_10006188	superfamily	190308	135	312	2.37E-08	53.0915	cl18163	Fringe superfamily	 - 	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#16623 - 	CGI_10005601	superfamily	247999	10	59	0.000771313	38.6256	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#16626 - 	CGI_10005604	superfamily	245847	9	79	1.53E-14	64.5001	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#16627 - 	CGI_10005605	superfamily	243099	6	142	5.72E-45	145.939	cl02575	Bcl-2_like superfamily	 - 	 - 	"Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly."
Q#16628 - 	CGI_10005606	superfamily	241619	123	154	0.00834821	34.3327	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#16628 - 	CGI_10005606	superfamily	241619	320	351	0.00834821	34.3327	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#16633 - 	CGI_10012605	superfamily	247805	35	233	9.47E-87	274.362	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16633 - 	CGI_10012605	superfamily	247905	257	378	2.25E-21	91.1452	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#16634 - 	CGI_10012606	superfamily	243083	1630	1718	3.12E-21	91.2764	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#16634 - 	CGI_10012606	superfamily	241617	321	380	0.000288512	41.2026	cl00110	MBD superfamily	 - 	 - 	"MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin.  MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family."
Q#16635 - 	CGI_10012607	superfamily	241645	11	87	5.96E-22	84.5484	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16636 - 	CGI_10012608	superfamily	241645	28	107	2.81E-20	78.7704	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16637 - 	CGI_10012609	superfamily	241645	20	90	1.13E-16	77.6148	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16637 - 	CGI_10012609	superfamily	241645	99	176	6.63E-16	75.3036	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16637 - 	CGI_10012609	superfamily	241645	224	313	0.000750201	39.934	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16638 - 	CGI_10012610	superfamily	241866	36	440	0	828.861	cl00445	Iso_dh superfamily	 - 	 - 	Isocitrate/isopropylmalate dehydrogenase; Isocitrate/isopropylmalate dehydrogenase.  
Q#16639 - 	CGI_10012611	superfamily	247794	253	616	0	611.333	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#16639 - 	CGI_10012611	superfamily	241952	803	1259	8.53E-174	525.434	cl00566	PntB superfamily	 - 	 - 	NAD/NADP transhydrogenase beta subunit [Energy production and conversion]
Q#16639 - 	CGI_10012611	superfamily	247794	53	244	5.94E-98	318.581	cl17240	FDH_GDH_like superfamily	C	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#16639 - 	CGI_10012611	superfamily	221763	679	767	7.57E-40	144.19	cl15081	DUF3814 superfamily	 - 	 - 	"Domain of unknown function (DUF3814); This is a domain of unknown function. It is often found in combination with pfam05222, pfam01262 and pfam02233 on alanine dehydrogenase and pyridine nucleotide transhydrogenase enzymes."
Q#16642 - 	CGI_10012614	superfamily	245835	15	228	1.14E-90	281.51	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#16642 - 	CGI_10012614	superfamily	247683	500	552	3.28E-23	93.253	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#16643 - 	CGI_10012615	superfamily	247805	276	421	8.20E-24	98.5635	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16644 - 	CGI_10012616	superfamily	197746	101	155	0.000141456	38.0911	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#16644 - 	CGI_10012616	superfamily	197746	162	203	0.00866724	33.0835	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#16648 - 	CGI_10005707	superfamily	243034	511	594	0.000395082	40.056	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#16648 - 	CGI_10005707	superfamily	221741	100	186	6.81E-20	86.6159	cl15057	Cadherin-like superfamily	 - 	 - 	"Cadherin-like beta sandwich domain; This domain is found in several bacterial, metazoan and chlorophyte algal proteins. A profile-profile comparison recovered the cadherin domain and a comparison of the predicted structure of this domain with the crystal structure of the cadherin showed a congruent seven stranded secondary structure. The domain is widespread in bacteria and seen in the firmicutes, actinobacteria, certain proteobacteria, bacteroides and chlamydiae with an expansion in Clostridium. In contrast, it is limited in its distribution in eukaryotes suggesting that it was derived through lateral transfer from bacteria. In prokaryotes, this domain is widely fused to other domains such as FNIII (Fibronectin Type III), TIG, SLH (S-layer homology), discoidin, cell-wall-binding repeat domain and alpha-amylase-like glycohydrolases. These associations are suggestive of a carbohydrate-binding function for this cadherin-like domain. In animal proteins it is associated with an ATP-grasp domain."
Q#16648 - 	CGI_10005707	superfamily	221741	6	93	2.89E-18	81.9935	cl15057	Cadherin-like superfamily	 - 	 - 	"Cadherin-like beta sandwich domain; This domain is found in several bacterial, metazoan and chlorophyte algal proteins. A profile-profile comparison recovered the cadherin domain and a comparison of the predicted structure of this domain with the crystal structure of the cadherin showed a congruent seven stranded secondary structure. The domain is widespread in bacteria and seen in the firmicutes, actinobacteria, certain proteobacteria, bacteroides and chlamydiae with an expansion in Clostridium. In contrast, it is limited in its distribution in eukaryotes suggesting that it was derived through lateral transfer from bacteria. In prokaryotes, this domain is widely fused to other domains such as FNIII (Fibronectin Type III), TIG, SLH (S-layer homology), discoidin, cell-wall-binding repeat domain and alpha-amylase-like glycohydrolases. These associations are suggestive of a carbohydrate-binding function for this cadherin-like domain. In animal proteins it is associated with an ATP-grasp domain."
Q#16649 - 	CGI_10005708	superfamily	246675	309	462	1.19E-107	338.158	cl14615	PI-PLCc_GDPD_SF superfamily	C	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#16649 - 	CGI_10005708	superfamily	247725	13	137	1.77E-37	138.092	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16649 - 	CGI_10005708	superfamily	246669	718	836	2.82E-37	137.673	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#16649 - 	CGI_10005708	superfamily	246675	583	686	3.04E-68	229.532	cl14615	PI-PLCc_GDPD_SF superfamily	N	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#16649 - 	CGI_10005708	superfamily	150071	215	309	8.84E-20	86.0882	cl08538	efhand_like superfamily	 - 	 - 	"Phosphoinositide-specific phospholipase C, efhand-like; Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme."
Q#16655 - 	CGI_10008864	superfamily	243092	230	513	7.66E-70	227.603	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16655 - 	CGI_10008864	superfamily	207680	99	117	8.14E-06	43.1155	cl02632	PRP4 superfamily	C	 - 	pre-mRNA processing factor 4 (PRP4) like; This small domain is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing.
Q#16656 - 	CGI_10008865	superfamily	241884	18	229	3.51E-122	348.48	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#16657 - 	CGI_10008866	superfamily	247754	78	132	1.43E-08	47.5478	cl17200	HTH_XRE superfamily	 - 	 - 	Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Q#16657 - 	CGI_10008866	superfamily	117100	5	73	8.54E-22	83.9448	cl07226	MBF1 superfamily	 - 	 - 	"Multiprotein bridging factor 1; This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (pfam01381) is found to its C-terminus."
Q#16658 - 	CGI_10008867	superfamily	241645	17	73	5.89E-19	83.4302	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16659 - 	CGI_10008868	superfamily	243034	216	302	3.75E-08	53.1528	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#16660 - 	CGI_10008869	superfamily	220715	14	147	3.66E-27	104.334	cl11025	NT-C2 superfamily	 - 	 - 	"N-terminal C2 in EEIG1 and EHBP1 proteins; This version of the C2 domain was initally identified in the vertebrate estrogen early-induced gene 1 (EEIG1), and its Drosophila ortholog required for uptake of dsRNA via the endocytotic machinery to induce RNAi silencing. It is also in C.elegans ortholog Sym-3 (SYnthetic lethal with Mec-3) and the mammalian protein EHBP1 (EH domain Binding Protein-1) that regulates endocytotic recycling and two plant proteins, RPG that regulates Rhizobium-directed polar growth and PMI1 (Plastid Movement Impaired 1) that is essential for intracellular movement of chloroplasts in response to blue light."
Q#16662 - 	CGI_10008871	superfamily	247739	14	193	8.71E-45	149.344	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#16663 - 	CGI_10008872	superfamily	241563	68	109	5.50E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16663 - 	CGI_10008872	superfamily	246954	135	207	0.00408072	38.5534	cl15415	Sec1 superfamily	NC	 - 	Sec1 family; Sec1 family.  
Q#16664 - 	CGI_10008873	superfamily	247805	43	130	4.86E-05	41.4759	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16665 - 	CGI_10008874	superfamily	247692	198	556	1.68E-63	213.537	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#16665 - 	CGI_10008874	superfamily	247692	30	232	2.40E-09	58.3601	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#16666 - 	CGI_10008875	superfamily	247692	71	410	4.40E-57	192.736	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#16667 - 	CGI_10008876	superfamily	247856	483	545	6.00E-09	52.9353	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16667 - 	CGI_10008876	superfamily	246925	185	402	5.63E-18	83.9441	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#16668 - 	CGI_10008877	superfamily	241832	4	218	1.84E-117	336.049	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16669 - 	CGI_10005072	superfamily	241583	12	127	6.99E-19	81.2661	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#16672 - 	CGI_10005075	superfamily	216363	133	238	1.40E-24	94.8445	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#16674 - 	CGI_10005077	superfamily	241568	34	71	0.0002324	38.598	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#16676 - 	CGI_10004740	superfamily	245206	33	322	9.70E-101	311.134	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16676 - 	CGI_10004740	superfamily	245206	361	618	7.46E-86	272.229	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16677 - 	CGI_10004741	superfamily	177822	42	291	3.40E-18	81.8901	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#16678 - 	CGI_10004742	superfamily	217410	7	165	1.41E-10	56.5936	cl18409	DDE_1 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere."
Q#16679 - 	CGI_10004743	superfamily	177822	24	146	0.000216137	39.9033	cl18088	PLN02164 superfamily	C	 - 	sulfotransferase
Q#16682 - 	CGI_10004746	superfamily	177822	4	129	7.45E-10	54.5409	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#16685 - 	CGI_10004749	superfamily	241578	238	432	2.38E-18	83.9768	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16685 - 	CGI_10004749	superfamily	217211	446	514	1.44E-07	49.9754	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#16685 - 	CGI_10004749	superfamily	219821	184	212	0.000188728	40.8174	cl07136	VWA_N superfamily	N	 - 	"VWA N-terminal; This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits."
Q#16686 - 	CGI_10010747	superfamily	244530	1	158	1.24E-25	99.9268	cl06844	SRR1 superfamily	N	 - 	SRR1; SRR1 proteins are signalling proteins involved in regulating the circadian clock in Arabidopsis.
Q#16687 - 	CGI_10010748	superfamily	243088	58	171	1.13E-09	55.0549	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#16689 - 	CGI_10010750	superfamily	241594	476	828	2.97E-165	486.302	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#16689 - 	CGI_10010750	superfamily	246669	14	137	2.55E-36	133.942	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#16689 - 	CGI_10010750	superfamily	241647	365	394	3.02E-11	59.849	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#16689 - 	CGI_10010750	superfamily	241647	289	317	9.19E-11	58.3082	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#16689 - 	CGI_10010750	superfamily	241647	257	287	1.41E-10	57.923	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#16689 - 	CGI_10010750	superfamily	241647	405	434	1.07E-08	52.5302	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#16690 - 	CGI_10010751	superfamily	246722	9	112	6.57E-50	158.133	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#16693 - 	CGI_10010755	superfamily	245205	213	287	1.44E-07	49.1585	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#16693 - 	CGI_10010755	superfamily	245596	368	501	4.79E-48	167.374	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16694 - 	CGI_10010756	superfamily	183292	1	32	0.00167491	35.5676	cl18135	PRK11728 superfamily	C	 - 	hydroxyglutarate oxidase; Provisional
Q#16696 - 	CGI_10002294	superfamily	243109	37	196	1.83E-92	269.883	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#16697 - 	CGI_10002295	superfamily	213405	11	119	1.63E-26	97.1948	cl17101	Fis1 superfamily	 - 	 - 	"Mitochondria Fission Protein Fis1, cytosolic domain; Fis1, along with Dnm1 and Mdv1, is an essential protein in mediating mitochondrial fission. Dnm1 and Fis1 are highly conserved, with a common mechanism in disparate species. In mutants of these proteins, mitochondrial fission is impaired, resulting in networks of undivided mitochondria. The Fis1 N-terminus is cytosolic and tethered to the mitochondrial outer membrane via a C-terminal transmembrane domain. Fis1 appears to act via the recruitment of division complexes to the mitochondrial outer membrane, via interactions with Mdv1 or Caf4. Fis1 has tandem TPR helix-turn-helix motifs which are known to mediate protein-protein interactions."
Q#16698 - 	CGI_10002296	superfamily	243074	101	147	1.13E-08	48.6569	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#16699 - 	CGI_10002297	superfamily	217617	71	170	4.83E-12	60.5077	cl15988	Sulfotransfer_2 superfamily	C	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#16701 - 	CGI_10004993	superfamily	241584	87	177	9.51E-17	75.6107	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16701 - 	CGI_10004993	superfamily	241567	291	348	0.00154176	38.4502	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#16702 - 	CGI_10004994	superfamily	241584	320	405	3.38E-11	60.9731	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16702 - 	CGI_10004994	superfamily	241584	127	215	3.00E-09	55.1951	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16702 - 	CGI_10004994	superfamily	241584	789	863	4.16E-05	42.8687	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16702 - 	CGI_10004994	superfamily	241584	525	585	0.00020274	40.5575	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16702 - 	CGI_10004994	superfamily	241584	231	314	0.00303567	37.0907	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16702 - 	CGI_10004994	superfamily	241567	682	779	2.16E-08	54.2434	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#16703 - 	CGI_10004995	superfamily	241584	256	324	1.10E-07	50.5727	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16703 - 	CGI_10004995	superfamily	241584	642	728	4.22E-07	49.0319	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16703 - 	CGI_10004995	superfamily	241584	77	151	1.06E-06	47.8763	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#16705 - 	CGI_10004997	superfamily	245225	29	426	1.13E-57	200.615	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#16706 - 	CGI_10010142	superfamily	215647	108	358	2.56E-67	217.476	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#16706 - 	CGI_10010142	superfamily	243029	22	89	5.72E-20	83.5541	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#16708 - 	CGI_10010144	superfamily	243029	212	277	8.94E-21	86.2505	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#16708 - 	CGI_10010144	superfamily	215647	307	363	3.76E-10	58.7741	cl18338	7tm_2 superfamily	NC	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#16708 - 	CGI_10010144	superfamily	215647	335	407	7.34E-08	51.8405	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#16708 - 	CGI_10010144	superfamily	245201	31	90	3.77E-05	44.0477	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16709 - 	CGI_10010145	superfamily	241687	17	94	4.02E-12	59.2681	cl00208	RNase_T2 superfamily	N	 - 	"Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far.  This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases).  Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen."
Q#16710 - 	CGI_10010146	superfamily	247068	47	148	3.65E-10	58.4789	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#16710 - 	CGI_10010146	superfamily	241611	354	532	1.74E-08	53.9316	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#16710 - 	CGI_10010146	superfamily	247068	159	245	0.000535926	39.6042	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#16711 - 	CGI_10010147	superfamily	247724	102	331	1.87E-38	141.145	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16711 - 	CGI_10010147	superfamily	191096	584	748	2.69E-71	231.904	cl12302	Fzo_mitofusin superfamily	 - 	 - 	fzo-like conserved region; Family of putative transmembrane GTPase. The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the human mitofusin protein.
Q#16712 - 	CGI_10010148	superfamily	219603	454	722	2.11E-104	327.098	cl06744	GCFC superfamily	 - 	 - 	"GC-rich sequence DNA-binding factor-like protein; Sequences found in this family are similar to a region of a human GC-rich sequence DNA-binding factor homolog. This is thought to be a protein involved in transcriptional regulation due to partial homologies to a transcription repressor and histone-interacting protein. This family also contains tuftelin interacting protein 11 which has been identified as both a nuclear and cytoplasmic protein, and has been implicated in the secretory pathway. Sip1, a septin interacting protein is also a member of this family."
Q#16712 - 	CGI_10010148	superfamily	221586	81	145	1.32E-21	91.6632	cl13843	TIP_N superfamily	C	 - 	"Tuftelin interacting protein N terminal; This domain family is found in eukaryotes, and is typically between 99 and 114 amino acids in length. The family is found in association with pfam08697, pfam01585. There are two completely conserved residues (G and F) that may be functionally important. TIP is involved in enamel assembly by interacting with one of the major proteins responsible for biomineralisation of enamel - tuftelin."
Q#16712 - 	CGI_10010148	superfamily	243107	214	243	8.99E-11	58.6728	cl02611	G-patch superfamily	C	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#16713 - 	CGI_10010149	superfamily	246974	8	303	2.14E-129	377.321	cl15477	diphth2_R superfamily	 - 	 - 	"diphthamide biosynthesis enzyme Dph1/Dph2 domain; Archaea and Eukaryotes, but not Eubacteria, share the property of having a covalently modified residue, 2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine, as a part of a cytosolic protein. The modified His, termed diphthamide, is part of translation elongation factor EF-2 and is the site for ADP-ribosylation by diphtheria toxin. This model includes both Dph1 and Dph2 from Saccharomyces cerevisiae, although only Dph2 is found in the Archaea (see TIGR03682). Dph2 has been shown to act analogously to the radical SAM (rSAM) family (pfam04055), with 4Fe-4S-assisted cleavage of S-adenosylmethionine to create a free radical, but a different organic radical than in rSAM."
Q#16714 - 	CGI_10010150	superfamily	242889	736	824	4.30E-14	69.5783	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#16717 - 	CGI_10010153	superfamily	241607	23	57	1.50E-05	39.5606	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16717 - 	CGI_10010153	superfamily	241607	141	165	3.75E-05	38.405	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16717 - 	CGI_10010153	superfamily	241607	63	97	4.95E-05	38.0198	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16717 - 	CGI_10010153	superfamily	241607	103	137	0.000657265	34.9382	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16718 - 	CGI_10010154	superfamily	241607	56	81	6.13E-08	44.9534	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16718 - 	CGI_10010154	superfamily	241607	16	50	3.76E-06	39.9458	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16719 - 	CGI_10010155	superfamily	241607	64	84	0.000275081	34.1819	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16719 - 	CGI_10010155	superfamily	241607	26	49	0.00855466	29.9306	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#16721 - 	CGI_10010157	superfamily	241572	164	253	3.14E-09	53.7817	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#16721 - 	CGI_10010157	superfamily	241572	49	138	4.91E-09	53.3965	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#16722 - 	CGI_10010158	superfamily	247856	273	325	2.31E-06	44.4609	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16723 - 	CGI_10003957	superfamily	248097	55	179	1.77E-22	88.091	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16724 - 	CGI_10001543	superfamily	241596	59	120	1.91E-05	41.4307	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#16730 - 	CGI_10009960	superfamily	222429	38	86	0.00943035	32.9829	cl18676	Myb_DNA-bind_5 superfamily	C	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#16736 - 	CGI_10006190	superfamily	245601	53	191	3.63E-18	81.3396	cl11399	HP superfamily	C	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#16738 - 	CGI_10006192	superfamily	219740	242	358	1.48E-06	48.9546	cl06992	Peptidase_S64 superfamily	N	 - 	"Peptidase family S64; This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1. The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS:S1) and to have a typical trypsin-like catalytic triad."
Q#16740 - 	CGI_10019942	superfamily	247743	216	383	1.85E-28	110.699	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16740 - 	CGI_10019942	superfamily	247743	2	106	8.11E-13	66.0155	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#16740 - 	CGI_10019942	superfamily	204202	452	495	0.00044059	38.3905	cl07827	Vps4_C superfamily	 - 	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#16741 - 	CGI_10019943	superfamily	241902	19	86	3.92E-18	73.2973	cl00493	trimeric_dUTPase superfamily	 - 	 - 	"Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA.  It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface."
Q#16742 - 	CGI_10019944	superfamily	243072	15	123	2.88E-27	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16745 - 	CGI_10019948	superfamily	247724	321	528	1.58E-55	188.898	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16746 - 	CGI_10019949	superfamily	241902	48	135	9.63E-31	117.21	cl00493	trimeric_dUTPase superfamily	 - 	 - 	"Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA.  It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface."
Q#16746 - 	CGI_10019949	superfamily	247724	552	740	4.42E-35	133.044	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#16747 - 	CGI_10019950	superfamily	243098	244	289	3.71E-06	44.5111	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#16747 - 	CGI_10019950	superfamily	243107	348	389	9.10E-11	57.9024	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#16748 - 	CGI_10019951	superfamily	241564	415	482	5.63E-29	109.277	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#16748 - 	CGI_10019951	superfamily	241564	271	336	5.10E-17	76.1503	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#16753 - 	CGI_10019957	superfamily	243161	5	69	4.31E-09	52.0522	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#16755 - 	CGI_10019959	superfamily	241563	187	222	0.00883208	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16756 - 	CGI_10019960	superfamily	241609	2	57	9.46E-17	67.7883	cl00100	KR superfamily	N	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#16760 - 	CGI_10019964	superfamily	247803	26	207	3.43E-53	174.254	cl17249	YlqF_related_GTPase superfamily	 - 	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#16761 - 	CGI_10019965	superfamily	247792	18	62	2.92E-09	54.7592	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16761 - 	CGI_10019965	superfamily	110440	863	890	1.34E-07	49.3285	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16761 - 	CGI_10019965	superfamily	110440	910	937	3.84E-07	48.1729	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16761 - 	CGI_10019965	superfamily	110440	960	984	4.11E-05	42.3949	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16761 - 	CGI_10019965	superfamily	110440	816	843	4.80E-05	42.0097	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16761 - 	CGI_10019965	superfamily	110440	768	796	0.000104532	41.2393	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16762 - 	CGI_10019966	superfamily	247792	93	148	5.00E-06	41.2113	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16764 - 	CGI_10019968	superfamily	247792	54	102	8.44E-08	48.9812	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16764 - 	CGI_10019968	superfamily	219412	253	329	0.00475218	35.6838	cl06465	DUF1515 superfamily	C	 - 	Protein of unknown function (DUF1515); This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown.
Q#16765 - 	CGI_10019969	superfamily	242918	59	303	6.57E-95	284.525	cl02172	Per1 superfamily	 - 	 - 	Per1-like; PER1 is required for GPI-phospholipase A2 activity and is involved in lipid remodelling of GPI-anchored proteins.
Q#16767 - 	CGI_10019972	superfamily	241563	61	96	0.00174454	37.4588	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16769 - 	CGI_10019974	superfamily	241623	215	314	9.30E-25	102.496	cl00119	PI3Kc_like superfamily	C	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#16769 - 	CGI_10019974	superfamily	245847	318	381	1.98E-05	42.929	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#16769 - 	CGI_10019974	superfamily	241742	188	211	0.000211959	40.3738	cl00271	PI3Ka superfamily	N	 - 	"Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture."
Q#16771 - 	CGI_10006995	superfamily	243096	193	333	7.87E-25	102.761	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#16771 - 	CGI_10006995	superfamily	247725	347	438	5.12E-27	106.234	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16773 - 	CGI_10006997	superfamily	242422	7	196	4.37E-19	81.4812	cl01306	LCM superfamily	 - 	 - 	Leucine carboxyl methyltransferase; Family of leucine carboxyl methyltransferases EC:2.1.1.-. This family may need divides a the full alignment contains a significantly shorter mouse sequence.
Q#16774 - 	CGI_10006998	superfamily	246710	339	480	1.14E-31	122.611	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#16774 - 	CGI_10006998	superfamily	246710	528	666	5.23E-31	120.685	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#16774 - 	CGI_10006998	superfamily	246710	859	988	2.54E-30	118.374	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#16774 - 	CGI_10006998	superfamily	246710	686	795	7.40E-19	85.2467	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#16774 - 	CGI_10006998	superfamily	245213	198	236	0.00064171	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16774 - 	CGI_10006998	superfamily	243060	1020	1117	1.10E-12	66.2484	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#16774 - 	CGI_10006998	superfamily	243555	66	162	0.000364608	41.6078	cl03871	Chitin_bind_3 superfamily	N	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#16775 - 	CGI_10006999	superfamily	241645	189	240	0.00583079	33.7798	cl00155	UBQ superfamily	C	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16776 - 	CGI_10007000	superfamily	247941	10	144	2.26E-15	68.9016	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#16777 - 	CGI_10007002	superfamily	241610	94	146	4.62E-18	73.8234	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#16777 - 	CGI_10007002	superfamily	241646	34	81	0.000269813	35.8894	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#16778 - 	CGI_10009504	superfamily	214531	141	184	6.34E-08	47.5965	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#16778 - 	CGI_10009504	superfamily	214531	186	227	5.93E-06	42.2037	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#16779 - 	CGI_10009505	superfamily	215821	27	68	3.16E-08	47.2351	cl18346	FKBP_C superfamily	N	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#16779 - 	CGI_10009505	superfamily	247856	75	143	3.57E-05	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16780 - 	CGI_10009506	superfamily	215821	6	70	0.000761395	36.0643	cl18346	FKBP_C superfamily	N	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#16781 - 	CGI_10009507	superfamily	215821	38	135	2.16E-20	82.6734	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#16781 - 	CGI_10009507	superfamily	247856	142	212	8.06E-05	38.6829	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16782 - 	CGI_10009508	superfamily	241573	52	373	6.81E-115	348.938	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#16782 - 	CGI_10009508	superfamily	246669	504	631	4.10E-30	115.453	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#16782 - 	CGI_10009508	superfamily	241653	385	475	4.83E-19	84.2944	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#16783 - 	CGI_10009509	superfamily	241639	709	1170	3.48E-146	458.955	cl00148	TOP4c superfamily	 - 	 - 	"DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth."
Q#16783 - 	CGI_10009509	superfamily	243181	263	415	1.43E-84	274.934	cl02783	TopoII_MutL_Trans superfamily	 - 	 - 	"MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2.  MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families."
Q#16783 - 	CGI_10009509	superfamily	242046	453	573	2.06E-70	233.346	cl00718	TOPRIM superfamily	 - 	 - 	"Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function."
Q#16783 - 	CGI_10009509	superfamily	241593	79	172	9.15E-06	45.7154	cl00075	HATPase_c superfamily	C	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#16784 - 	CGI_10009510	superfamily	241644	7	159	9.23E-61	187.024	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#16785 - 	CGI_10009511	superfamily	245201	148	382	1.48E-67	227.034	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16786 - 	CGI_10009512	superfamily	241993	2	105	1.40E-23	91.6063	cl00630	YdcF-like superfamily	 - 	 - 	"YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX,  which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis."
Q#16788 - 	CGI_10009514	superfamily	222366	833	1112	6.07E-120	395.93	cl16381	E3_UbLigase_R4 superfamily	C	 - 	E3 ubiquitin-protein ligase UBR4; This is a family of E## ubiquitin ligase enzymes.
Q#16788 - 	CGI_10009514	superfamily	217293	32	219	2.03E-30	121.586	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16788 - 	CGI_10009514	superfamily	191182	539	611	3.83E-28	111.624	cl04917	Nsp1_C superfamily	C	 - 	Nsp1-like C-terminal region; This family probably forms a coiled-coil. This important region of Nsp1 is involved in binding Nup82.
Q#16788 - 	CGI_10009514	superfamily	222274	295	375	2.97E-13	68.2815	cl18658	Nucleoporin_FG superfamily	 - 	 - 	"Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145."
Q#16788 - 	CGI_10009514	superfamily	222003	1285	1381	5.24E-05	43.0642	cl17871	Hydrolase_like superfamily	 - 	 - 	HAD-hyrolase-like; HAD-hyrolase-like.  
Q#16788 - 	CGI_10009514	superfamily	202474	226	270	0.00150699	40.3297	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16788 - 	CGI_10009514	superfamily	248469	1230	1332	0.0034555	38.1199	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#16789 - 	CGI_10009515	superfamily	245596	598	798	1.03E-78	261.859	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16789 - 	CGI_10009515	superfamily	245596	476	531	1.07E-08	56.5472	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16790 - 	CGI_10009516	superfamily	245596	112	329	5.11E-75	245.295	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16790 - 	CGI_10009516	superfamily	245596	26	82	1.33E-09	58.088	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16791 - 	CGI_10009517	superfamily	245596	385	613	4.47E-79	255.695	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16791 - 	CGI_10009517	superfamily	245596	299	358	5.82E-10	58.8584	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#16792 - 	CGI_10009518	superfamily	241832	430	532	5.93E-42	148.594	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16792 - 	CGI_10009518	superfamily	243077	19	73	1.01E-17	78.7413	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#16792 - 	CGI_10009518	superfamily	241832	363	424	0.000131871	41.057	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16792 - 	CGI_10009518	superfamily	241832	115	213	7.71E-45	156.531	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16792 - 	CGI_10009518	superfamily	241832	538	647	3.46E-38	138.194	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16792 - 	CGI_10009518	superfamily	241832	656	735	2.78E-24	98.9033	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16793 - 	CGI_10009519	superfamily	193687	2	146	1.62E-74	222.86	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#16794 - 	CGI_10007189	superfamily	241749	29	169	5.99E-26	97.8417	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#16795 - 	CGI_10007190	superfamily	241571	311	437	2.52E-07	49.3331	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#16795 - 	CGI_10007190	superfamily	245213	442	475	0.000127178	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16795 - 	CGI_10007190	superfamily	241583	87	274	1.79E-38	140.014	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#16796 - 	CGI_10007191	superfamily	245213	655	683	0.00096144	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16796 - 	CGI_10007191	superfamily	245213	454	484	0.00698343	35.6902	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16796 - 	CGI_10007191	superfamily	241583	96	283	8.74E-40	146.562	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#16796 - 	CGI_10007191	superfamily	246918	693	745	6.62E-18	79.9383	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16796 - 	CGI_10007191	superfamily	246918	750	802	5.45E-17	77.2419	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16796 - 	CGI_10007191	superfamily	246918	865	916	5.78E-17	77.2419	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16796 - 	CGI_10007191	superfamily	246918	808	859	2.35E-16	75.3159	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16796 - 	CGI_10007191	superfamily	243051	937	1074	1.64E-13	69.7141	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#16797 - 	CGI_10007192	superfamily	241613	153	184	7.29E-05	39.8826	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#16797 - 	CGI_10007192	superfamily	241613	202	242	0.000100043	39.4974	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#16797 - 	CGI_10007192	superfamily	241571	33	127	0.00415619	35.4659	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#16798 - 	CGI_10007193	superfamily	202203	42	107	9.06E-34	120.751	cl03534	E2F_TDP superfamily	 - 	 - 	"E2F/DP family winged-helix DNA-binding domain; This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins."
Q#16801 - 	CGI_10007196	superfamily	207794	218	572	9.05E-145	429.325	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#16801 - 	CGI_10007196	superfamily	111707	146	216	3.94E-15	73.218	cl03741	Glyco_hydro_20b superfamily	N	 - 	"Glycosyl hydrolase family 20, domain 2; This domain has a zincin-like fold."
Q#16802 - 	CGI_10007197	superfamily	217904	3	503	7.28E-141	422.204	cl04404	Gpi16 superfamily	 - 	 - 	"Gpi16 subunit, GPI transamidase component; GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to newly synthesised proteins. Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small C-terminal, cytosolic extension with an ER retrieval motif."
Q#16803 - 	CGI_10007198	superfamily	202224	1434	1549	1.21E-24	101.989	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#16803 - 	CGI_10007198	superfamily	210240	1176	1216	1.11E-16	76.5326	cl15840	JmjN superfamily	 - 	 - 	jmjN domain; jmjN domain.  
Q#16803 - 	CGI_10007198	superfamily	243120	1242	1330	6.47E-14	69.9153	cl02633	ARID superfamily	 - 	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#16805 - 	CGI_10006142	superfamily	247769	148	201	7.30E-05	41.1709	cl17215	HDc superfamily	C	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#16808 - 	CGI_10006145	superfamily	247856	228	279	0.00183862	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#16809 - 	CGI_10006146	superfamily	247742	128	173	0.00924379	34.5097	cl17188	enolase_like superfamily	NC	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#16810 - 	CGI_10012904	superfamily	245226	271	432	1.56E-20	87.7412	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#16812 - 	CGI_10012906	superfamily	241563	156	190	0.00135703	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16814 - 	CGI_10012908	superfamily	248275	1	106	1.35E-26	97.4578	cl17721	zf-C2H2_jaz superfamily	 - 	 - 	"Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation."
Q#16816 - 	CGI_10012910	superfamily	241613	522	556	1.19E-08	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#16816 - 	CGI_10012910	superfamily	241613	559	593	2.38E-08	51.4386	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#16816 - 	CGI_10012910	superfamily	241613	487	515	3.94E-07	47.9718	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#16816 - 	CGI_10012910	superfamily	243075	107	186	1.88E-32	122.041	cl02536	SAND superfamily	 - 	 - 	"SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain."
Q#16818 - 	CGI_10012913	superfamily	222150	322	347	0.000723573	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16818 - 	CGI_10012913	superfamily	222150	209	234	0.00849382	33.9045	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16819 - 	CGI_10012914	superfamily	242422	46	141	2.04E-19	86.874	cl01306	LCM superfamily	C	 - 	Leucine carboxyl methyltransferase; Family of leucine carboxyl methyltransferases EC:2.1.1.-. This family may need divides a the full alignment contains a significantly shorter mouse sequence.
Q#16819 - 	CGI_10012914	superfamily	243146	568	614	2.53E-05	42.6615	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16820 - 	CGI_10012915	superfamily	217293	2	129	3.18E-25	100.785	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16820 - 	CGI_10012915	superfamily	202474	136	224	1.61E-24	98.88	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16820 - 	CGI_10012915	superfamily	202474	264	287	5.70E-05	42.2557	cl08379	Neur_chan_memb superfamily	N	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16823 - 	CGI_10012918	superfamily	243110	229	283	0.000519125	39.3349	cl02616	MACPF superfamily	C	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#16824 - 	CGI_10012919	superfamily	243190	23	96	4.11E-28	98.5342	cl02794	Cyt_c_Oxidase_VIb superfamily	 - 	 - 	"Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex."
Q#16825 - 	CGI_10012920	superfamily	247038	539	619	2.73E-06	45.9152	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#16825 - 	CGI_10012920	superfamily	241750	218	515	7.05E-69	229.852	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#16825 - 	CGI_10012920	superfamily	241750	78	131	0.000161291	43.0299	cl00281	metallo-dependent_hydrolases superfamily	C	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#16829 - 	CGI_10009260	superfamily	243072	103	224	1.80E-34	127.115	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16829 - 	CGI_10009260	superfamily	216554	331	443	4.66E-28	110.647	cl15977	zf-DHHC superfamily	C	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#16829 - 	CGI_10009260	superfamily	216554	491	574	0.00719313	36.6886	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#16829 - 	CGI_10009260	superfamily	243072	40	91	0.00869161	35.4371	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#16830 - 	CGI_10009261	superfamily	216082	9	439	2.32E-74	254.294	cl08284	Glyco_hydro_15 superfamily	C	 - 	Glycosyl hydrolases family 15; In higher organisms this family is represented by phosphorylase kinase subunits.
Q#16830 - 	CGI_10009261	superfamily	216082	911	1024	1.61E-11	66.7023	cl08284	Glyco_hydro_15 superfamily	N	 - 	Glycosyl hydrolases family 15; In higher organisms this family is represented by phosphorylase kinase subunits.
Q#16831 - 	CGI_10009262	superfamily	202478	19	99	2.78E-05	42.7879	cl03789	UcrQ superfamily	 - 	 - 	UcrQ family; The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This family represents the 9.5 kDa subunit of the complex.
Q#16833 - 	CGI_10009264	superfamily	241564	195	259	1.33E-09	53.8087	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#16838 - 	CGI_10009269	superfamily	248097	1	109	1.10E-16	70.757	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16839 - 	CGI_10009270	superfamily	248097	92	219	1.87E-17	75.3794	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16840 - 	CGI_10009271	superfamily	248097	104	182	1.94E-12	62.6678	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16840 - 	CGI_10009271	superfamily	248097	238	304	1.42E-07	48.8006	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16841 - 	CGI_10009272	superfamily	248097	92	220	6.66E-19	79.2314	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16842 - 	CGI_10009273	superfamily	248097	171	298	2.93E-18	78.461	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16843 - 	CGI_10009274	superfamily	248097	91	218	2.71E-21	85.7798	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16844 - 	CGI_10009275	superfamily	248097	88	216	1.31E-17	75.7646	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16846 - 	CGI_10009277	superfamily	247794	16	314	1.72E-143	410.247	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#16847 - 	CGI_10009278	superfamily	222430	344	484	1.50E-46	160.489	cl16445	Nup54 superfamily	 - 	 - 	"Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them."
Q#16848 - 	CGI_10009279	superfamily	248097	6	137	1.74E-16	70.757	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16849 - 	CGI_10013853	superfamily	245213	273	308	1.98E-09	54.1798	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16849 - 	CGI_10013853	superfamily	245213	347	382	5.74E-09	53.0242	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16849 - 	CGI_10013853	superfamily	245213	310	345	4.04E-08	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16849 - 	CGI_10013853	superfamily	245213	237	271	6.59E-08	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16849 - 	CGI_10013853	superfamily	243124	86	232	7.35E-37	135.632	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#16849 - 	CGI_10013853	superfamily	243124	605	716	4.58E-20	87.8676	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#16849 - 	CGI_10013853	superfamily	243124	429	487	9.56E-09	53.9701	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#16872 - 	CGI_10007783	superfamily	243061	1	102	1.97E-37	123.606	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#16873 - 	CGI_10007784	superfamily	248458	113	248	2.90E-15	75.8133	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16873 - 	CGI_10007784	superfamily	248458	314	488	2.73E-10	60.7905	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16874 - 	CGI_10007785	superfamily	244882	73	507	1.14E-94	296.095	cl08270	Peptidase_S10 superfamily	 - 	 - 	Serine carboxypeptidase; Serine carboxypeptidase.  
Q#16875 - 	CGI_10007786	superfamily	202715	109	206	5.61E-41	136.554	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#16876 - 	CGI_10007787	superfamily	241832	1	61	2.02E-35	118.385	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#16877 - 	CGI_10006729	superfamily	243082	109	170	9.07E-11	59.419	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#16881 - 	CGI_10006733	superfamily	248013	303	342	0.00383001	34.882	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#16888 - 	CGI_10015280	superfamily	248293	3	87	0.000837057	34.6419	cl17739	MADF_DNA_bdg superfamily	 - 	 - 	Alcohol dehydrogenase transcription factor Myb/SANT-like; The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains.
Q#16890 - 	CGI_10015282	superfamily	245835	452	657	6.81E-65	217.183	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#16890 - 	CGI_10015282	superfamily	248264	703	793	9.77E-16	75.7365	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#16890 - 	CGI_10015282	superfamily	243066	20	57	0.000286475	40.2933	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#16891 - 	CGI_10015283	superfamily	245823	66	584	0	611.593	cl11976	SNF superfamily	 - 	 - 	Sodium:neurotransmitter symporter family; Sodium:neurotransmitter symporter family.  
Q#16893 - 	CGI_10015285	superfamily	246748	630	659	0.00814833	37.5836	cl14876	Zinc_peptidase_like superfamily	N	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#16894 - 	CGI_10015286	superfamily	190308	254	457	9.96E-57	190.993	cl18163	Fringe superfamily	 - 	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#16895 - 	CGI_10015287	superfamily	245201	8	262	1.27E-64	218.58	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#16895 - 	CGI_10015287	superfamily	221402	712	921	6.35E-42	154.008	cl13493	DUF3543 superfamily	 - 	 - 	Domain of unknown function (DUF3543); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 217 to 291 amino acids in length. This domain is found associated with pfam00069. This domain has a single completely conserved residue A that may be functionally important.
Q#16896 - 	CGI_10015288	superfamily	247799	456	512	2.80E-09	54.4883	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#16896 - 	CGI_10015288	superfamily	243098	621	667	1.60E-07	49.1335	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#16898 - 	CGI_10015290	superfamily	220416	35	321	1.72E-62	203.807	cl10783	Morph_protein1 superfamily	 - 	 - 	"Defects in morphology protein 1, mitochondrial precursor; Members of this family of proteins are thought to be involved in cellular morphology, though little else is known about them."
Q#16902 - 	CGI_10015294	superfamily	241574	43	177	3.48E-39	132.732	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#16904 - 	CGI_10015296	superfamily	241574	44	178	1.01E-39	133.888	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#16905 - 	CGI_10015297	superfamily	222150	788	813	6.68E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16905 - 	CGI_10015297	superfamily	222150	306	331	1.07E-05	43.9197	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16905 - 	CGI_10015297	superfamily	222150	38	63	3.89E-05	42.3789	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16905 - 	CGI_10015297	superfamily	222150	643	668	0.000229416	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16907 - 	CGI_10015299	superfamily	222150	155	180	0.000184131	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16907 - 	CGI_10015299	superfamily	222150	267	291	0.000301644	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#16908 - 	CGI_10015300	superfamily	247727	142	281	0.000826063	38.5651	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#16909 - 	CGI_10015301	superfamily	241583	209	408	1.43E-85	276.812	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#16909 - 	CGI_10015301	superfamily	216572	14	131	2.94E-15	74.2334	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#16909 - 	CGI_10015301	superfamily	204025	1096	1126	7.22E-07	47.6313	cl07344	PLAC superfamily	 - 	 - 	PLAC (protease and lacunin) domain; The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins. It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin.
Q#16909 - 	CGI_10015301	superfamily	246918	910	964	0.000201643	40.6479	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16909 - 	CGI_10015301	superfamily	246918	1041	1091	0.000267134	40.2627	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16909 - 	CGI_10015301	superfamily	246918	974	1031	0.00229097	37.5663	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16909 - 	CGI_10015301	superfamily	246918	524	559	0.00486817	36.4107	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16909 - 	CGI_10015301	superfamily	221428	586	636	0.00572289	36.5975	cl13541	Salp15 superfamily	N	 - 	"Salivary protein of 15kDa inhibits CD4+ T cell activation; This is a family of 15kDa salivary proteins from Acari Arachnids that is induced on feeding and assists the parasite to remain attached to its arthropod host. By repressing calcium fluxes triggered by TCR engagement, Salp15 inhibits CD4+ T cell activation. Salp15 shows weak similarity to Inhibin A, a member of the TGF-beta superfamily that inhibits the production of cytokines and the proliferation of T cells."
Q#16910 - 	CGI_10015302	superfamily	243146	79	131	1.48E-06	45.3579	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16910 - 	CGI_10015302	superfamily	243146	193	242	4.74E-05	41.1207	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16910 - 	CGI_10015302	superfamily	243146	120	167	0.000852544	37.2063	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#16911 - 	CGI_10015303	superfamily	244530	8	93	1.37E-23	91.4524	cl06844	SRR1 superfamily	N	 - 	SRR1; SRR1 proteins are signalling proteins involved in regulating the circadian clock in Arabidopsis.
Q#16912 - 	CGI_10007978	superfamily	218118	54	115	4.33E-05	38.3641	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#16913 - 	CGI_10007979	superfamily	241578	2509	2666	4.02E-15	76.1762	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16913 - 	CGI_10007979	superfamily	241578	2307	2462	1.78E-14	74.2502	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16913 - 	CGI_10007979	superfamily	241578	1408	1566	3.54E-12	67.3166	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16913 - 	CGI_10007979	superfamily	241578	1164	1294	2.92E-10	61.1534	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16913 - 	CGI_10007979	superfamily	247068	420	511	5.94E-05	44.2266	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#16913 - 	CGI_10007979	superfamily	247068	2856	2950	0.00020491	42.6858	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#16913 - 	CGI_10007979	superfamily	152683	1940	2042	3.27E-10	60.3793	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#16913 - 	CGI_10007979	superfamily	241578	969	1136	6.01E-07	50.8497	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16913 - 	CGI_10007979	superfamily	246918	1851	1897	3.89E-06	47.1963	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16913 - 	CGI_10007979	superfamily	241578	273	400	7.61E-06	47.2862	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16913 - 	CGI_10007979	superfamily	152683	799	900	9.26E-06	46.8973	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#16913 - 	CGI_10007979	superfamily	216897	644	702	0.000102777	43.4389	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#16913 - 	CGI_10007979	superfamily	246918	711	756	0.00471306	37.9515	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16913 - 	CGI_10007979	superfamily	246918	15	60	0.00568059	37.9515	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#16914 - 	CGI_10006284	superfamily	248012	34	140	4.83E-09	53.7357	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#16915 - 	CGI_10006285	superfamily	248012	31	160	7.11E-08	50.3996	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#16918 - 	CGI_10006194	superfamily	241574	33	205	6.52E-63	198.964	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#16920 - 	CGI_10006196	superfamily	241752	2005	2123	9.83E-30	117.42	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#16920 - 	CGI_10006196	superfamily	241554	1545	1685	4.75E-25	104.265	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#16920 - 	CGI_10006196	superfamily	241554	1168	1295	1.72E-20	90.7827	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#16920 - 	CGI_10006196	superfamily	241554	1353	1493	1.43E-16	79.2267	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#16920 - 	CGI_10006196	superfamily	247723	571	643	1.06E-06	48.8028	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#16921 - 	CGI_10006197	superfamily	243090	170	282	1.44E-40	146.314	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#16921 - 	CGI_10006197	superfamily	241645	420	492	4.79E-28	109.386	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16921 - 	CGI_10006197	superfamily	241645	491	557	1.39E-07	50.3599	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#16921 - 	CGI_10006197	superfamily	245875	693	714	7.67E-06	44.2317	cl12112	GoLoco superfamily	 - 	 - 	GoLoco motif; GoLoco motif.  
Q#16923 - 	CGI_10006199	superfamily	247725	714	847	1.21E-48	170.651	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#16923 - 	CGI_10006199	superfamily	241622	432	508	7.25E-17	77.9922	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#16923 - 	CGI_10006199	superfamily	241862	139	391	4.00E-24	103.975	cl00437	COG0428 superfamily	 - 	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#16924 - 	CGI_10006200	superfamily	246709	31	251	1.72E-130	373.073	cl14782	RNase_H superfamily	 - 	 - 	"RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription."
Q#16926 - 	CGI_10006202	superfamily	241900	89	143	8.53E-12	60.3084	cl00490	EEP superfamily	NC	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#16926 - 	CGI_10006202	superfamily	241900	19	88	0.000615616	37.9668	cl00490	EEP superfamily	C	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#16927 - 	CGI_10006203	superfamily	193607	287	417	2.41E-65	207.424	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#16927 - 	CGI_10006203	superfamily	247792	238	279	1.57E-10	56.6852	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16929 - 	CGI_10003455	superfamily	241629	42	149	5.08E-19	86.0348	cl00133	SCP superfamily	N	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#16929 - 	CGI_10003455	superfamily	247097	575	606	3.29E-06	45.8333	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#16930 - 	CGI_10003456	superfamily	247057	749	816	3.05E-19	83.3543	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#16930 - 	CGI_10003456	superfamily	221744	114	322	3.76E-10	59.7571	cl18614	CABIT superfamily	N	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#16931 - 	CGI_10000528	superfamily	209898	51	73	2.54E-05	37.383	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#16933 - 	CGI_10000532	superfamily	243092	123	210	8.60E-05	43.4776	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#16935 - 	CGI_10001800	superfamily	241632	1	145	4.58E-46	155.103	cl00137	SERPIN superfamily	N	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#16936 - 	CGI_10001801	superfamily	241632	3	79	2.78E-20	81.8847	cl00137	SERPIN superfamily	C	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#16937 - 	CGI_10001802	superfamily	241632	1	177	3.71E-56	182.838	cl00137	SERPIN superfamily	N	 - 	"SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia."
Q#16938 - 	CGI_10001803	superfamily	241629	69	200	6.85E-40	138.602	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#16939 - 	CGI_10001805	superfamily	248097	8	123	6.13E-16	68.831	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16940 - 	CGI_10004596	superfamily	245231	21	107	1.48E-25	97.2063	cl10019	PurM-like superfamily	NC	 - 	"AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain."
Q#16942 - 	CGI_10004598	superfamily	216101	76	460	5.59E-124	376.248	cl08288	Carn_acyltransf superfamily	N	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#16943 - 	CGI_10004599	superfamily	248013	73	121	2.00E-10	57.2739	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#16943 - 	CGI_10004599	superfamily	243091	339	463	3.54E-39	140.162	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#16943 - 	CGI_10004599	superfamily	243114	232	331	3.24E-35	128.682	cl02622	Pre-SET superfamily	 - 	 - 	Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.
Q#16945 - 	CGI_10000691	superfamily	243077	26	78	6.57E-13	60.6369	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#16947 - 	CGI_10002218	superfamily	247792	142	198	3.93E-11	56.1151	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#16948 - 	CGI_10002219	superfamily	217505	21	448	4.57E-159	459.788	cl04021	Serinc superfamily	 - 	 - 	Serine incorporator (Serinc); This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid. Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis.
Q#16952 - 	CGI_10006149	superfamily	245213	23	64	0.00286757	36.456	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16952 - 	CGI_10006149	superfamily	245213	118	159	0.00588778	35.6856	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16953 - 	CGI_10006150	superfamily	241578	363	402	1.20E-05	45.4536	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16953 - 	CGI_10006150	superfamily	241578	152	195	1.85E-05	45.0684	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16953 - 	CGI_10006150	superfamily	241578	572	611	2.43E-05	44.6832	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16953 - 	CGI_10006150	superfamily	241578	442	480	0.000256712	41.6016	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16953 - 	CGI_10006150	superfamily	245213	282	315	0.0027505	36.0708	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#16953 - 	CGI_10006150	superfamily	241578	403	434	0.00399496	37.7496	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16954 - 	CGI_10006151	superfamily	241563	63	97	7.59E-05	40.7336	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#16955 - 	CGI_10006152	superfamily	110440	350	378	0.00600431	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#16956 - 	CGI_10001602	superfamily	243035	152	265	0.000874495	37.5794	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#16957 - 	CGI_10021155	superfamily	193307	19	93	4.84E-12	57.2661	cl14916	MFS_1_like superfamily	 - 	 - 	MFS_1 like family; In fungal members this domain is found at the C-terminus of putative transporter proteins.
Q#16958 - 	CGI_10021156	superfamily	220238	51	151	2.43E-26	99.2888	cl18552	DUF2012 superfamily	 - 	 - 	Protein of unknown function (DUF2012); This is a eukaryotic family of uncharacterized proteins.
Q#16960 - 	CGI_10021158	superfamily	246675	13	307	2.35E-98	294.149	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#16961 - 	CGI_10021159	superfamily	241795	6	135	1.76E-89	259.323	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#16963 - 	CGI_10021161	superfamily	245206	4	54	4.80E-10	52.9735	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#16964 - 	CGI_10021162	superfamily	241795	9	140	1.70E-91	266.612	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#16964 - 	CGI_10021162	superfamily	147395	152	193	1.87E-15	67.2244	cl04973	Dpy-30 superfamily	 - 	 - 	Dpy-30 motif; This motif is found in a wide variety of domain contexts. It is found in the Dpy-30 proteins hence the motifs name. It is about 40 residues long and is probably fomed of two alpha-helices. It may be a dimerisation motif analogous to pfam02197 (Bateman A pers obs).
Q#16966 - 	CGI_10021164	superfamily	248019	24	124	4.96E-20	85.7988	cl17465	DAGK_cat superfamily	C	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#16966 - 	CGI_10021164	superfamily	248019	394	480	0.00579257	37.9423	cl17465	DAGK_cat superfamily	N	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#16966 - 	CGI_10021164	superfamily	248019	111	262	0.00913556	37.1719	cl17465	DAGK_cat superfamily	NC	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#16967 - 	CGI_10021165	superfamily	245840	10	186	1.53E-48	158.284	cl12022	Ribosomal_L18e superfamily	 - 	 - 	Ribosomal protein L18e/L15; This family includes eukaryotic L18 as well as prokaryotic L15.
Q#16971 - 	CGI_10021169	superfamily	247905	374	483	2.32E-33	124.658	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#16971 - 	CGI_10021169	superfamily	244562	572	663	2.36E-22	92.2447	cl06960	GUCT superfamily	 - 	 - 	"RNA-binding GUCT domain found in the RNA helicase II/Gu protein family; This family includes vertebrate RNA helicase II/Gualpha (RH-II/Gualpha) and RNA helicase II/Gubeta (RH-II/Gubeta), both of which consist of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain, and a Gu C-terminal (GUCT) domain. They localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. The family also contains plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75), Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins. RH7 is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with the typical GUCT domain found in the RNA helicase II/Gu protein family."
Q#16971 - 	CGI_10021169	superfamily	247805	157	336	2.07E-60	202.33	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#16972 - 	CGI_10021170	superfamily	241606	16	121	1.16E-25	98.9025	cl00096	IRF superfamily	 - 	 - 	Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
Q#16973 - 	CGI_10021171	superfamily	241606	22	128	8.70E-31	113.925	cl00096	IRF superfamily	 - 	 - 	Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
Q#16977 - 	CGI_10021175	superfamily	248458	109	248	1.54E-15	76.5837	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16977 - 	CGI_10021175	superfamily	248458	323	500	5.04E-11	63.1017	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#16980 - 	CGI_10021178	superfamily	246908	441	538	2.67E-32	119.455	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#16981 - 	CGI_10021179	superfamily	241640	795	1023	1.32E-75	249.116	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#16981 - 	CGI_10021179	superfamily	241578	466	596	1.90E-05	44.8642	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#16981 - 	CGI_10021179	superfamily	241640	188	282	2.47E-09	57.2862	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#16984 - 	CGI_10021182	superfamily	242406	4	86	3.79E-10	52.2085	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#16985 - 	CGI_10021183	superfamily	217293	22	227	5.53E-32	120.43	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16985 - 	CGI_10021183	superfamily	202474	234	284	1.71E-09	56.1229	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#16986 - 	CGI_10021184	superfamily	217293	37	229	5.81E-31	117.349	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#16987 - 	CGI_10021185	superfamily	241567	158	397	8.31E-55	183.185	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#16989 - 	CGI_10021187	superfamily	245226	11	146	6.02E-51	174.059	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#16989 - 	CGI_10021187	superfamily	245226	500	533	1.03E-05	44.6318	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#16990 - 	CGI_10021188	superfamily	245226	610	810	8.99E-36	135.49	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#16992 - 	CGI_10005421	superfamily	248012	581	725	1.06E-11	63.1112	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#16992 - 	CGI_10005421	superfamily	241646	90	120	0.000549293	38.5858	cl00156	WAP superfamily	C	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#16992 - 	CGI_10005421	superfamily	214507	293	347	0.00136962	37.4096	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#16993 - 	CGI_10005422	superfamily	247912	1	333	4.61E-44	159.204	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16993 - 	CGI_10005422	superfamily	221337	383	468	3.10E-06	45.3855	cl13401	DUF3471 superfamily	 - 	 - 	"Domain of unknown function (DUF3471); This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144."
Q#16994 - 	CGI_10005423	superfamily	247912	509	842	7.40E-35	136.477	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16994 - 	CGI_10005423	superfamily	247912	1	334	3.14E-24	104.506	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16994 - 	CGI_10005423	superfamily	221337	380	411	0.0012491	38.4519	cl13401	DUF3471 superfamily	C	 - 	"Domain of unknown function (DUF3471); This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144."
Q#16995 - 	CGI_10005424	superfamily	247912	4	305	3.40E-22	95.646	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16996 - 	CGI_10005425	superfamily	247912	46	373	1.03E-15	76.7712	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16997 - 	CGI_10005426	superfamily	247912	32	96	4.28E-13	68.682	cl17358	Beta-lactamase superfamily	C	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16997 - 	CGI_10005426	superfamily	247912	176	304	5.16E-05	43.6441	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#16998 - 	CGI_10005427	superfamily	248097	14	101	1.94E-10	54.9638	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#16999 - 	CGI_10005428	superfamily	248097	69	190	4.99E-22	87.3206	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17000 - 	CGI_10005429	superfamily	248097	73	194	4.77E-18	76.535	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17001 - 	CGI_10005430	superfamily	246918	17	69	8.33E-13	58.7523	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17003 - 	CGI_10005432	superfamily	246597	362	558	3.40E-39	142.047	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#17003 - 	CGI_10005432	superfamily	219833	7	250	3.02E-20	89.7631	cl07152	Pol_alpha_B_N superfamily	 - 	 - 	DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. Also see pfam04058.
Q#17006 - 	CGI_10000907	superfamily	245864	4	134	3.33E-26	103.512	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#17007 - 	CGI_10015628	superfamily	247058	2	186	1.11E-55	182.76	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#17007 - 	CGI_10015628	superfamily	202367	298	328	7.51E-07	47.5344	cl18226	3HCDH_N superfamily	C	 - 	"3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda crystallin."
Q#17008 - 	CGI_10015629	superfamily	199166	287	506	1.48E-10	60.0336	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#17008 - 	CGI_10015629	superfamily	243074	229	274	4.91E-07	47.1161	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#17009 - 	CGI_10015630	superfamily	114903	23	114	2.40E-10	56.0647	cl05626	BAMBI superfamily	N	 - 	"BMP and activin membrane-bound inhibitor (BAMBI) N-terminal domain; This family consists of several eukaryotic BMP and activin membrane-bound inhibitor (BAMBI) proteins. Members of the transforming growth factor-beta (TGF-beta) superfamily, including TGF-beta, bone morphogenetic proteins (BMPs), activins and nodals, are vital for regulating growth and differentiation. BAMBI is related to TGF-beta-family type I receptors but lacks an intracellular kinase domain. BAMBI is co-expressed with the ventralising morphogen BMP4 during Xenopus embryogenesis and requires BMP signalling for its expression. The protein stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling."
Q#17010 - 	CGI_10015631	superfamily	218259	324	459	4.51E-36	130.467	cl04742	Bile_Hydr_Trans superfamily	 - 	 - 	"Acyl-CoA thioester hydrolase/BAAT N-terminal region; This family consists of the amino termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT). This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism. For example, in peroxisomes, the hydrolase acts on bile-CoA esters."
Q#17010 - 	CGI_10015631	superfamily	192535	20	283	0.000216898	41.8126	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#17013 - 	CGI_10015634	superfamily	247757	565	679	3.22E-20	88.221	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#17014 - 	CGI_10015635	superfamily	245225	516	956	6.64E-55	200.547	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17014 - 	CGI_10015635	superfamily	245225	41	469	2.31E-48	181.287	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17014 - 	CGI_10015635	superfamily	245225	1244	1418	6.83E-13	71.8511	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17014 - 	CGI_10015635	superfamily	242034	1657	1716	0.00215413	39.4472	cl00695	Lysine_decarbox superfamily	N	 - 	"Possible lysine decarboxylase; The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear."
Q#17017 - 	CGI_10015638	superfamily	245596	108	412	0	568.801	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#17018 - 	CGI_10015639	superfamily	116538	649	779	5.34E-43	153.6	cl06801	Vps54 superfamily	 - 	 - 	"Vps54-like protein; This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog , the human homolog, and the mouse homolog. In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs."
Q#17019 - 	CGI_10015640	superfamily	241760	4	50	1.10E-18	79.644	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#17019 - 	CGI_10015640	superfamily	247804	64	108	4.66E-09	52.1926	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#17019 - 	CGI_10015640	superfamily	203011	362	436	0.00056655	37.9569	cl04515	SWIRM superfamily	 - 	 - 	SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
Q#17020 - 	CGI_10015641	superfamily	243084	1361	1473	4.19E-35	131.749	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#17020 - 	CGI_10015641	superfamily	204507	22	122	6.90E-35	130.867	cl11169	WAC_Acf1_DNA_bd superfamily	 - 	 - 	"ATP-utilising chromatin assembly and remodelling N-terminal; ACF (for ATP-utilising chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA."
Q#17020 - 	CGI_10015641	superfamily	247999	1131	1179	9.11E-16	74.0639	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#17020 - 	CGI_10015641	superfamily	247999	1229	1272	3.67E-09	55.1892	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#17020 - 	CGI_10015641	superfamily	243137	402	461	1.52E-08	53.4054	cl02674	DDT superfamily	 - 	 - 	"DDT domain; This domain is approximately 60 residues in length, and is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is exclusively associated with nuclear domains, and is thought to be arranged into three alpha helices."
Q#17021 - 	CGI_10015642	superfamily	247749	1	326	0	598.841	cl17195	LDH_MDH_like superfamily	 - 	 - 	"NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others."
Q#17022 - 	CGI_10015643	superfamily	241868	4	45	5.55E-05	39.7851	cl00447	Nudix_Hydrolase superfamily	C	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#17023 - 	CGI_10015644	superfamily	218223	17	273	7.32E-09	54.6822	cl04698	Radial_spoke superfamily	N	 - 	"Radial spokehead-like protein; This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene."
Q#17024 - 	CGI_10015645	superfamily	243061	1023	1123	5.92E-21	92.0198	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17024 - 	CGI_10015645	superfamily	243061	159	261	5.23E-17	80.4638	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17024 - 	CGI_10015645	superfamily	243061	1847	1950	7.43E-09	56.321	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17024 - 	CGI_10015645	superfamily	243035	2498	2595	0.00019338	42.9722	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17025 - 	CGI_10015646	superfamily	220161	316	448	7.86E-22	90.8738	cl07783	Rubis-subs-bind superfamily	 - 	 - 	"Rubisco LSMT substrate-binding; Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex."
Q#17026 - 	CGI_10015647	superfamily	243092	313	406	0.00994106	36.9292	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17027 - 	CGI_10015648	superfamily	241572	30	128	3.21E-17	77.2788	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#17027 - 	CGI_10015648	superfamily	241572	144	197	0.00170024	37.2181	cl00050	CYCLIN superfamily	C	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#17028 - 	CGI_10015649	superfamily	247724	19	114	3.88E-11	56.816	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17030 - 	CGI_10000773	superfamily	247068	131	177	0.00198423	35.4031	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17031 - 	CGI_10001016	superfamily	245814	39	125	0.0084768	32.8625	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17033 - 	CGI_10011408	superfamily	245205	19	96	6.78E-17	70.7297	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#17034 - 	CGI_10011409	superfamily	241613	24	59	4.24E-07	45.2754	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#17037 - 	CGI_10011412	superfamily	216423	72	337	9.02E-88	277.966	cl18367	Glyco_hydro_35 superfamily	 - 	 - 	Glycosyl hydrolases family 35; Glycosyl hydrolases family 35.  
Q#17038 - 	CGI_10011413	superfamily	217740	16	190	1.29E-21	88.1873	cl18427	Scramblase superfamily	 - 	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#17039 - 	CGI_10011414	superfamily	247684	266	696	3.62E-80	266.065	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17039 - 	CGI_10011414	superfamily	247684	33	260	2.38E-33	132.786	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17040 - 	CGI_10011415	superfamily	247684	40	382	2.88E-63	212.908	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17042 - 	CGI_10011417	superfamily	247684	40	471	2.05E-89	285.325	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17045 - 	CGI_10011420	superfamily	241621	74	158	2.82E-12	61.6165	cl00116	PDGF superfamily	 - 	 - 	"Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain"
Q#17048 - 	CGI_10011423	superfamily	241572	51	135	6.06E-12	61.1004	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#17049 - 	CGI_10011424	superfamily	202474	145	224	7.47E-31	115.829	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17049 - 	CGI_10011424	superfamily	217293	49	126	2.54E-12	63.0355	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17051 - 	CGI_10011426	superfamily	247755	230	484	3.45E-165	479.555	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#17051 - 	CGI_10011426	superfamily	247755	500	744	3.95E-143	422.587	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#17051 - 	CGI_10011426	superfamily	217870	158	189	1.30E-06	46.3361	cl04386	RLI superfamily	 - 	 - 	"Possible Fer4-like domain in RNase L inhibitor, RLI; Possible metal-binding domain in endoribonuclease RNase L inhibitor. Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, pfam00037. Also often found adjacent to the DUF367 domain pfam04034 in uncharacterized proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons, and could possibly play a more general role in the regulation of RNA stability in mammalian cells. Inhibitory activity requires concentration-dependent association of RLI with RNase L."
Q#17051 - 	CGI_10011426	superfamily	243197	202	223	0.000151371	40.3084	cl02805	Fer4 superfamily	 - 	 - 	"4Fe-4S binding domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich."
Q#17053 - 	CGI_10011428	superfamily	216056	70	220	1.23E-30	116.255	cl08279	Peptidase_M16 superfamily	 - 	 - 	Insulinase (Peptidase family M16); Insulinase (Peptidase family M16).  
Q#17053 - 	CGI_10011428	superfamily	218490	225	429	5.42E-22	93.3099	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#17054 - 	CGI_10001319	superfamily	247724	46	215	1.57E-16	76.0461	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17055 - 	CGI_10001321	superfamily	245201	1	125	4.03E-45	149.535	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17056 - 	CGI_10001343	superfamily	245029	43	90	0.00868515	31.8492	cl09190	MAPEG superfamily	N	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#17057 - 	CGI_10001344	superfamily	245029	18	130	3.48E-19	78.0732	cl09190	MAPEG superfamily	 - 	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#17059 - 	CGI_10002025	superfamily	247068	131	223	1.47E-20	87.7541	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17059 - 	CGI_10002025	superfamily	247068	502	585	1.48E-14	70.4201	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17059 - 	CGI_10002025	superfamily	247068	244	335	2.07E-14	70.0349	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17059 - 	CGI_10002025	superfamily	247068	37	122	3.52E-09	55.0122	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17063 - 	CGI_10007320	superfamily	248213	60	107	0.000262598	38.3249	cl17659	DivIC superfamily	C	 - 	Septum formation initiator; DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil.
Q#17066 - 	CGI_10007323	superfamily	246680	598	676	0.000368665	39.241	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#17069 - 	CGI_10007326	superfamily	193257	228	429	2.47E-17	82.7259	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#17070 - 	CGI_10007327	superfamily	193253	225	470	1.20E-19	88.9405	cl15084	MT superfamily	C	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#17070 - 	CGI_10007327	superfamily	193256	32	193	1.34E-13	69.5912	cl18189	AAA_8 superfamily	N	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#17071 - 	CGI_10007328	superfamily	222647	38	88	0.00146934	36.2458	cl16771	FlxA superfamily	NC	 - 	"FlxA-like protein; This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation."
Q#17072 - 	CGI_10007329	superfamily	193251	824	1113	1.83E-26	111.181	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#17072 - 	CGI_10007329	superfamily	193256	1214	1306	8.79E-05	44.5532	cl18189	AAA_8 superfamily	C	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#17073 - 	CGI_10002099	superfamily	241600	1	86	2.45E-37	131.209	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#17073 - 	CGI_10002099	superfamily	242566	147	182	4.02E-05	40.0766	cl01536	UPF0154 superfamily	C	 - 	Uncharacterized protein family (UPF0154); This family contains a set of short bacterial proteins of unknown function.
Q#17074 - 	CGI_10002100	superfamily	243072	413	532	3.88E-25	100.921	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17074 - 	CGI_10002100	superfamily	243072	128	248	1.31E-21	90.9058	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17074 - 	CGI_10002100	superfamily	243072	317	468	1.29E-20	88.2094	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17074 - 	CGI_10002100	superfamily	243072	33	184	6.77E-15	71.6458	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17075 - 	CGI_10002481	superfamily	243119	101	145	0.000114794	37.7985	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#17077 - 	CGI_10010175	superfamily	245816	280	399	3.55E-06	45.2994	cl11964	CYTH-like_Pase superfamily	N	 - 	"CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; CYTH-like superfamily enzymes hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB), and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions."
Q#17079 - 	CGI_10010177	superfamily	243166	44	254	1.29E-12	63.4666	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#17081 - 	CGI_10010179	superfamily	217062	24	268	9.16E-43	149.727	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#17082 - 	CGI_10010180	superfamily	247683	33	83	0.000146417	40.1387	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17084 - 	CGI_10010182	superfamily	243100	43	91	4.30E-07	46.4529	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#17085 - 	CGI_10001250	superfamily	241563	61	97	0.00332873	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17087 - 	CGI_10012883	superfamily	243092	28	270	6.99E-30	117.821	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17089 - 	CGI_10012885	superfamily	243045	113	165	8.25E-10	56.8727	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#17089 - 	CGI_10012885	superfamily	241596	30	71	1.19E-08	52.6015	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#17089 - 	CGI_10012885	superfamily	243045	278	356	2.29E-06	46.4723	cl02459	PAS superfamily	N	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#17090 - 	CGI_10012886	superfamily	248264	45	214	3.86E-17	77.6625	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#17092 - 	CGI_10012888	superfamily	241596	25	78	8.54E-11	56.0683	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#17092 - 	CGI_10012888	superfamily	248097	155	283	1.67E-15	70.3718	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17093 - 	CGI_10012889	superfamily	248097	124	234	6.93E-18	77.6906	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17094 - 	CGI_10012890	superfamily	248097	17	144	1.66E-19	79.2314	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17096 - 	CGI_10012892	superfamily	241570	558	668	1.47E-17	80.4478	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#17096 - 	CGI_10012892	superfamily	243045	26	124	3.85E-07	49.5539	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#17096 - 	CGI_10012892	superfamily	219619	428	477	7.82E-07	47.9728	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#17098 - 	CGI_10012894	superfamily	245596	704	903	2.84E-78	260.703	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#17098 - 	CGI_10012894	superfamily	245596	581	638	2.13E-08	55.3916	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#17099 - 	CGI_10012895	superfamily	241698	8	208	2.22E-74	225.606	cl00220	cysteine_hydrolases superfamily	 - 	 - 	"Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function."
Q#17100 - 	CGI_10012896	superfamily	245206	36	305	6.67E-89	270.303	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#17101 - 	CGI_10012897	superfamily	247692	19	370	1.34E-46	164.001	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#17103 - 	CGI_10012899	superfamily	247792	17	76	0.00173762	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17103 - 	CGI_10012899	superfamily	197380	466	627	7.62E-06	46.4609	cl16909	SdiA-regulated superfamily	 - 	 - 	"SdiA-regulated; This model represents a bacterial family of proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators. The C-terminal domain included in the alignment forms a five-bladed beta-propeller structure. The X-ray structure of Escherichia coli yjiK (C-terminal domain) exhibits binding of calcium ions (Ca++) in what appears to be an evolutionarily conserved site. Sequence analysis suggests a distant relationship to proteins that are characterized as containing NHL-repeats. The latter also form beta-propeller structures, with several examples known to form six-bladed beta-propellers. Several of the six-bladed beta-propellers containing NHL repeats have been characterized functionally, including members with enzymatic functions that are dependent on metal ions. No functional characterization is available for this family of five-bladed propellers, though."
Q#17103 - 	CGI_10012899	superfamily	241563	173	207	8.32E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17104 - 	CGI_10012900	superfamily	241962	1110	1211	8.10E-39	141.692	cl00584	CutA1 superfamily	 - 	 - 	"CutA1 divalent ion tolerance protein; Several gene loci with a possible involvement in cellular tolerance to copper have been identified. One such locus in eubacteria and archaebacteria, cutA, is thought to be involved in cellular tolerance to a wide variety of divalent cations other than copper. The cutA locus consists of two operons, of one and two genes. The CutA1 protein is a cytoplasmic protein, encoded by the single-gene operon and has been linked to divalent cation tolerance. It has no recognised structural motifs. This family also contains putative proteins from eukaryotes (human and Drosophila)."
Q#17105 - 	CGI_10012901	superfamily	242494	10	146	1.85E-28	103.929	cl01418	Cupin_5 superfamily	 - 	 - 	Cupin superfamily (DUF985); Family of uncharacterized proteins found in bacteria and eukaryotes that belongs to the Cupin superfamily.
Q#17106 - 	CGI_10012902	superfamily	243034	423	530	1.53E-10	58.9308	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#17106 - 	CGI_10012902	superfamily	243034	198	300	6.68E-10	57.39	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#17106 - 	CGI_10012902	superfamily	243034	500	605	2.87E-09	55.464	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#17106 - 	CGI_10012902	superfamily	243034	270	368	9.05E-07	47.76	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#17106 - 	CGI_10012902	superfamily	243034	362	449	0.00175759	37.7448	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#17107 - 	CGI_10012903	superfamily	247907	73	184	4.99E-05	40.1244	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#17107 - 	CGI_10012903	superfamily	241811	1	19	0.000241306	37.1801	cl00355	Ribosomal_S14 superfamily	N	 - 	Ribosomal protein S14p/S29e; This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
Q#17110 - 	CGI_10002249	superfamily	241563	18	50	7.12E-05	40.3983	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17111 - 	CGI_10002250	superfamily	245596	22	236	3.10E-69	214.368	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#17112 - 	CGI_10008577	superfamily	241563	210	241	3.74E-07	47.2819	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17112 - 	CGI_10008577	superfamily	247792	69	120	3.99E-07	47.4404	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17113 - 	CGI_10008578	superfamily	219619	135	187	6.48E-16	71.4699	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#17113 - 	CGI_10008578	superfamily	219619	259	336	1.98E-12	61.8399	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#17114 - 	CGI_10008579	superfamily	241749	28	169	1.48E-31	112.479	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#17115 - 	CGI_10008580	superfamily	243090	316	428	7.09E-44	150.789	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#17116 - 	CGI_10008581	superfamily	247710	106	467	4.92E-150	435.773	cl17114	metX superfamily	 - 	 - 	homoserine O-acetyltransferase; Provisional
Q#17117 - 	CGI_10002835	superfamily	199166	210	377	1.11E-18	83.1456	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#17117 - 	CGI_10002835	superfamily	199166	97	250	4.00E-17	78.9084	cl15308	AMN1 superfamily	 - 	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#17117 - 	CGI_10002835	superfamily	243074	12	56	1.82E-08	50.5829	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#17118 - 	CGI_10002836	superfamily	247675	29	197	2.40E-67	211.785	cl17011	Arginase_HDAC superfamily	C	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#17119 - 	CGI_10002497	superfamily	247692	75	278	5.54E-30	116.237	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#17119 - 	CGI_10002497	superfamily	247692	1	44	2.99E-06	46.87	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#17122 - 	CGI_10003326	superfamily	248264	150	295	7.56E-38	133.131	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#17122 - 	CGI_10003326	superfamily	243161	1	52	9.17E-08	48.5446	cl02739	THAP superfamily	N	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#17123 - 	CGI_10007788	superfamily	243072	103	224	9.32E-35	124.033	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17123 - 	CGI_10007788	superfamily	243072	165	288	4.88E-29	108.625	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17123 - 	CGI_10007788	superfamily	243072	9	158	1.95E-26	101.306	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17124 - 	CGI_10007789	superfamily	247856	175	223	0.000300438	37.9125	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17124 - 	CGI_10007789	superfamily	247999	90	147	0.00314385	34.7736	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#17125 - 	CGI_10007790	superfamily	247856	106	150	0.000132098	38.2977	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17125 - 	CGI_10007790	superfamily	247856	133	187	0.000495151	36.7569	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17126 - 	CGI_10007791	superfamily	217394	25	462	3.60E-134	410.994	cl08387	Alg6_Alg8 superfamily	 - 	 - 	"ALG6, ALG8 glycosyltransferase family; N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue, and Alg8 transfers the second one. In the human alg6 gene, a C->T transition, which causes Ala333 to be replaced with Val, has been identified as the cause of a congenital disorder of glycosylation, designated as type Ic OMIM:603147."
Q#17126 - 	CGI_10007791	superfamily	220363	512	826	2.84E-82	269.192	cl15585	DUF2036 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2036); This family of proteins includes members ranging in size from approximately 300 to 460 residues. There are a number of well-conserved domains along the length.
Q#17128 - 	CGI_10007793	superfamily	215827	145	314	2.13E-23	98.6947	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#17130 - 	CGI_10007795	superfamily	207662	28	102	1.17E-29	110.344	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#17130 - 	CGI_10007795	superfamily	245599	311	458	4.47E-12	63.7811	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#17131 - 	CGI_10007796	superfamily	245864	30	485	7.58E-120	361.981	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#17134 - 	CGI_10007799	superfamily	247905	1	69	1.07E-16	71.8852	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#17135 - 	CGI_10002702	superfamily	241554	287	352	4.46E-12	62.6631	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#17137 - 	CGI_10004862	superfamily	241832	54	196	1.93E-61	190.892	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#17138 - 	CGI_10004863	superfamily	241629	72	103	2.80E-05	42.122	cl00133	SCP superfamily	N	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#17139 - 	CGI_10004864	superfamily	241629	159	300	1.94E-29	111.639	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#17140 - 	CGI_10004865	superfamily	241629	89	225	3.63E-33	122.629	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#17141 - 	CGI_10004866	superfamily	148147	69	237	6.03E-10	55.6727	cl05718	Anemone_cytotox superfamily	 - 	 - 	"Sea anemone cytotoxic protein; Sea anemones are a rich source of cytotoxic proteins. Cytolysins comprise a group of more than 30 highly basic proteins with molecular masses of about 20 kDa. Cytolysins isolated from the sea anemone, Heteractis magnifica, include magnificalysin I (HMg I), magnificalysin II (HMg II) and Heteractis magnifica toxin (HMgtxn). These are highly homologous at their N-terminals. HMg I and II have molecular masses of approximately 19 kDa, and pI values of 9.4 and 10.0, respectively. Cytolysins isolated from other sea anemones Actinia tenebrosa (Tenebrosin-C, TN-C), Actinia equina (Equinatoxin, EqT) and Stichodactyla helianthus (ShC) exhibit pore-forming, haemolytic, cytotoxic, and heart stimulatory activities."
Q#17142 - 	CGI_10004867	superfamily	241763	137	392	4.31E-74	232.129	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#17142 - 	CGI_10004867	superfamily	244586	54	110	8.99E-16	71.1206	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#17143 - 	CGI_10004112	superfamily	247775	219	514	8.52E-38	142.724	cl17221	ArsB_NhaD_permease superfamily	N	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#17143 - 	CGI_10004112	superfamily	247775	26	145	5.86E-17	81.4773	cl17221	ArsB_NhaD_permease superfamily	C	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#17144 - 	CGI_10004113	superfamily	245206	22	243	3.99E-49	163.224	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#17145 - 	CGI_10004114	superfamily	247856	96	157	4.51E-16	69.4989	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17145 - 	CGI_10004114	superfamily	247856	22	84	1.01E-08	49.0833	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17146 - 	CGI_10004115	superfamily	247856	26	88	5.56E-12	57.5577	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17146 - 	CGI_10004115	superfamily	247856	100	158	1.05E-10	54.0909	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17147 - 	CGI_10003182	superfamily	219677	41	73	0.000100102	37.4172	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#17150 - 	CGI_10003185	superfamily	216198	260	354	4.06E-11	58.8644	cl08295	Transglut_C superfamily	 - 	 - 	"Transglutaminase family, C-terminal ig like domain; Transglutaminase family, C-terminal ig like domain.  "
Q#17150 - 	CGI_10003185	superfamily	216198	157	217	0.00270491	35.7525	cl08295	Transglut_C superfamily	C	 - 	"Transglutaminase family, C-terminal ig like domain; Transglutaminase family, C-terminal ig like domain.  "
Q#17151 - 	CGI_10003186	superfamily	241764	4	79	7.54E-30	113.899	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#17151 - 	CGI_10003186	superfamily	247743	130	288	3.60E-18	82.5791	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17151 - 	CGI_10003186	superfamily	201479	458	578	1.98E-30	116.96	cl02994	Transglut_N superfamily	 - 	 - 	Transglutaminase family; Transglutaminase family.  
Q#17151 - 	CGI_10003186	superfamily	247916	727	770	3.32E-09	54.3111	cl17362	Transglut_core superfamily	C	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#17151 - 	CGI_10003186	superfamily	204202	368	403	9.23E-08	49.9465	cl07827	Vps4_C superfamily	C	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#17152 - 	CGI_10002753	superfamily	243035	143	263	6.92E-22	88.8309	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17152 - 	CGI_10002753	superfamily	243035	52	123	7.55E-07	46.459	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17153 - 	CGI_10002754	superfamily	243072	82	202	2.44E-34	126.729	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17153 - 	CGI_10002754	superfamily	243072	472	584	1.76E-13	67.7938	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17153 - 	CGI_10002754	superfamily	243072	10	103	5.78E-09	54.3118	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17153 - 	CGI_10002754	superfamily	243072	176	236	5.93E-09	54.3118	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17154 - 	CGI_10002755	superfamily	245602	556	735	1.43E-22	100.009	cl11402	GH31 superfamily	N	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#17154 - 	CGI_10002755	superfamily	245602	350	606	8.96E-14	71.4778	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#17155 - 	CGI_10002756	superfamily	243035	64	180	2.00E-28	110.402	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17155 - 	CGI_10002756	superfamily	243035	388	500	3.40E-25	101.157	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17155 - 	CGI_10002756	superfamily	243035	197	297	4.18E-15	72.2673	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17155 - 	CGI_10002756	superfamily	243035	525	615	1.17E-14	71.1117	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17156 - 	CGI_10004471	superfamily	217380	171	454	3.98E-89	285.373	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#17158 - 	CGI_10004473	superfamily	221488	145	344	6.54E-65	206.374	cl13659	zf-SNAP50_C superfamily	 - 	 - 	"snRNA-activating protein of 50kDa MW C terminal; This domain family is found in eukaryotes, and is typically between 196 and 207 amino acids in length. There is a conserved CEH sequence motif. SNAP50 is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs."
Q#17159 - 	CGI_10004474	superfamily	247723	303	378	5.33E-18	78.5068	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17159 - 	CGI_10004474	superfamily	247723	191	246	7.48E-10	55.6208	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17160 - 	CGI_10004475	superfamily	221490	480	516	1.08E-11	62.2398	cl13660	CAF1A superfamily	C	 - 	"Chromatin assembly factor 1 subunit A; The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints."
Q#17162 - 	CGI_10004477	superfamily	247683	294	347	5.53E-34	120.442	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17162 - 	CGI_10004477	superfamily	245835	25	250	4.66E-98	292.676	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#17165 - 	CGI_10003390	superfamily	248458	549	689	0.000628926	41.1453	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17165 - 	CGI_10003390	superfamily	233349	163	328	1.29E-17	84.8544	cl11688	GPH_sucrose superfamily	C	 - 	"GPH family sucrose/H+ symporter; This model represents sucrose/proton symporters, found in plants, from the Glycoside-Pentoside-Hexuronide (GPH)/cation symporter family. These proteins are predicted to have 12 transmembrane domains. Members may export sucrose (e.g. SUT1, SUT4) from green parts to the phloem for long-distance transport or import sucrose (e.g SUT2) to sucrose sinks such as the tap root of the carrot."
Q#17165 - 	CGI_10003390	superfamily	233349	460	587	9.33E-06	47.49	cl11688	GPH_sucrose superfamily	NC	 - 	"GPH family sucrose/H+ symporter; This model represents sucrose/proton symporters, found in plants, from the Glycoside-Pentoside-Hexuronide (GPH)/cation symporter family. These proteins are predicted to have 12 transmembrane domains. Members may export sucrose (e.g. SUT1, SUT4) from green parts to the phloem for long-distance transport or import sucrose (e.g SUT2) to sucrose sinks such as the tap root of the carrot."
Q#17166 - 	CGI_10003391	superfamily	222150	341	368	3.52E-06	44.6901	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17166 - 	CGI_10003391	superfamily	222150	312	338	1.19E-05	43.1493	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17166 - 	CGI_10003391	superfamily	222150	401	427	3.19E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17166 - 	CGI_10003391	superfamily	222150	283	308	0.000797609	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17166 - 	CGI_10003391	superfamily	222150	373	398	0.00135806	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17167 - 	CGI_10003392	superfamily	247724	14	178	1.50E-97	285.789	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17167 - 	CGI_10003392	superfamily	243077	214	263	5.30E-13	61.7925	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#17168 - 	CGI_10003393	superfamily	243072	17	93	4.56E-18	74.7274	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17169 - 	CGI_10003394	superfamily	247792	16	58	5.87E-08	49.7516	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17170 - 	CGI_10003395	superfamily	207654	516	581	5.63E-28	109.069	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	207654	444	509	3.40E-25	100.98	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	207654	868	933	8.77E-25	99.8246	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	207654	797	861	1.23E-22	93.6614	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	207654	675	740	1.21E-20	88.2686	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	207654	1027	1092	4.73E-19	83.6462	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	207654	951	1017	4.82E-19	83.6462	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	207654	608	665	2.55E-17	78.6386	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#17170 - 	CGI_10003395	superfamily	245008	40	102	8.65E-09	53.7168	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#17171 - 	CGI_10003396	superfamily	202009	87	136	2.12E-17	73.3004	cl09271	NAC superfamily	 - 	 - 	NAC domain; NAC domain.  
Q#17173 - 	CGI_10002350	superfamily	247856	157	220	3.45E-07	46.3869	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17175 - 	CGI_10002352	superfamily	247684	7	411	6.69E-29	120.46	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17178 - 	CGI_10008401	superfamily	247724	17	114	8.20E-06	42.8288	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17179 - 	CGI_10008402	superfamily	241874	4	551	0	632.292	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#17180 - 	CGI_10008403	superfamily	247724	60	217	7.06E-21	90.4106	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17181 - 	CGI_10008404	superfamily	245716	125	147	4.82E-06	41.8461	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#17182 - 	CGI_10008405	superfamily	243197	93	115	9.32E-06	39.9232	cl02805	Fer4 superfamily	 - 	 - 	"4Fe-4S binding domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich."
Q#17182 - 	CGI_10008405	superfamily	243197	58	77	0.00166843	33.76	cl02805	Fer4 superfamily	 - 	 - 	"4Fe-4S binding domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich."
Q#17183 - 	CGI_10008406	superfamily	241594	684	1066	1.58E-130	402.714	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#17185 - 	CGI_10008408	superfamily	216686	106	283	2.39E-23	95.0825	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#17186 - 	CGI_10008409	superfamily	245230	2	444	0	583.89	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#17187 - 	CGI_10008410	superfamily	220786	84	181	1.10E-05	42.377	cl11141	Ribosomal_L50 superfamily	 - 	 - 	"Ribosomal subunit 39S; The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units. Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components. In E. coli, in the absence of the enzyme pseudouridine synthase (RluD) synthase, there is an accumulation of 50S and 30S subunits and the appearance of abnormal particles (62S and 39S), with concomitant loss of 70S ribosomes."
Q#17188 - 	CGI_10008411	superfamily	248010	856	978	3.62E-08	53.154	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#17189 - 	CGI_10008412	superfamily	212166	3	245	1.67E-75	251.107	cl17009	SSH-N superfamily	 - 	 - 	"N-terminal domain conserved in slingshot (SSH) phosphatases; This domain or region conserved in Bilateria is found N-terminal to the DEK_C-like and catalytic domains of slingshot phosphatases. Slingshot is a cofilin-specific phosphatase. Dephosphorylation reactivates cofilin, which in turn depolymerizes actin and is thus required for actin filament reorganization. Slingshot is a member of the dual-specificity protein phosphatase family. This N-terminal SSH region may be involved in P-cofilin binding (the model C-terminus plus the DEK_C-like domain, which are characterized as the "B" domain in some of the literature), and may be required for the F-actin mediated activation of slingshot (the N-terminal region of this model, sometimes referred to as the "A" domain)."
Q#17189 - 	CGI_10008412	superfamily	241574	321	456	3.95E-46	163.934	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17189 - 	CGI_10008412	superfamily	204056	264	316	1.23E-09	56.3373	cl07395	DEK_C superfamily	 - 	 - 	DEK C terminal domain; DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family. This domain is also found in chitin synthase proteins and in protein phosphatases.
Q#17190 - 	CGI_10008413	superfamily	243066	30	82	3.00E-12	59.5533	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#17191 - 	CGI_10008414	superfamily	243100	189	231	3.70E-10	54.1569	cl02576	B_zip1 superfamily	C	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#17192 - 	CGI_10006030	superfamily	241563	65	102	1.25E-05	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17192 - 	CGI_10006030	superfamily	187408	147	282	0.000285481	41.944	cl14654	V_Alix_like superfamily	NC	 - 	"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain."
Q#17195 - 	CGI_10006033	superfamily	246911	11	98	2.79E-28	109.285	cl15262	PUB superfamily	 - 	 - 	"PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.   The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes (except for fungi) and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97."
Q#17195 - 	CGI_10006033	superfamily	247916	278	358	9.46E-19	82.8338	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#17195 - 	CGI_10006033	superfamily	245322	502	583	3.10E-12	63.4401	cl10509	DUF750 superfamily	 - 	 - 	"Domain of unknown function (DUF750); This family of proteins with unknown function shows similarity to PNG-1, a enzyme responsible for de-N-glycosylation of misfolded glycoproteins in the cytosol. However, unlike PNG-1, this protein does not contain a catalytic triad in its transglutaminase domain."
Q#17195 - 	CGI_10006033	superfamily	217753	342	410	3.88E-06	45.8374	cl10615	Rad4 superfamily	NC	 - 	Rad4 transglutaminase-like domain; Rad4 transglutaminase-like domain.  
Q#17197 - 	CGI_10006035	superfamily	247805	246	381	6.36E-21	91.2448	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#17197 - 	CGI_10006035	superfamily	247905	477	570	6.51E-08	52.2401	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#17197 - 	CGI_10006035	superfamily	243778	623	713	1.77E-25	103.073	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#17197 - 	CGI_10006035	superfamily	219532	840	960	4.00E-07	49.6202	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#17197 - 	CGI_10006035	superfamily	247805	339	517	0.00575599	38.9502	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#17198 - 	CGI_10006036	superfamily	246597	283	469	3.84E-55	184.804	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#17198 - 	CGI_10006036	superfamily	152648	5	55	2.70E-14	68.1511	cl13624	Dpoe2NT superfamily	N	 - 	"DNA polymerases epsilon N terminal; This domain is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam04042. There is a single completely conserved residue F that may be functionally important. This domain is the N terminal domain of DNA polymerase epsilon subunit B. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. This domain has close structural relation to AAA+ protein C terminal domains."
Q#17201 - 	CGI_10006039	superfamily	246748	358	601	2.05E-100	313.76	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#17201 - 	CGI_10006039	superfamily	244870	143	339	5.65E-74	241.04	cl08238	PA superfamily	 - 	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#17201 - 	CGI_10006039	superfamily	202944	629	752	3.93E-30	115.831	cl07854	TFR_dimer superfamily	 - 	 - 	Transferrin receptor-like dimerisation domain; This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
Q#17201 - 	CGI_10006039	superfamily	246748	59	115	7.07E-10	59.5285	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#17202 - 	CGI_10006040	superfamily	244870	142	337	2.79E-71	233.336	cl08238	PA superfamily	 - 	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#17202 - 	CGI_10006040	superfamily	246748	357	566	6.91E-77	250.973	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#17202 - 	CGI_10006040	superfamily	202944	600	717	2.77E-28	110.438	cl07854	TFR_dimer superfamily	 - 	 - 	Transferrin receptor-like dimerisation domain; This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
Q#17202 - 	CGI_10006040	superfamily	246748	59	115	1.59E-09	58.3729	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#17203 - 	CGI_10002786	superfamily	247044	10	122	6.35E-56	179.341	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#17203 - 	CGI_10002786	superfamily	247044	136	214	1.60E-20	84.2112	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#17203 - 	CGI_10002786	superfamily	247044	239	322	1.15E-19	81.912	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#17204 - 	CGI_10002787	superfamily	248458	194	322	0.00171881	38.4489	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17206 - 	CGI_10002789	superfamily	220647	18	180	0.000676055	37.6924	cl18565	L_HGMIC_fpl superfamily	 - 	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#17207 - 	CGI_10002790	superfamily	248279	6	85	8.82E-13	64.6655	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#17207 - 	CGI_10002790	superfamily	247999	332	382	6.77E-08	49.4112	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#17207 - 	CGI_10002790	superfamily	247999	186	235	1.39E-07	48.2556	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#17210 - 	CGI_10012565	superfamily	241752	316	661	2.48E-101	315.749	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#17210 - 	CGI_10012565	superfamily	242589	192	289	1.65E-49	168.352	cl01581	WGR superfamily	 - 	 - 	"WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain."
Q#17210 - 	CGI_10012565	superfamily	190460	21	99	2.65E-28	110.729	cl03756	PARP_reg superfamily	N	 - 	"Poly(ADP-ribose) polymerase, regulatory domain; Poly(ADP-ribose) polymerase catalyzes the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#17212 - 	CGI_10012567	superfamily	242059	246	474	3.24E-35	136.477	cl00738	MBOAT superfamily	N	 - 	"MBOAT, membrane-bound O-acyltransferase family; The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue."
Q#17213 - 	CGI_10012568	superfamily	246921	58	97	2.91E-10	57.0001	cl15299	FG-GAP superfamily	C	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#17215 - 	CGI_10012570	superfamily	245201	3	303	0	590.174	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17217 - 	CGI_10012572	superfamily	243072	98	223	4.08E-33	125.574	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17217 - 	CGI_10012572	superfamily	243072	230	389	9.14E-31	119.025	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17217 - 	CGI_10012572	superfamily	243072	32	157	2.51E-30	117.87	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17217 - 	CGI_10012572	superfamily	243072	330	457	3.68E-30	117.099	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17217 - 	CGI_10012572	superfamily	243072	398	525	4.02E-30	117.099	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17217 - 	CGI_10012572	superfamily	243072	802	930	2.69E-29	114.788	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17217 - 	CGI_10012572	superfamily	243072	565	694	3.59E-29	114.403	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17217 - 	CGI_10012572	superfamily	243072	635	761	3.59E-27	108.625	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17219 - 	CGI_10012574	superfamily	245607	10	113	2.38E-46	147.922	cl11414	Cytochrom_C superfamily	 - 	 - 	"Cytochrome c; The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, pfam06181, has now been merged into this family."
Q#17220 - 	CGI_10012575	superfamily	241760	248	288	3.88E-10	56.5864	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#17220 - 	CGI_10012575	superfamily	247792	368	410	9.97E-09	52.448	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17220 - 	CGI_10012575	superfamily	247792	164	219	0.00924834	35.114	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17221 - 	CGI_10012576	superfamily	241597	141	211	3.29E-14	64.9475	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#17222 - 	CGI_10012577	superfamily	206035	151	248	2.87E-31	112.641	cl16440	Enkurin superfamily	 - 	 - 	"Calmodulin-binding; This is a family of apparent calmodulin-binding proteins found at high levels in the testis and vomeronasal organ and at lower levels in certain other tissues. Enkurin is a scaffold protein that binds PI3 kinase to sperm transient receptor potential (canonical) (TRPC) channels. The mammalian transient receptor potential (canonical) channels are the primary candidates for the Ca(2+) entry pathway activated by the hormones, growth factors, and neurotransmitters that exert their effect through activation of PLC. Calmodulin binds to the C-terminus of all TRPC channels, and dissociation of calmodulin from TRPC4 results in profound activation of the channel."
Q#17223 - 	CGI_10012578	superfamily	241644	11	134	1.23E-17	80.3241	cl00154	UBCc superfamily	C	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#17224 - 	CGI_10012579	superfamily	245936	87	285	9.68E-58	185.446	cl12283	IPK superfamily	 - 	 - 	Inositol polyphosphate kinase; ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
Q#17224 - 	CGI_10012579	superfamily	245936	1	39	2.99E-10	56.7892	cl12283	IPK superfamily	C	 - 	Inositol polyphosphate kinase; ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
Q#17226 - 	CGI_10003806	superfamily	247684	20	462	1.31E-97	306.511	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17227 - 	CGI_10003807	superfamily	247684	13	433	5.24E-85	272.999	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17228 - 	CGI_10003808	superfamily	241691	60	297	7.16E-47	159.355	cl00213	DNA_BRE_C superfamily	 - 	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#17228 - 	CGI_10003808	superfamily	206538	277	325	8.69E-16	70.719	cl16833	Topo_C_assoc superfamily	N	 - 	C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.
Q#17230 - 	CGI_10003025	superfamily	241584	802	892	7.18E-22	94.4855	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	1398	1492	8.73E-22	94.1003	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	1297	1386	5.45E-21	91.7891	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	903	986	2.09E-20	90.2483	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2075	2166	9.47E-20	88.3223	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	1196	1289	9.88E-20	87.9371	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2884	2978	2.13E-19	87.1667	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	1980	2063	9.54E-19	85.2407	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	703	794	4.23E-18	83.3147	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2379	2472	7.01E-18	82.5443	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	1670	1763	7.59E-18	82.5443	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2683	2776	8.17E-18	82.5443	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	1772	1863	8.45E-18	82.5443	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2481	2571	1.17E-17	82.1591	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	1874	1965	4.46E-17	80.2331	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2989	3079	5.77E-17	80.2331	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	3191	3282	1.10E-16	79.0775	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2286	2367	2.20E-15	75.6107	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2582	2671	4.88E-15	74.4551	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2177	2261	5.41E-14	71.3735	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	2784	2875	1.22E-12	67.5215	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	241584	3088	3171	2.28E-11	63.6695	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17230 - 	CGI_10003025	superfamily	245814	1498	1565	8.84E-11	61.3511	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	1023	1093	1.54E-08	54.8027	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	2	57	1.50E-05	45.9431	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	1119	1190	8.58E-14	70.3024	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	630	699	1.14E-13	69.9172	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	1593	1666	4.61E-10	59.5168	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	534	605	3.24E-07	50.9669	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	436	498	1.73E-06	49.0409	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	360	424	1.14E-05	46.3445	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	80	157	1.22E-05	46.3445	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	169	246	1.37E-05	46.3445	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17230 - 	CGI_10003025	superfamily	245814	259	335	3.62E-05	44.8037	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17231 - 	CGI_10003026	superfamily	245670	210	298	1.30E-24	103.815	cl11519	DENN superfamily	N	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#17231 - 	CGI_10003026	superfamily	243635	113	166	5.85E-10	58.1149	cl04085	uDENN superfamily	N	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#17232 - 	CGI_10016448	superfamily	241571	727	828	1.58E-41	148.715	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#17232 - 	CGI_10016448	superfamily	241571	408	517	7.25E-41	146.789	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#17232 - 	CGI_10016448	superfamily	241571	563	675	1.72E-32	123.291	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#17232 - 	CGI_10016448	superfamily	241571	299	406	4.69E-24	99.0238	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#17232 - 	CGI_10016448	superfamily	241571	833	921	4.83E-18	81.6898	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#17232 - 	CGI_10016448	superfamily	241583	120	297	1.59E-111	343.655	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#17232 - 	CGI_10016448	superfamily	241578	499	557	8.11E-08	52.7723	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17232 - 	CGI_10016448	superfamily	241578	676	712	3.99E-06	47.7648	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17234 - 	CGI_10016450	superfamily	207627	355	442	6.25E-17	77.6751	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#17234 - 	CGI_10016450	superfamily	216653	57	216	4.60E-16	76.0967	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#17234 - 	CGI_10016450	superfamily	207627	470	559	2.93E-14	69.9759	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#17234 - 	CGI_10016450	superfamily	216653	664	819	2.13E-11	62.2295	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#17235 - 	CGI_10016451	superfamily	246680	16	95	4.53E-08	50.4118	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#17237 - 	CGI_10016453	superfamily	217605	567	921	2.68E-97	319.453	cl04144	Tuberin superfamily	 - 	 - 	"Tuberin; Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. The TSC2 gene codes for tuberin and interacts with hamartin pfam04388, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking."
Q#17237 - 	CGI_10016453	superfamily	216901	1521	1711	2.59E-47	170.074	cl03466	Rap_GAP superfamily	 - 	 - 	Rap/ran-GAP; Rap/ran-GAP.  
Q#17239 - 	CGI_10016455	superfamily	246751	92	387	2.79E-118	351.931	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#17239 - 	CGI_10016455	superfamily	241546	394	495	1.38E-08	52.6828	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#17241 - 	CGI_10016457	superfamily	247805	28	69	2.35E-06	42.7096	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#17242 - 	CGI_10016458	superfamily	245847	190	335	3.84E-19	82.2193	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#17242 - 	CGI_10016458	superfamily	241619	85	134	0.000900737	36.7913	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#17244 - 	CGI_10016460	superfamily	245847	137	207	6.26E-10	57.9517	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#17244 - 	CGI_10016460	superfamily	241619	35	81	0.00132815	37.5617	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#17246 - 	CGI_10016462	superfamily	241563	63	99	3.78E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17249 - 	CGI_10016465	superfamily	241574	135	334	5.65E-24	97.6565	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17249 - 	CGI_10016465	superfamily	241574	2	85	5.89E-23	94.5749	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17251 - 	CGI_10016467	superfamily	243061	11	112	5.71E-38	135.547	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17251 - 	CGI_10016467	superfamily	243061	119	220	2.55E-35	128.614	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17251 - 	CGI_10016467	superfamily	243061	448	549	2.96E-35	128.229	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17251 - 	CGI_10016467	superfamily	243061	340	441	9.08E-31	115.902	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17251 - 	CGI_10016467	superfamily	243061	225	333	2.30E-22	92.405	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17251 - 	CGI_10016467	superfamily	243061	556	601	9.46E-08	50.4182	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17252 - 	CGI_10002774	superfamily	215754	36	119	6.90E-22	87.694	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#17252 - 	CGI_10002774	superfamily	215754	125	219	2.29E-20	83.4568	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#17252 - 	CGI_10002774	superfamily	215754	224	260	5.00E-06	43.396	cl02813	Mito_carr superfamily	C	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#17253 - 	CGI_10002775	superfamily	241583	253	460	6.65E-15	74.1889	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#17256 - 	CGI_10013681	superfamily	242667	1	164	5.30E-92	290.26	cl01720	Phage_Nu1 superfamily	 - 	 - 	"Phage DNA packaging protein Nu1; Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA."
Q#17256 - 	CGI_10013681	superfamily	233457	741	897	3.30E-48	178.15	cl18843	portal_lambda superfamily	N	 - 	"phage portal protein, lambda family; This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa [Mobile and extrachromosomal element functions, Prophage functions]."
Q#17256 - 	CGI_10013681	superfamily	233457	669	725	2.07E-10	62.5898	cl18843	portal_lambda superfamily	C	 - 	"phage portal protein, lambda family; This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa [Mobile and extrachromosomal element functions, Prophage functions]."
Q#17257 - 	CGI_10013691	superfamily	243078	22	138	2.48E-47	153.529	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#17259 - 	CGI_10013693	superfamily	243095	2	47	0.0017793	37.2813	cl02570	RhoGAP superfamily	N	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#17260 - 	CGI_10013694	superfamily	241574	319	446	4.11E-48	169.326	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17260 - 	CGI_10013694	superfamily	241626	66	179	7.31E-25	102.36	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#17263 - 	CGI_10013697	superfamily	242466	8	156	7.06E-54	169.672	cl01379	TspO_MBR superfamily	 - 	 - 	"TspO/MBR family; Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates. In, the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues."
Q#17265 - 	CGI_10013699	superfamily	241559	2	34	0.000355034	36.8736	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#17266 - 	CGI_10013700	superfamily	243105	37	334	1.78E-96	295.152	cl02603	TEA superfamily	N	 - 	TEA/ATTS domain family; TEA/ATTS domain family.  
Q#17268 - 	CGI_10013702	superfamily	243092	53	81	0.00141587	33.4796	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17270 - 	CGI_10013704	superfamily	245819	65	233	2.68E-25	104.969	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#17270 - 	CGI_10013704	superfamily	245819	399	557	3.24E-11	62.9819	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#17270 - 	CGI_10013704	superfamily	247743	587	743	1.79E-10	60.2912	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17271 - 	CGI_10013705	superfamily	216981	155	254	0.00380873	35.201	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#17272 - 	CGI_10013706	superfamily	247692	63	566	0	573.815	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#17273 - 	CGI_10013707	superfamily	245814	231	303	4.11E-14	68.6699	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17273 - 	CGI_10013707	superfamily	245814	574	644	1.75E-11	60.9659	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17273 - 	CGI_10013707	superfamily	245814	132	197	0.000514219	39.0095	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17276 - 	CGI_10021926	superfamily	247724	127	150	0.00256046	35.8431	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17277 - 	CGI_10021927	superfamily	247724	78	275	2.39E-27	105.949	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17278 - 	CGI_10021928	superfamily	247724	222	326	2.93E-21	89.3858	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17279 - 	CGI_10021929	superfamily	247724	85	205	7.32E-16	72.8222	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17280 - 	CGI_10021930	superfamily	247724	116	306	1.26E-33	124.054	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17281 - 	CGI_10021931	superfamily	247725	1357	1493	6.84E-77	252.2	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#17281 - 	CGI_10021931	superfamily	243096	1191	1357	1.22E-30	121.251	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#17281 - 	CGI_10021931	superfamily	243054	840	1071	1.20E-10	62.078	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#17281 - 	CGI_10021931	superfamily	247069	693	839	4.87E-10	59.6646	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#17282 - 	CGI_10021932	superfamily	247905	808	937	7.57E-30	118.109	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#17282 - 	CGI_10021932	superfamily	247805	512	661	4.25E-23	98.9487	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#17282 - 	CGI_10021932	superfamily	248013	407	459	3.31E-06	47.2587	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#17282 - 	CGI_10021932	superfamily	248013	313	380	7.08E-05	43.4067	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#17282 - 	CGI_10021932	superfamily	207699	2256	2299	5.72E-12	63.8523	cl02688	BRK superfamily	 - 	 - 	BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.
Q#17282 - 	CGI_10021932	superfamily	207699	2181	2219	1.32E-11	62.6967	cl02688	BRK superfamily	 - 	 - 	BRK domain; The function of this domain is unknown. It is often found associated with helicases and transcription factors.
Q#17283 - 	CGI_10021933	superfamily	202014	498	695	2.42E-65	219.21	cl03387	RB_A superfamily	 - 	 - 	Retinoblastoma-associated protein A domain; This domain has the cyclin fold as predicted.
Q#17283 - 	CGI_10021933	superfamily	221325	64	207	8.59E-46	162.486	cl13385	DUF3452 superfamily	 - 	 - 	"Domain of unknown function (DUF3452); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with pfam01858, pfam01857. This domain has a single completely conserved residue W that may be functionally important."
Q#17283 - 	CGI_10021933	superfamily	216744	812	849	1.76E-08	53.9245	cl18378	RB_B superfamily	N	 - 	"Retinoblastoma-associated protein B domain; The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B domain. The B domain has a cyclin fold."
Q#17284 - 	CGI_10021934	superfamily	247787	29	191	3.20E-33	120.381	cl17233	RecA-like_NTPases superfamily	C	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#17288 - 	CGI_10021938	superfamily	247724	7	178	5.86E-119	337.209	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17289 - 	CGI_10021939	superfamily	247856	128	176	2.63E-07	47.5425	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17289 - 	CGI_10021939	superfamily	247856	258	306	2.63E-07	47.5425	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17289 - 	CGI_10021939	superfamily	247856	193	248	0.000369397	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17289 - 	CGI_10021939	superfamily	247856	323	378	0.000411093	37.9125	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17292 - 	CGI_10021942	superfamily	245814	185	251	1.18E-09	55.1879	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17293 - 	CGI_10021943	superfamily	221591	249	469	6.24E-58	191.98	cl13854	SUFU_C superfamily	 - 	 - 	"Suppressor of Fused Gli/Ci N terminal binding domain; This domain family is found in eukaryotes, and is typically between 192 and 219 amino acids in length. The family is found in association with pfam05076. There is a conserved HGRHFT sequence motif. This family is the C terminal domain of the Suppressor of Fused protein (Su(fu)). Su(fu) is a repressor of the Gli and Ci transcription factors of the Hedgehog signalling cascade. It functions by binding these proteins and preventing their translocation to the nucleus. The C terminal domain is only found in eukaryotic Su(fu) proteins; it is not present in bacterial homologues. The C terminal domain binds to the N terminal of Gli/Ci while the N terminal of Su(fu) binds to the C terminal of Gli/Ci. This dual binding mechanism is likely an evolutionary advancement in this signalling cascade which is not present in bacterial homologues."
Q#17293 - 	CGI_10021943	superfamily	218418	56	237	3.92E-28	109.334	cl04922	SUFU superfamily	 - 	 - 	"Suppressor of fused protein (SUFU); SUFU, encoding the human orthologue of Drosophila suppressor of fused, appears to have a conserved role in the repression of Hedgehog signaling. SUFU exerts its repressor role by physically interacting with GLI proteins in both the cytoplasm and the nucleus. SUFU has been found to be a tumour-suppressor gene that predisposes individuals to medulloblastoma by modulating the SHH signaling pathway. Genomic contextual analysis of bacterial SUFU versions revealed that they are immunity proteins against diverse nuclease toxins in polymorphic toxin systems."
Q#17294 - 	CGI_10021944	superfamily	247744	489	607	7.38E-30	115.322	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#17294 - 	CGI_10021944	superfamily	241622	264	344	1.20E-15	73.3698	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#17294 - 	CGI_10021944	superfamily	247683	365	427	3.20E-31	116.763	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17295 - 	CGI_10021945	superfamily	245201	60	332	2.39E-56	188.861	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17296 - 	CGI_10021946	superfamily	243072	165	292	6.42E-35	124.803	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17296 - 	CGI_10021946	superfamily	241584	4	98	9.71E-06	42.8687	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17296 - 	CGI_10021946	superfamily	243072	137	169	6.19E-06	42.5412	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17297 - 	CGI_10021947	superfamily	243056	500	734	1.09E-51	179.425	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#17298 - 	CGI_10021948	superfamily	142634	1051	1469	0	769.834	cl11429	RNAP_largest_subunit_C superfamily	 - 	 - 	"Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria."
Q#17298 - 	CGI_10021948	superfamily	245715	239	539	1.18E-152	477.781	cl11591	RNA_pol_Rpb1_2 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion."
Q#17298 - 	CGI_10021948	superfamily	218370	11	347	1.41E-117	378.951	cl04880	RNA_pol_Rpb1_1 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand."
Q#17298 - 	CGI_10021948	superfamily	218368	889	1072	1.97E-96	312.104	cl04878	RNA_pol_Rpb1_6 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II."
Q#17298 - 	CGI_10021948	superfamily	218361	518	685	5.09E-58	200.925	cl04873	RNA_pol_Rpb1_3 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking."
Q#17298 - 	CGI_10021948	superfamily	218372	710	816	5.03E-44	158.688	cl04881	RNA_pol_Rpb1_4 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors."
Q#17299 - 	CGI_10021949	superfamily	218390	198	254	6.06E-17	78.5113	cl04895	PARG_cat superfamily	N	 - 	"Poly (ADP-ribose) glycohydrolase (PARG); Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death."
Q#17301 - 	CGI_10021951	superfamily	151071	129	173	2.02E-19	77.9485	cl11152	APP_amyloid superfamily	 - 	 - 	"beta-amyloid precursor protein C-terminus; This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with family A4_EXTRA, pfam02177, further towards the N-terminus."
Q#17302 - 	CGI_10021952	superfamily	248458	43	461	1.18E-26	109.326	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17304 - 	CGI_10021954	superfamily	247805	655	790	1.07E-24	103.186	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#17304 - 	CGI_10021954	superfamily	247905	849	976	1.67E-11	64.1812	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#17304 - 	CGI_10021954	superfamily	247792	1874	1908	0.000572999	40.1216	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17304 - 	CGI_10021954	superfamily	243778	1028	1118	4.05E-13	68.0195	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#17304 - 	CGI_10021954	superfamily	219532	1156	1250	0.000681786	40.3754	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#17306 - 	CGI_10008957	superfamily	241874	39	333	1.17E-159	462.531	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#17308 - 	CGI_10008959	superfamily	241640	293	462	1.96E-06	46.7969	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#17309 - 	CGI_10008960	superfamily	246664	1	91	1.58E-49	165.13	cl14561	An_peroxidase_like superfamily	N	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#17310 - 	CGI_10008961	superfamily	246664	42	435	0	608.88	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#17311 - 	CGI_10008962	superfamily	245598	190	777	2.66E-119	373.98	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#17311 - 	CGI_10008962	superfamily	246669	65	170	1.08E-23	97.7184	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#17312 - 	CGI_10008963	superfamily	222366	5221	6022	0	1090.45	cl16381	E3_UbLigase_R4 superfamily	 - 	 - 	E3 ubiquitin-protein ligase UBR4; This is a family of E## ubiquitin ligase enzymes.
Q#17313 - 	CGI_10008964	superfamily	243039	718	851	2.13E-54	188.585	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#17313 - 	CGI_10008964	superfamily	241736	94	346	1.06E-95	311.221	cl00263	TFold superfamily	 - 	 - 	"Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1),  6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and share a fold-related binding site with a glutamate or glutamine residue anchoring the substrate and a lot of conserved interactions. They also share a similar oligomerization mode: several T-folds join together to form a beta(2n)alpha(n) barrel, then two barrels join together in a head-to-head fashion to made up the native enzymes. The functional enzyme is a tetramer for UO, a hexamer for PTPS, an octamer for DHNA/DHNTPE and a decamer for GTPCH-1. The substrate is located in a deep and narrow pocket at the interface between monomers. In PTPS, the active site is located at the interface of three monomers, two from one trimer and one from the other trimer. In GTPCH-1, it is also located at the interface of three subunits, two from one pentamer and one from the other pentamer. There are four equivalent active sites in UO, six in PTPS, eight in DHNA/DHNTPE and ten in GTPCH-1.   Each globular multimeric enzyme encloses a tunnel which is lined with charged residues for DHNA and UO, and with basic residues in PTPS. The N and C-terminal ends are located on one side of the T-fold while the residues involved in the catalytic activity are located at the opposite side. In PTPS, UO and DHNA/DHNTPE, the N and C-terminal extremities of the enzyme are located on the exterior side of the functional multimeric enzyme. In GTPCH-1, the extra C-terminal helix places the extremity inside the tunnel."
Q#17313 - 	CGI_10008964	superfamily	243066	1088	1184	1.56E-16	77.7312	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#17313 - 	CGI_10008964	superfamily	190233	447	500	2.52E-07	49.7602	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#17313 - 	CGI_10008964	superfamily	190233	500	558	1.20E-06	47.8342	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#17313 - 	CGI_10008964	superfamily	198867	1284	1334	0.00982479	36.1653	cl06652	BACK superfamily	C	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#17316 - 	CGI_10012280	superfamily	241600	216	428	4.34E-83	256.398	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#17316 - 	CGI_10012280	superfamily	241600	63	165	4.68E-32	121.193	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#17318 - 	CGI_10012282	superfamily	241785	1	84	6.02E-41	139.069	cl00324	Ribosomal_L3 superfamily	N	 - 	Ribosomal protein L3; Ribosomal protein L3.  
Q#17320 - 	CGI_10012284	superfamily	243035	31	152	1.50E-29	111.558	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17320 - 	CGI_10012284	superfamily	243035	174	265	5.08E-13	65.7189	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17322 - 	CGI_10012286	superfamily	238191	34	560	1.30E-111	345.086	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#17325 - 	CGI_10012289	superfamily	243051	291	453	1.29E-54	182.192	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#17325 - 	CGI_10012289	superfamily	245835	71	281	0.00918733	36.1798	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#17326 - 	CGI_10012290	superfamily	222150	490	515	1.33E-06	46.6161	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17326 - 	CGI_10012290	superfamily	222150	518	542	7.48E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17326 - 	CGI_10012290	superfamily	222150	376	403	0.00017005	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17326 - 	CGI_10012290	superfamily	222150	463	487	0.00106088	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17326 - 	CGI_10012290	superfamily	222150	406	431	0.00242807	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17327 - 	CGI_10012291	superfamily	242876	20	160	6.83E-67	202.97	cl02092	Clat_adaptor_s superfamily	 - 	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#17328 - 	CGI_10012292	superfamily	248458	12	189	4.16E-11	63.1017	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17328 - 	CGI_10012292	superfamily	248458	337	477	8.17E-08	52.7013	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17329 - 	CGI_10012293	superfamily	247675	37	325	4.85E-171	480.048	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#17332 - 	CGI_10012296	superfamily	245201	60	108	2.14E-06	48.5245	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17333 - 	CGI_10012297	superfamily	217293	1	177	1.06E-74	234.835	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17333 - 	CGI_10012297	superfamily	202474	184	410	4.13E-66	213.284	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17334 - 	CGI_10012298	superfamily	217293	26	249	1.60E-89	275.666	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17334 - 	CGI_10012298	superfamily	202474	256	482	2.90E-64	210.203	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17335 - 	CGI_10012299	superfamily	217293	33	259	7.60E-82	255.635	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17335 - 	CGI_10012299	superfamily	202474	266	479	8.54E-52	177.076	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17336 - 	CGI_10012300	superfamily	217293	1	222	8.28E-63	205.559	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17336 - 	CGI_10012300	superfamily	202474	229	466	2.92E-62	204.81	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17337 - 	CGI_10012301	superfamily	202474	151	406	1.82E-47	163.979	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17337 - 	CGI_10012301	superfamily	217293	28	144	2.20E-31	119.275	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17338 - 	CGI_10012302	superfamily	202474	111	332	2.34E-49	167.446	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17338 - 	CGI_10012302	superfamily	217293	2	104	1.50E-23	96.5479	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17339 - 	CGI_10012303	superfamily	217293	36	246	3.90E-77	243.309	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17339 - 	CGI_10012303	superfamily	202474	253	482	4.06E-50	172.453	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17340 - 	CGI_10012304	superfamily	217293	52	261	2.75E-85	264.11	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17340 - 	CGI_10012304	superfamily	202474	268	471	1.91E-18	83.4721	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17342 - 	CGI_10006348	superfamily	220622	31	174	2.71E-68	209.301	cl10879	Mesd superfamily	 - 	 - 	"Chaperone for wingless signalling and trafficking of LDL receptor; Mesd is a family of highly conserved proteins found from nematodes to humans. The final C-terminal residues, KEDL, are the endoplasmic reticulum retention sequence as it is an ER protein specifically required for the intracellular trafficking of members of the low-density lipoprotein family of receptors (LDLRs). The N- and C-terminal sequences are predicted to adopt a random coil conformation, with the exception of an isolated predicted helix within the N-terminal region, The central folded domain flanked by natively unstructured regions is the necessary structure for facilitating maturation of LRP6 (Low-Density Lipoprotein Receptor-Related Protein 6 Maturation)."
Q#17343 - 	CGI_10006349	superfamily	245225	17	183	5.71E-32	120.045	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17345 - 	CGI_10006351	superfamily	245225	1	146	1.15E-26	105.471	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17347 - 	CGI_10025340	superfamily	241578	272	411	2.40E-11	61.1534	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17347 - 	CGI_10025340	superfamily	241568	22	73	0.006984	34.746	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#17350 - 	CGI_10025343	superfamily	243050	63	118	8.23E-36	127.092	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#17350 - 	CGI_10025343	superfamily	243050	4	55	6.04E-34	121.766	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#17350 - 	CGI_10025343	superfamily	241599	259	317	1.13E-20	85.758	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#17352 - 	CGI_10025345	superfamily	245208	54	434	0	540.318	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#17353 - 	CGI_10025346	superfamily	241583	161	317	2.69E-91	280.63	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#17353 - 	CGI_10025346	superfamily	243048	353	549	1.19E-40	146.302	cl02471	HX superfamily	 - 	 - 	Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat.
Q#17353 - 	CGI_10025346	superfamily	216518	72	134	0.000703512	37.8949	cl18368	PG_binding_1 superfamily	 - 	 - 	Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.
Q#17355 - 	CGI_10025348	superfamily	241583	107	264	2.57E-80	247.503	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#17355 - 	CGI_10025348	superfamily	243048	316	436	1.07E-19	86.2112	cl02471	HX superfamily	N	 - 	Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat.
Q#17355 - 	CGI_10025348	superfamily	216518	18	70	1.17E-07	48.6805	cl18368	PG_binding_1 superfamily	 - 	 - 	Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.
Q#17356 - 	CGI_10025349	superfamily	191444	134	198	0.00740895	33.4517	cl05558	IL17 superfamily	N	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#17357 - 	CGI_10025350	superfamily	244083	162	258	1.39E-35	125.106	cl05417	PLA2_like superfamily	 - 	 - 	"PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers."
Q#17358 - 	CGI_10025351	superfamily	241590	289	348	3.48E-17	74.2656	cl00072	GYF superfamily	 - 	 - 	GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
Q#17360 - 	CGI_10025353	superfamily	247724	7	142	1.86E-86	254.281	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17361 - 	CGI_10025355	superfamily	215866	68	218	2.74E-49	166.732	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#17361 - 	CGI_10025355	superfamily	243212	241	370	8.51E-28	107.045	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#17362 - 	CGI_10025356	superfamily	215866	27	177	4.03E-45	154.791	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#17362 - 	CGI_10025356	superfamily	243212	200	328	4.07E-24	96.2589	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#17363 - 	CGI_10025357	superfamily	243035	97	223	1.95E-24	94.9941	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17364 - 	CGI_10025358	superfamily	243072	97	217	2.14E-36	127.115	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17365 - 	CGI_10025359	superfamily	215866	9	157	2.18E-26	101.633	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#17365 - 	CGI_10025359	superfamily	243212	180	287	2.64E-15	70.0653	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#17366 - 	CGI_10025360	superfamily	215866	7	160	1.80E-33	122.819	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#17366 - 	CGI_10025360	superfamily	243212	183	306	2.70E-15	71.9913	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#17367 - 	CGI_10025361	superfamily	241570	223	322	9.97E-07	48.8614	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#17367 - 	CGI_10025361	superfamily	241570	144	203	1.34E-06	48.4762	cl00047	CAP_ED superfamily	N	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#17367 - 	CGI_10025361	superfamily	215866	1125	1267	3.07E-37	138.997	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#17367 - 	CGI_10025361	superfamily	215866	753	899	4.94E-28	112.419	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#17367 - 	CGI_10025361	superfamily	243212	922	1051	2.64E-20	89.7105	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#17367 - 	CGI_10025361	superfamily	243212	1290	1419	5.43E-19	85.8585	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#17368 - 	CGI_10025362	superfamily	241739	117	403	4.76E-125	367.27	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#17369 - 	CGI_10025363	superfamily	243066	67	171	3.60E-19	82.6653	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#17369 - 	CGI_10025363	superfamily	198867	187	290	4.10E-08	50.8028	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#17370 - 	CGI_10025364	superfamily	247743	620	779	3.97E-13	68.3267	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17370 - 	CGI_10025364	superfamily	191262	860	1070	1.84E-78	256.376	cl18170	Lon_C superfamily	 - 	 - 	"Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops."
Q#17370 - 	CGI_10025364	superfamily	197740	144	210	9.31E-09	53.9804	cl15344	LON superfamily	C	 - 	"Found in ATP-dependent protease La (LON); N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs."
Q#17371 - 	CGI_10025365	superfamily	246669	287	423	8.82E-82	250.037	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#17371 - 	CGI_10025365	superfamily	246669	152	277	1.49E-61	197.573	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#17372 - 	CGI_10025366	superfamily	241615	79	117	0.000140044	38.6205	cl00107	LysM superfamily	 - 	 - 	"Lysine Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes."
Q#17374 - 	CGI_10025368	superfamily	247802	80	277	2.68E-118	354.141	cl17248	RIO superfamily	 - 	 - 	"RIO kinase family, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They function as non-ribosomal factors necessary for late 18S rRNA processing. RIO1 is also required for proper cell cycle progression and chromosome maintenance. The biological substrates for RIO kinases are still unknown."
Q#17374 - 	CGI_10025368	superfamily	220140	9	92	1.38E-34	126.507	cl07723	Rio2_N superfamily	 - 	 - 	"Rio2, N-terminal; Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains."
Q#17374 - 	CGI_10025368	superfamily	245622	499	572	4.57E-06	45.6782	cl11446	Rhomboid superfamily	N	 - 	"Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite."
Q#17375 - 	CGI_10025369	superfamily	217505	51	525	8.62E-117	355.014	cl04021	Serinc superfamily	 - 	 - 	Serine incorporator (Serinc); This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid. Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis.
Q#17376 - 	CGI_10025370	superfamily	244539	1249	1396	1.98E-36	139.362	cl06868	FNR_like superfamily	C	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#17376 - 	CGI_10025370	superfamily	247856	820	880	2.05E-07	50.2389	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17376 - 	CGI_10025370	superfamily	246664	1	583	0	563.461	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#17376 - 	CGI_10025370	superfamily	242267	1075	1208	1.86E-05	44.9736	cl01043	Ferric_reduct superfamily	 - 	 - 	"Ferric reductase like transmembrane component; This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease."
Q#17377 - 	CGI_10025371	superfamily	241997	10	120	1.66E-23	89.1753	cl00638	RNA_pol_Rpb4 superfamily	 - 	 - 	RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II.
Q#17378 - 	CGI_10025372	superfamily	148511	35	98	2.01E-05	41.8005	cl06134	Selenoprotein_S superfamily	NC	 - 	Selenoprotein S (SelS); This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. The function of this family is unknown.
Q#17380 - 	CGI_10025374	superfamily	243072	388	515	2.41E-28	111.321	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17381 - 	CGI_10025375	superfamily	245201	144	391	2.46E-62	207.089	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17382 - 	CGI_10025376	superfamily	241592	23	119	7.12E-44	141.704	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#17383 - 	CGI_10025377	superfamily	245335	28	277	6.13E-125	363.875	cl10571	GT_MraY-like superfamily	 - 	 - 	"Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound polyprenol phosphate, which is the initiation step of protein N-glycosylation in eukaryotes and peptidoglycan biosynthesis in bacteria. One member, D-N-acetylhexosamine 1-phosphate transferase (GPT) is a eukaryotic enzyme, which is specific for UDP-GlcNAc as donor substrate and dolichol-phosphate as the membrane bound acceptor. The bacterial members MraY, WecA, and WbpL/WbcO utilize undecaprenol phosphate as the acceptor substrate, but use different UDP-sugar donor substrates. MraY-type transferases are highly specific for UDP-N-acetylmuramate-pentapeptide, whereas WecA proteins are selective for UDP-N-acetylglucosamine (UDP-GlcNAc). The WbcO/WbpL substrate specificity has not yet been determined, but the structure of their biosynthetic endproducts implies that UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or UDPN-acetyl-D-quinosamine (UDP-QuiNAc) are used. The eukaryotic reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for N-glycosylation. The prokaryotic reactions lead to the formation of polyprenol-linked oligosaccharides involved in bacterial cell wall and peptidoglycan assembly. Archaeal and eukaryotic enzymes may use the same substrates and are evolutionarily closer than the bacterial enzyme. Archaea possess the same N-glycosylation pathway as eukaryotes. A glycosyl transferase gene Mv1751 in M. voltae encodes for the enzyme that carries out the first step in the pathway, the attachment of GlcNAc to a dolichol lipid carrier in the membrane. A lethal mutation in the alg7 (GPT) gene in Saccharomyces cerevisiae was successfully complemented with Mv1751, the archaea gene."
Q#17384 - 	CGI_10025378	superfamily	241559	26	141	7.31E-21	86.2107	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#17384 - 	CGI_10025378	superfamily	109460	213	237	4.42E-05	40.4846	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#17384 - 	CGI_10025378	superfamily	109460	294	317	6.83E-05	40.0994	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#17384 - 	CGI_10025378	superfamily	109460	334	357	0.00111481	36.6326	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#17384 - 	CGI_10025378	superfamily	109460	174	197	0.00714366	34.3214	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#17385 - 	CGI_10025379	superfamily	109460	92	116	0.000413309	38.1734	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#17385 - 	CGI_10025379	superfamily	109460	52	76	0.00739678	34.7066	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#17387 - 	CGI_10025381	superfamily	241584	310	392	2.50E-07	48.6467	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17387 - 	CGI_10025381	superfamily	245814	239	293	5.44E-07	47.4839	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17390 - 	CGI_10025384	superfamily	241572	20	168	5.05E-05	41.7581	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#17391 - 	CGI_10025385	superfamily	247692	318	880	0	654.605	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#17391 - 	CGI_10025385	superfamily	247692	990	1507	2.05E-171	528.645	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#17391 - 	CGI_10025385	superfamily	219040	11	101	1.19E-10	60.5565	cl05791	DMAP_binding superfamily	 - 	 - 	"DMAP1-binding Domain; This domain binds DMAP1, a transcriptional co-repressor."
Q#17392 - 	CGI_10025386	superfamily	248345	29	157	1.35E-30	112.753	cl17791	SAC3_GANP superfamily	 - 	 - 	"SAC3/GANP/Nin1/mts3/eIF-3 p25 family; This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits."
Q#17393 - 	CGI_10025387	superfamily	247727	52	157	1.95E-09	52.0471	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#17394 - 	CGI_10025388	superfamily	222420	390	470	0.000531482	39.1552	cl16438	DUF4199 superfamily	N	 - 	Protein of unknown function (DUF4199); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 167 and 182 amino acids in length.
Q#17394 - 	CGI_10025388	superfamily	220413	61	133	0.0083174	35.3807	cl10778	Nop25 superfamily	C	 - 	"Nucleolar protein 12 (25kDa); Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export."
Q#17395 - 	CGI_10025389	superfamily	245008	72	151	8.42E-34	119.241	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#17395 - 	CGI_10025389	superfamily	244949	181	269	1.77E-39	134.3	cl08426	AMPKBI superfamily	 - 	 - 	"5'-AMP-activated protein kinase beta subunit, interation domain; This region is found in the beta subunit of the 5'-AMP-activated protein kinase complex, and its yeast homologues Sip1, Sip2 and Gal83, which are found in the SNF1 kinase complex. This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known. The isoamylase N-terminal domain (pfam02922) is sometimes found in proteins belonging to this family."
Q#17398 - 	CGI_10025392	superfamily	243092	169	313	6.12E-20	88.9312	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17398 - 	CGI_10025392	superfamily	243074	60	107	1.08E-08	51.7385	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#17399 - 	CGI_10025393	superfamily	248458	49	227	9.89E-14	71.1909	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17400 - 	CGI_10025394	superfamily	246925	195	492	9.45E-36	135.176	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#17401 - 	CGI_10025395	superfamily	192098	334	401	2.06E-24	99.6006	cl07295	RPAP1_C superfamily	 - 	 - 	"RPAP1-like, C-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans."
Q#17401 - 	CGI_10025395	superfamily	192099	215	262	1.26E-12	64.9668	cl07296	RPAP1_N superfamily	 - 	 - 	"RPAP1-like, N-terminal; Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans."
Q#17404 - 	CGI_10025398	superfamily	247792	184	222	0.000820208	36.2696	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17405 - 	CGI_10025399	superfamily	241728	46	179	2.45E-65	200.963	cl00253	Dtyr_deacylase superfamily	 - 	 - 	D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding
Q#17406 - 	CGI_10025400	superfamily	247058	7	110	3.42E-37	128.832	cl15762	crotonase-like superfamily	N	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#17407 - 	CGI_10009407	superfamily	245818	48	205	2.72E-25	97.2427	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#17408 - 	CGI_10009408	superfamily	218331	91	228	9.63E-41	140.867	cl08427	PAP_RNA-bind superfamily	 - 	 - 	Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.
Q#17413 - 	CGI_10009415	superfamily	147539	22	172	1.46E-69	210.717	cl05128	TRAP-delta superfamily	 - 	 - 	"Translocon-associated protein, delta subunit precursor (TRAP-delta); This family consists of several eukaryotic translocon-associated protein, delta subunit precursors (TRAP-delta or SSR-delta). The exact function of this protein is unknown."
Q#17414 - 	CGI_10009416	superfamily	245835	16	93	9.51E-25	93.5998	cl12013	BAR superfamily	C	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#17416 - 	CGI_10009418	superfamily	241563	98	136	3.64E-07	47.6671	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17416 - 	CGI_10009418	superfamily	110440	522	549	0.000171117	39.6985	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#17418 - 	CGI_10009420	superfamily	243072	512	548	0.0012299	37.7483	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17419 - 	CGI_10009421	superfamily	245201	436	668	3.33E-101	313.353	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17419 - 	CGI_10009421	superfamily	247723	116	187	1.20E-28	109.779	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17419 - 	CGI_10009421	superfamily	243157	296	351	4.57E-13	66.048	cl02720	PB1 superfamily	N	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#17419 - 	CGI_10009421	superfamily	247723	17	91	1.84E-08	52.1743	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17419 - 	CGI_10009421	superfamily	247723	225	268	0.000612596	38.47	cl17169	RRM_SF superfamily	NC	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17421 - 	CGI_10011725	superfamily	184428	2	326	2.48E-62	203.26	cl14742	PRK13971 superfamily	 - 	 - 	hydroxyproline-2-epimerase; Provisional
Q#17422 - 	CGI_10011726	superfamily	220626	86	334	8.73E-54	181.665	cl18564	GpcrRhopsn4 superfamily	 - 	 - 	"Rhodopsin-like GPCR transmembrane domain; This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans. GPCRs are integral membrane receptors whose intracellular actions are mediated by signalling pathways involving G proteins and downstream secondary messengers."
Q#17425 - 	CGI_10011729	superfamily	241581	1141	1246	9.21E-13	66.641	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#17425 - 	CGI_10011729	superfamily	241596	451	510	4.83E-12	63.3871	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#17425 - 	CGI_10011729	superfamily	243107	1344	1389	5.09E-12	63.333	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#17425 - 	CGI_10011729	superfamily	216347	321	376	5.69E-09	58.7013	cl08309	Cu_amine_oxid superfamily	C	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#17425 - 	CGI_10011729	superfamily	145726	70	159	1.61E-06	47.7254	cl08353	Cu_amine_oxidN2 superfamily	 - 	 - 	"Copper amine oxidase, N2 domain; This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ)."
Q#17426 - 	CGI_10011730	superfamily	203209	51	229	3.22E-11	61.3256	cl12305	STOP superfamily	 - 	 - 	"STOP protein; Neurons contain abundant subsets of highly stable microtubules that resist de-polymerising conditions such as exposure to the cold. Stable microtubules are thought to be essential for neuronal development, maintenance, and function. STOP is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity. Additionally knowledge of STOPs function and properties may help in the treatment of neuroleptics in illnesses such as schizophrenia, currently thought to result from synaptic defects."
Q#17426 - 	CGI_10011730	superfamily	203209	217	363	0.000236107	40.9101	cl12305	STOP superfamily	N	 - 	"STOP protein; Neurons contain abundant subsets of highly stable microtubules that resist de-polymerising conditions such as exposure to the cold. Stable microtubules are thought to be essential for neuronal development, maintenance, and function. STOP is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity. Additionally knowledge of STOPs function and properties may help in the treatment of neuroleptics in illnesses such as schizophrenia, currently thought to result from synaptic defects."
Q#17427 - 	CGI_10011731	superfamily	246669	1030	1118	9.18E-08	52.8395	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#17427 - 	CGI_10011731	superfamily	247724	1665	1825	2.72E-41	152.49	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17427 - 	CGI_10011731	superfamily	248012	2307	2396	1.21E-11	64.5213	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#17427 - 	CGI_10011731	superfamily	199166	27	181	0.000318384	43.47	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#17430 - 	CGI_10011734	superfamily	242274	191	342	2.18E-09	56.3657	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#17431 - 	CGI_10011735	superfamily	243030	40	70	0.00420999	34.9155	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#17434 - 	CGI_10011739	superfamily	241563	7	45	1.05E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17438 - 	CGI_10014004	superfamily	219165	165	542	3.00E-172	495.668	cl06019	LMF1 superfamily	 - 	 - 	"Lipase maturation factor; This family of transmembrane proteins includes the lipase maturation factor, LMF1. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states. The precise role of LMF1 in lipase folding has yet to be determined."
Q#17439 - 	CGI_10014005	superfamily	241574	125	261	6.36E-57	182.808	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17439 - 	CGI_10014005	superfamily	241626	3	90	5.95E-09	52.6694	cl00125	RHOD superfamily	N	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#17442 - 	CGI_10014008	superfamily	241563	18	50	0.00156003	36.5463	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17443 - 	CGI_10014009	superfamily	241626	144	265	5.90E-57	182.034	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#17444 - 	CGI_10014010	superfamily	241626	159	281	1.34E-53	173.944	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#17445 - 	CGI_10014011	superfamily	241626	159	281	1.22E-51	168.552	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#17447 - 	CGI_10014013	superfamily	243092	62	236	0.00014185	41.5516	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17448 - 	CGI_10014014	superfamily	245847	204	365	0.000373077	39.8474	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#17449 - 	CGI_10014015	superfamily	241574	207	396	6.58E-42	150.814	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17452 - 	CGI_10014018	superfamily	241574	72	140	3.80E-05	38.8791	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17455 - 	CGI_10003733	superfamily	247743	1084	1241	4.13E-07	50.2223	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17455 - 	CGI_10003733	superfamily	247743	774	919	8.52E-05	43.2887	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17455 - 	CGI_10003733	superfamily	247743	1459	1602	0.000108958	42.9035	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17455 - 	CGI_10003733	superfamily	247743	251	316	2.55E-09	57.3052	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17455 - 	CGI_10003733	superfamily	247743	508	598	1.71E-06	48.4456	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17456 - 	CGI_10019976	superfamily	245602	330	646	1.16E-150	446.752	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#17457 - 	CGI_10019977	superfamily	216981	1083	1207	2.27E-15	75.2617	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#17457 - 	CGI_10019977	superfamily	216981	582	707	1.45E-14	72.5654	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#17458 - 	CGI_10019978	superfamily	241570	374	467	1.56E-15	74.2846	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#17464 - 	CGI_10019984	superfamily	246680	150	211	1.42E-05	41.5522	cl14633	DD_superfamily superfamily	N	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#17464 - 	CGI_10019984	superfamily	245874	1	71	1.16E-14	67.0662	cl12111	TNFR superfamily	 - 	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#17466 - 	CGI_10019986	superfamily	243146	426	478	7.17E-05	40.6195	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17466 - 	CGI_10019986	superfamily	243146	467	508	0.00695956	34.9447	cl02701	Kelch_3 superfamily	C	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17468 - 	CGI_10019988	superfamily	192581	34	68	0.00064423	34.7463	cl11073	TFIIIC_sub6 superfamily	 - 	 - 	TFIIIC subunit; This is a family of proteins subunits of TFIIIC. TFIIIC in yeast and humans is required for transcription of tRNA and 5 S RNA genes by RNA polymerase III. Yeast members of this family are fused to phosphoglycerate mutase domain.
Q#17469 - 	CGI_10019989	superfamily	243034	71	183	2.26E-08	50.8416	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#17471 - 	CGI_10019991	superfamily	241758	11	157	1.88E-26	98.5962	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#17472 - 	CGI_10019992	superfamily	243119	445	487	0.000370561	38.5689	cl02629	CBM_14 superfamily	C	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#17472 - 	CGI_10019992	superfamily	243119	233	291	0.000493198	38.1837	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#17473 - 	CGI_10019993	superfamily	243119	285	327	8.86E-05	39.7245	cl02629	CBM_14 superfamily	C	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#17473 - 	CGI_10019993	superfamily	243119	95	131	0.000982982	36.653	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#17478 - 	CGI_10019998	superfamily	241596	58	115	3.84E-12	58.3795	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#17479 - 	CGI_10019999	superfamily	218522	1	159	3.55E-51	163.271	cl05018	UPF0220 superfamily	 - 	 - 	Uncharacterized protein family (UPF0220); This family of proteins is functionally uncharacterized.
Q#17484 - 	CGI_10020005	superfamily	245847	86	226	7.05E-18	77.2117	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#17488 - 	CGI_10006435	superfamily	248264	395	554	2.14E-38	138.139	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#17488 - 	CGI_10006435	superfamily	243161	136	171	1.11E-07	49.7002	cl02739	THAP superfamily	NC	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#17488 - 	CGI_10006435	superfamily	222429	13	91	7.81E-07	47.2352	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#17488 - 	CGI_10006435	superfamily	222263	307	404	8.22E-06	44.2309	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#17489 - 	CGI_10006436	superfamily	243072	1236	1361	9.78E-38	140.211	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17489 - 	CGI_10006436	superfamily	243072	1500	1625	1.11E-36	137.13	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17489 - 	CGI_10006436	superfamily	243072	1405	1526	6.17E-36	134.819	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17489 - 	CGI_10006436	superfamily	243072	1170	1295	1.59E-35	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17489 - 	CGI_10006436	superfamily	243072	1096	1229	2.13E-23	98.6098	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17489 - 	CGI_10006436	superfamily	243072	1373	1403	1.40E-05	44.4672	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17491 - 	CGI_10006438	superfamily	241573	19	342	6.79E-113	343.93	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#17491 - 	CGI_10006438	superfamily	246669	510	631	1.01E-28	111.601	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#17491 - 	CGI_10006438	superfamily	241653	354	487	1.16E-23	97.7764	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#17492 - 	CGI_10006439	superfamily	213389	171	346	2.31E-12	65.7735	cl17092	STING_C superfamily	 - 	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#17492 - 	CGI_10006439	superfamily	213389	529	686	4.54E-12	64.6179	cl17092	STING_C superfamily	 - 	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#17493 - 	CGI_10006440	superfamily	241638	181	329	2.85E-24	96.26	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#17494 - 	CGI_10003633	superfamily	215825	56	425	6.76E-160	466.009	cl02828	Calreticulin superfamily	 - 	 - 	Calreticulin family; Calreticulin family.  
Q#17496 - 	CGI_10007607	superfamily	247068	799	892	4.04E-17	79.2797	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	476	614	2.10E-14	71.5757	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	51	142	7.04E-13	66.9533	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	1368	1460	2.72E-12	65.4125	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	379	464	2.26E-11	62.7161	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	260	359	5.87E-11	61.5605	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	1283	1355	6.58E-11	61.1753	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	155	248	2.53E-08	53.4714	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	904	995	9.99E-08	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	1007	1097	7.36E-06	46.1526	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17496 - 	CGI_10007607	superfamily	247068	1110	1198	6.33E-05	43.071	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17497 - 	CGI_10007608	superfamily	247068	484	581	2.17E-20	88.1393	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17497 - 	CGI_10007608	superfamily	247068	594	683	4.19E-17	78.5093	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17497 - 	CGI_10007608	superfamily	247068	167	319	1.35E-12	65.4125	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17497 - 	CGI_10007608	superfamily	247068	768	852	2.34E-11	61.5605	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17497 - 	CGI_10007608	superfamily	247068	338	476	4.76E-05	42.6858	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17498 - 	CGI_10007609	superfamily	247856	174	234	1.72E-10	56.7873	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17499 - 	CGI_10007610	superfamily	217324	35	155	9.14E-19	79.4149	cl03844	Folate_rec superfamily	 - 	 - 	Folate receptor family; This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anchor. The proteins contain 16 conserved cysteines that form eight disulphide bridges.
Q#17500 - 	CGI_10007611	superfamily	246723	368	553	1.13E-05	46.9127	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#17500 - 	CGI_10007611	superfamily	246723	233	368	0.000146128	43.4459	cl14813	GluZincin superfamily	C	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#17501 - 	CGI_10007612	superfamily	245819	883	1018	5.76E-55	189.327	cl11967	Nucleotidyl_cyc_III superfamily	C	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#17501 - 	CGI_10007612	superfamily	245225	28	434	1.90E-103	331.988	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17501 - 	CGI_10007612	superfamily	245201	565	810	3.21E-42	156.157	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17502 - 	CGI_10007613	superfamily	241584	26	118	7.03E-11	56.7359	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17506 - 	CGI_10003077	superfamily	219026	9	283	6.80E-90	271.025	cl05768	GPI2 superfamily	 - 	 - 	"Phosphatidylinositol N-acetylglucosaminyltransferase; Glycosylphosphatidylinositol (GPI) represents an important anchoring molecule for cell surface proteins. The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to phosphatidylinositol (PI). This step involves products of three or four genes in both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively."
Q#17508 - 	CGI_10003079	superfamily	213389	137	302	6.94E-56	182.489	cl17092	STING_C superfamily	 - 	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#17510 - 	CGI_10004850	superfamily	217293	26	162	3.97E-31	113.882	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17512 - 	CGI_10004852	superfamily	245608	15	215	2.61E-75	228.737	cl11421	FAA_hydrolase superfamily	 - 	 - 	"Fumarylacetoacetate (FAA) hydrolase family; This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase, encoded by mhpD in E. coli, is involved in the phenylpropionic acid pathway of E. coli and catalyzes the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli is involved in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida is a 4-Oxalocrotonate decarboxylase."
Q#17519 - 	CGI_10004859	superfamily	109845	111	150	3.80E-09	48.9191	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#17519 - 	CGI_10004859	superfamily	109845	26	70	4.12E-05	38.1335	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#17519 - 	CGI_10004859	superfamily	109845	2	40	8.72E-05	37.3631	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#17519 - 	CGI_10004859	superfamily	109845	81	125	0.00485429	32.7407	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#17520 - 	CGI_10004860	superfamily	109845	64	103	6.20E-10	50.4599	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#17520 - 	CGI_10004860	superfamily	109845	34	78	0.000644233	33.8963	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#17521 - 	CGI_10005091	superfamily	245225	34	164	7.29E-69	217.881	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17522 - 	CGI_10005092	superfamily	245225	1	289	1.45E-97	311.099	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#17522 - 	CGI_10005092	superfamily	215648	382	622	4.16E-74	241.346	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#17522 - 	CGI_10005092	superfamily	219467	302	351	1.12E-12	63.8915	cl08456	NCD3G superfamily	 - 	 - 	"Nine Cysteines Domain of family 3 GPCR; This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins."
Q#17524 - 	CGI_10002373	superfamily	246669	11	111	8.93E-24	89.5648	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#17525 - 	CGI_10002374	superfamily	241868	295	430	6.05E-67	212.012	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#17525 - 	CGI_10002374	superfamily	243072	21	102	2.33E-16	75.1126	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17525 - 	CGI_10002374	superfamily	204192	252	280	1.21E-05	42.2162	cl07801	zf-NADH-PPase superfamily	 - 	 - 	NADH pyrophosphatase zinc ribbon domain; This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Q#17525 - 	CGI_10002374	superfamily	220167	184	249	0.0042145	35.4601	cl07800	NUDIX-like superfamily	N	 - 	"NADH pyrophosphatase-like rudimentary NUDIX domain; The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP."
Q#17526 - 	CGI_10002375	superfamily	243176	240	748	0	735.567	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#17526 - 	CGI_10002375	superfamily	243176	18	185	2.31E-90	293.743	cl02777	chaperonin_like superfamily	C	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#17530 - 	CGI_10006154	superfamily	248241	8	275	1.03E-31	122.042	cl17687	5_nucleotid superfamily	N	 - 	"5' nucleotidase family; This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5."
Q#17531 - 	CGI_10006155	superfamily	248241	7	265	7.54E-21	90.0705	cl17687	5_nucleotid superfamily	 - 	 - 	"5' nucleotidase family; This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5."
Q#17532 - 	CGI_10006156	superfamily	247743	539	682	8.78E-13	66.7859	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17532 - 	CGI_10006156	superfamily	243514	678	744	1.63E-09	56.5255	cl03749	STAT_int superfamily	N	 - 	"STAT protein, protein interaction domain; STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017."
Q#17535 - 	CGI_10008135	superfamily	242406	1	63	1.32E-06	43.7341	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#17536 - 	CGI_10008137	superfamily	241600	1	131	3.55E-31	112.334	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#17537 - 	CGI_10008138	superfamily	214781	532	620	2.72E-14	70.834	cl02747	NRF superfamily	 - 	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#17537 - 	CGI_10008138	superfamily	214781	102	190	9.81E-14	69.2932	cl02747	NRF superfamily	 - 	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#17537 - 	CGI_10008138	superfamily	226122	889	1072	0.00177894	40.4343	cl18744	NolL superfamily	N	 - 	Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]
Q#17538 - 	CGI_10020990	superfamily	241550	382	524	1.23E-92	290.692	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#17538 - 	CGI_10020990	superfamily	217810	522	709	2.09E-60	202.099	cl04341	tRNA-synt_1c_C superfamily	 - 	 - 	"tRNA synthetases class I (E and Q), anti-codon binding domain; Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln)."
Q#17538 - 	CGI_10020990	superfamily	241550	220	321	7.87E-59	200.17	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#17538 - 	CGI_10020990	superfamily	218149	3	115	2.71E-36	134.702	cl04588	tRNA_synt_1c_R1 superfamily	N	 - 	"Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1; This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function."
Q#17538 - 	CGI_10020990	superfamily	218148	116	213	2.39E-19	83.9496	cl04587	tRNA_synt_1c_R2 superfamily	 - 	 - 	"Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2; This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function."
Q#17539 - 	CGI_10020991	superfamily	243092	129	263	0.000757345	39.6256	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17539 - 	CGI_10020991	superfamily	110440	308	335	0.00932999	33.5353	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#17540 - 	CGI_10020992	superfamily	241563	102	138	7.66E-05	40.7336	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17540 - 	CGI_10020992	superfamily	110440	522	548	0.000282969	38.9281	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#17540 - 	CGI_10020992	superfamily	191851	141	252	0.00354519	37.6095	cl06708	DUF1640 superfamily	 - 	 - 	Protein of unknown function (DUF1640); This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Q#17540 - 	CGI_10020992	superfamily	110440	563	590	0.00781739	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#17541 - 	CGI_10020993	superfamily	243128	755	944	3.75E-33	129.017	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#17541 - 	CGI_10020993	superfamily	243128	959	1154	9.48E-33	127.862	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#17541 - 	CGI_10020993	superfamily	217861	1243	1334	2.22E-17	82.0386	cl04380	Upf2 superfamily	N	 - 	"Up-frameshift suppressor 2; Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay."
Q#17541 - 	CGI_10020993	superfamily	243128	400	592	9.37E-12	65.0743	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#17541 - 	CGI_10020993	superfamily	198850	40	103	6.16E-09	54.8323	cl04907	L51_S25_CI-B8 superfamily	 - 	 - 	"Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain; The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins."
Q#17543 - 	CGI_10020995	superfamily	216981	161	301	1.62E-20	87.5881	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#17544 - 	CGI_10020996	superfamily	220135	3	156	2.87E-42	153.441	cl07707	PPP4R2 superfamily	C	 - 	"PPP4R2; PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes."
Q#17545 - 	CGI_10020997	superfamily	247684	205	573	1.59E-48	174.187	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17545 - 	CGI_10020997	superfamily	247725	87	134	0.000348142	39.6444	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#17546 - 	CGI_10020998	superfamily	247068	7	104	1.71E-28	111.636	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17546 - 	CGI_10020998	superfamily	247068	216	312	3.29E-27	107.784	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17546 - 	CGI_10020998	superfamily	247068	117	209	1.50E-22	94.6877	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17546 - 	CGI_10020998	superfamily	247068	321	420	1.61E-22	94.3025	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17546 - 	CGI_10020998	superfamily	247068	429	530	2.81E-22	93.9173	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#17549 - 	CGI_10021001	superfamily	241944	5	505	0	846.707	cl00554	NAD_binding_5 superfamily	 - 	 - 	"Myo-inositol-1-phosphate synthase; This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyzes the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol. Inositol phosphates play an important role in signal transduction."
Q#17550 - 	CGI_10021002	superfamily	217293	33	243	1.06E-67	218.656	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17550 - 	CGI_10021002	superfamily	202474	268	499	9.77E-12	63.4417	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17551 - 	CGI_10021003	superfamily	247727	42	156	3.48E-13	65.9142	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#17551 - 	CGI_10021003	superfamily	247727	276	390	1.30E-12	64.3734	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#17552 - 	CGI_10021004	superfamily	245819	351	525	2.98E-50	172.764	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#17552 - 	CGI_10021004	superfamily	219526	112	256	3.15E-35	131.587	cl06648	HNOBA superfamily	C	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#17553 - 	CGI_10021005	superfamily	217252	341	452	1.68E-41	144.245	cl08372	Pyr_redox_dim superfamily	 - 	 - 	"Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases."
Q#17553 - 	CGI_10021005	superfamily	215691	171	251	1.97E-16	74.1594	cl15766	Pyr_redox superfamily	 - 	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#17553 - 	CGI_10021005	superfamily	248054	121	200	1.39E-05	44.6007	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#17554 - 	CGI_10021006	superfamily	241626	166	285	3.05E-56	180.878	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#17556 - 	CGI_10021008	superfamily	245213	317	356	9.34E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17556 - 	CGI_10021008	superfamily	245874	357	430	7.84E-05	43.1838	cl12111	TNFR superfamily	C	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#17556 - 	CGI_10021008	superfamily	245835	1092	1176	0.000549573	41.7233	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#17556 - 	CGI_10021008	superfamily	247725	7	27	0.00495958	37.5096	cl17171	PH-like superfamily	NC	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#17557 - 	CGI_10021009	superfamily	247916	128	198	5.95E-11	58.5483	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#17559 - 	CGI_10021011	superfamily	110440	910	937	0.00312807	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#17559 - 	CGI_10021011	superfamily	110440	752	777	0.00476072	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#17561 - 	CGI_10021013	superfamily	246616	12	287	2.48E-114	334.518	cl14105	MetH superfamily	 - 	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#17562 - 	CGI_10021014	superfamily	189332	19	276	5.58E-73	243.845	cl14874	Luminal_IRE1_like superfamily	 - 	 - 	"The Luminal domain, a dimerization domain, of Inositol-requiring protein 1-like proteins; The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), eukaryotic translation Initiation Factor 2-Alpha Kinase 3  (EIF2AK3), and similar proteins. IRE1 and EIF2AK3 are serine/threonine protein kinases (STKs) and are type I transmembrane proteins that are localized in the endoplasmic reticulum (ER). They are kinase receptors that are activated through the release of BiP, a chaperone bound to their luminal domains under unstressed conditions. This results in dimerization through their luminal domains, allowing trans-autophosphorylation of their kinase domains and activation. They play roles in the signaling of the unfolded protein response (UPR), which is activated when protein misfolding is detected in the ER in order to decrease the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), contains an endoribonuclease domain in its cytoplasmic side and acts as an ER stress sensor. It is the oldest and most conserved component of the UPR in eukaryotes. Its activation results in the cleavage of its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans, promoting a splicing event that enables translation into a transcription factor which activates the UPR. EIF2AK3, also called PKR-like Endoplasmic Reticulum Kinase (PERK), phosphorylates the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. It functions as the central regulator of translational control during the UPR pathway. In addition to the eIF-2 alpha subunit, EIF2AK3 also phosphorylates Nrf2, a leucine zipper transcription factor which regulates cellular redox status and promotes cell survival during the UPR."
Q#17562 - 	CGI_10021014	superfamily	245201	732	911	5.18E-29	117.599	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17562 - 	CGI_10021014	superfamily	245201	444	508	1.07E-13	70.7285	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17563 - 	CGI_10021015	superfamily	247736	26	86	1.56E-08	49.9669	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#17564 - 	CGI_10021016	superfamily	247736	25	93	3.24E-12	58.056	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#17565 - 	CGI_10021017	superfamily	247736	69	130	8.59E-12	57.2856	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#17566 - 	CGI_10021018	superfamily	246683	14	264	2.17E-78	245.108	cl14648	Aldose_epim superfamily	 - 	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#17570 - 	CGI_10006559	superfamily	241886	3	324	8.35E-111	327.594	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#17571 - 	CGI_10006560	superfamily	241886	3	327	2.48E-101	314.497	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#17571 - 	CGI_10006560	superfamily	241886	355	655	7.71E-90	284.452	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#17572 - 	CGI_10006561	superfamily	241886	1	297	8.82E-95	285.607	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#17575 - 	CGI_10002794	superfamily	247684	11	172	1.78E-44	153.202	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17576 - 	CGI_10002795	superfamily	247684	12	427	2.66E-87	278.777	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17577 - 	CGI_10002796	superfamily	242169	13	93	5.98E-13	59.8982	cl00886	Robl_LC7 superfamily	 - 	 - 	"Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role."
Q#17578 - 	CGI_10020946	superfamily	238192	1	176	1.85E-47	163.945	cl18939	Cyt_C5_DNA_methylase superfamily	C	 - 	"Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability."
Q#17578 - 	CGI_10020946	superfamily	238192	223	365	1.45E-11	63.023	cl18939	Cyt_C5_DNA_methylase superfamily	N	 - 	"Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability."
Q#17580 - 	CGI_10020948	superfamily	146263	1	98	4.10E-16	73.8779	cl04138	SK_channel superfamily	 - 	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#17580 - 	CGI_10020948	superfamily	219619	174	250	2.24E-08	50.6692	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#17580 - 	CGI_10020948	superfamily	198825	271	341	0.00545997	34.7517	cl03763	CaMBD superfamily	 - 	 - 	"Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other."
Q#17583 - 	CGI_10020951	superfamily	222150	74	99	3.96E-06	43.9197	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17583 - 	CGI_10020951	superfamily	222150	47	69	0.00973619	34.2897	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17584 - 	CGI_10020952	superfamily	246925	182	417	2.81E-05	45.4242	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#17584 - 	CGI_10020952	superfamily	246925	543	630	0.000170295	43.113	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#17585 - 	CGI_10020953	superfamily	243058	216	334	7.26E-21	88.9107	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#17585 - 	CGI_10020953	superfamily	243058	139	248	3.75E-19	83.9031	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#17585 - 	CGI_10020953	superfamily	243058	300	416	2.52E-15	73.1175	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#17586 - 	CGI_10020954	superfamily	247769	623	799	1.98E-12	65.8237	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#17586 - 	CGI_10020954	superfamily	248010	187	345	4.99E-18	82.4292	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#17586 - 	CGI_10020954	superfamily	248010	371	527	1.86E-17	80.8884	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#17587 - 	CGI_10020955	superfamily	248312	5	160	1.59E-05	41.5788	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#17588 - 	CGI_10020956	superfamily	246723	45	724	1.10E-126	392.822	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#17589 - 	CGI_10020957	superfamily	246723	120	202	1.33E-20	89.2846	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#17590 - 	CGI_10020958	superfamily	246723	6	98	8.02E-20	83.1214	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#17591 - 	CGI_10020959	superfamily	217293	24	229	1.99E-25	101.941	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17591 - 	CGI_10020959	superfamily	202474	251	287	5.93E-06	45.7225	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17592 - 	CGI_10020960	superfamily	246723	71	684	1.66E-108	343.902	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#17593 - 	CGI_10020961	superfamily	241794	9	149	4.65E-77	228.07	cl00334	Ribosomal_S9 superfamily	 - 	 - 	Ribosomal protein S9/S16; This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes.
Q#17594 - 	CGI_10020962	superfamily	241573	32	309	6.09E-43	157.108	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#17594 - 	CGI_10020962	superfamily	241653	513	661	7.58E-11	60.412	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#17595 - 	CGI_10020963	superfamily	247684	23	442	2.40E-96	302.659	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#17596 - 	CGI_10020964	superfamily	241607	224	257	7.67E-07	46.8794	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#17597 - 	CGI_10020965	superfamily	245864	34	460	2.59E-75	245.651	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#17601 - 	CGI_10020969	superfamily	242220	25	224	2.19E-59	187.416	cl00957	Translin superfamily	 - 	 - 	"Translin family; Members of this family include Translin that interacts with DNA and forms a ring around the DNA. This family also includes human translin-associated protein X, which was found to interact with translin with yeast two-hybrid screen."
Q#17602 - 	CGI_10020970	superfamily	247792	138	182	1.13E-09	53.6036	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17602 - 	CGI_10020970	superfamily	210118	198	217	0.00134915	36.16	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#17603 - 	CGI_10020971	superfamily	247755	1076	1299	2.97E-108	342.1	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#17603 - 	CGI_10020971	superfamily	248376	726	1049	1.00E-55	197.246	cl17822	MutS_III superfamily	 - 	 - 	"MutS domain III; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in."
Q#17603 - 	CGI_10020971	superfamily	216613	400	517	7.53E-39	142.328	cl03286	MutS_I superfamily	 - 	 - 	"MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in."
Q#17603 - 	CGI_10020971	superfamily	243083	65	169	3.72E-31	120.184	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#17603 - 	CGI_10020971	superfamily	218486	531	687	2.14E-11	63.1489	cl04975	MutS_II superfamily	 - 	 - 	"MutS domain II; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam01624, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. This domain corresponds to domain II in Thermus aquaticus MutS as characterized in, and has similarity resembles RNAse-H-like domains (see pfam00075)."
Q#17605 - 	CGI_10020973	superfamily	243222	44	457	0	702.464	cl02872	DHQ_Fe-ADH superfamily	 - 	 - 	"Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing  alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement.  ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H."
Q#17606 - 	CGI_10020974	superfamily	218721	293	562	2.30E-39	149.188	cl05344	TROVE superfamily	N	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#17607 - 	CGI_10020975	superfamily	241682	86	245	3.79E-84	250.522	cl00203	Ribosomal_L30_like superfamily	 - 	 - 	"Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome.  The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs.  L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea."
Q#17607 - 	CGI_10020975	superfamily	203848	14	84	4.56E-28	103.078	cl06906	Ribosomal_L30_N superfamily	 - 	 - 	Ribosomal L30 N-terminal domain; This presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018.
Q#17608 - 	CGI_10020976	superfamily	243310	1	182	2.10E-30	114.643	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#17609 - 	CGI_10020977	superfamily	243310	27	265	1.23E-78	241.374	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#17610 - 	CGI_10020978	superfamily	245206	1	244	1.32E-74	233.291	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#17611 - 	CGI_10020979	superfamily	248012	59	118	9.72E-05	37.9425	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#17614 - 	CGI_10020982	superfamily	247858	9	149	6.58E-13	62.4054	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#17616 - 	CGI_10020984	superfamily	241622	91	172	1.01E-26	98.4078	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#17616 - 	CGI_10020984	superfamily	243136	13	64	1.79E-09	50.7056	cl02672	L27 superfamily	 - 	 - 	L27 domain; The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.
Q#17617 - 	CGI_10020985	superfamily	243066	7	95	1.13E-22	93.7716	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#17617 - 	CGI_10020985	superfamily	222150	659	683	0.000198273	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17618 - 	CGI_10020986	superfamily	220097	30	113	2.11E-07	47.0133	cl08518	Phospholip_A2_3 superfamily	N	 - 	"Prokaryotic phospholipase A2; The prokaryotic phospholipase A2 domain is predominantly found in bacterial and fungal phospholipases, as well as various hypothetical and putative proteins. It enables the liberation of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments."
Q#17620 - 	CGI_10020988	superfamily	248312	4	152	2.61E-05	40.8084	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#17621 - 	CGI_10003366	superfamily	222313	63	93	0.000263286	38.7122	cl18662	Methyltransf_32 superfamily	C	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#17622 - 	CGI_10003367	superfamily	245304	41	335	1.51E-148	443.154	cl10459	Peptidases_S8_S53 superfamily	 - 	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#17622 - 	CGI_10003367	superfamily	201820	425	511	3.51E-33	123.89	cl08326	P_proprotein superfamily	 - 	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#17622 - 	CGI_10003367	superfamily	248097	773	870	1.73E-10	59.5862	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17623 - 	CGI_10003368	superfamily	246676	308	471	2.23E-29	113.594	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#17623 - 	CGI_10003368	superfamily	243146	57	107	2.40E-06	44.9727	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17623 - 	CGI_10003368	superfamily	243146	168	219	0.00559937	34.9575	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17624 - 	CGI_10000974	superfamily	245201	113	366	1.70E-14	72.184	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17625 - 	CGI_10004413	superfamily	241733	5	83	1.30E-50	158.098	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#17628 - 	CGI_10004416	superfamily	248458	32	110	1.91E-07	50.3901	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17630 - 	CGI_10005445	superfamily	243100	56	104	3.37E-06	44.2179	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#17631 - 	CGI_10005446	superfamily	242902	384	514	4.98E-16	75.8208	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#17631 - 	CGI_10005446	superfamily	246027	184	222	0.0073208	36.888	cl12560	DUF2806 superfamily	N	 - 	Protein of unknown function (DUF2806); This bacterial family of proteins has no known function.
Q#17633 - 	CGI_10005448	superfamily	216554	58	215	3.55E-46	160.723	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#17636 - 	CGI_10005451	superfamily	222150	335	358	0.00018683	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17636 - 	CGI_10005451	superfamily	246975	350	370	0.00410261	35.0153	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#17636 - 	CGI_10005451	superfamily	222150	362	386	0.00587027	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#17636 - 	CGI_10005451	superfamily	246975	321	342	0.00785722	34.2449	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#17637 - 	CGI_10003661	superfamily	245226	307	476	7.26E-28	109.312	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#17638 - 	CGI_10003662	superfamily	241563	97	138	2.49E-07	47.474	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17638 - 	CGI_10003662	superfamily	241563	48	89	7.26E-05	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17640 - 	CGI_10001374	superfamily	247724	6	145	1.38E-55	174.638	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17641 - 	CGI_10018748	superfamily	241567	51	298	4.92E-94	281.411	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#17645 - 	CGI_10018752	superfamily	219953	58	164	8.75E-25	94.5579	cl07317	DUF1777 superfamily	N	 - 	Protein of unknown function (DUF1777); This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins.
Q#17646 - 	CGI_10018753	superfamily	243061	143	243	1.98E-38	137.088	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17646 - 	CGI_10018753	superfamily	243061	362	463	6.61E-38	135.933	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17646 - 	CGI_10018753	superfamily	243061	470	570	1.04E-37	135.162	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17646 - 	CGI_10018753	superfamily	243061	35	136	4.23E-36	130.925	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17646 - 	CGI_10018753	superfamily	243061	250	350	9.32E-29	110.509	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17646 - 	CGI_10018753	superfamily	243061	579	624	1.29E-17	79.3082	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17647 - 	CGI_10018754	superfamily	241578	345	502	8.18E-39	142.045	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17647 - 	CGI_10018754	superfamily	241613	707	739	0.00187268	37.1862	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#17647 - 	CGI_10018754	superfamily	243061	124	225	7.10E-40	142.866	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17647 - 	CGI_10018754	superfamily	243061	16	117	5.98E-37	134.777	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17647 - 	CGI_10018754	superfamily	243061	230	330	2.02E-36	133.236	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17647 - 	CGI_10018754	superfamily	246918	537	588	1.60E-14	69.5379	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17647 - 	CGI_10018754	superfamily	246918	651	702	2.30E-14	69.1527	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17647 - 	CGI_10018754	superfamily	246918	594	627	3.48E-09	54.1299	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17648 - 	CGI_10018755	superfamily	241578	555	716	7.33E-41	148.979	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17648 - 	CGI_10018755	superfamily	241578	350	508	1.21E-25	105.451	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17648 - 	CGI_10018755	superfamily	241578	754	914	2.48E-21	92.7398	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17648 - 	CGI_10018755	superfamily	245213	965	1004	2.95E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17648 - 	CGI_10018755	superfamily	243061	132	232	2.11E-41	148.259	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17648 - 	CGI_10018755	superfamily	243061	24	125	1.40E-40	145.948	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17648 - 	CGI_10018755	superfamily	243061	237	339	1.20E-34	129.384	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17649 - 	CGI_10018756	superfamily	206077	535	585	1.66E-18	80.3595	cl18287	AA_permease_C superfamily	 - 	 - 	C-terminus of AA_permease; This is the C-terminus of AA-permease enzymes that is not captured by the models pfam00324 and pfam13520.
Q#17650 - 	CGI_10018757	superfamily	247792	56	95	2.10E-05	42.4328	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17650 - 	CGI_10018757	superfamily	128778	229	301	0.0078234	35.7035	cl17972	BBC superfamily	C	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#17651 - 	CGI_10018758	superfamily	217293	31	240	2.89E-50	172.047	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17651 - 	CGI_10018758	superfamily	202474	247	463	1.36E-10	59.9749	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17652 - 	CGI_10018759	superfamily	217293	532	731	9.22E-58	197.47	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17652 - 	CGI_10018759	superfamily	217293	42	250	8.57E-47	167.039	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17652 - 	CGI_10018759	superfamily	202474	257	475	1.13E-11	64.2121	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17653 - 	CGI_10018760	superfamily	217293	35	242	2.23E-61	201.322	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17653 - 	CGI_10018760	superfamily	202474	249	462	1.06E-10	59.9749	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17654 - 	CGI_10018761	superfamily	217293	37	242	5.59E-53	179.366	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#17654 - 	CGI_10018761	superfamily	202474	249	462	4.34E-12	64.2121	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#17658 - 	CGI_10018765	superfamily	241754	381	1135	0	825.26	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#17659 - 	CGI_10018766	superfamily	241622	189	279	3.08E-17	74.9106	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#17660 - 	CGI_10018767	superfamily	247829	3	276	2.01E-106	313.259	cl17275	PRTase_typeII superfamily	 - 	 - 	"Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate phosphoribosyltransferase (NAPRTase), to be used in the synthesis of NAD. QAPRTase catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide, an important step in the de novo synthesis of NAD. NAPRTase catalyses a similar reaction leading to NAMN and pyrophosphate, using nicotinic acid an PPRP as substrates, used in the NAD salvage pathway."
Q#17661 - 	CGI_10018768	superfamily	222754	61	175	1.16E-25	103.504	cl18690	SM-ATX superfamily	 - 	 - 	SM domain found in Ataxin-2; SM domain found in Ataxin-2.
Q#17661 - 	CGI_10018768	superfamily	219155	208	275	1.22E-06	47.3241	cl10004	LsmAD superfamily	 - 	 - 	LsmAD domain; This domain is found associated with Lsm domain.
Q#17662 - 	CGI_10018769	superfamily	243056	111	310	1.84E-68	216.842	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#17664 - 	CGI_10018771	superfamily	246925	1005	1139	7.57E-14	72.7733	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#17666 - 	CGI_10018773	superfamily	243066	51	155	1.14E-27	107.703	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#17666 - 	CGI_10018773	superfamily	243146	460	507	1.46E-07	48.8247	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17666 - 	CGI_10018773	superfamily	243146	498	548	4.83E-07	47.271	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17666 - 	CGI_10018773	superfamily	198867	163	256	5.29E-07	48.1064	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#17666 - 	CGI_10018773	superfamily	243146	409	460	1.33E-06	46.0123	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17666 - 	CGI_10018773	superfamily	243146	348	395	4.83E-06	44.5746	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17666 - 	CGI_10018773	superfamily	243146	310	344	0.00725934	35.1166	cl02701	Kelch_3 superfamily	N	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17668 - 	CGI_10018775	superfamily	190261	67	140	2.40E-32	119.961	cl03504	RFX_DNA_binding superfamily	 - 	 - 	RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Q#17669 - 	CGI_10018776	superfamily	244603	174	483	2.51E-63	215.651	cl07072	COG4 superfamily	 - 	 - 	COG4 transport protein; This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi an intra Golgi transport.
Q#17671 - 	CGI_10018778	superfamily	245201	25	269	5.32E-70	232.512	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17673 - 	CGI_10018780	superfamily	248097	11	125	1.49E-15	68.0606	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17674 - 	CGI_10018781	superfamily	214531	13	48	1.63E-07	49.9077	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#17674 - 	CGI_10018781	superfamily	111397	1030	1109	7.05E-07	48.8767	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#17674 - 	CGI_10018781	superfamily	214531	50	91	2.88E-05	43.3593	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#17674 - 	CGI_10018781	superfamily	248289	889	947	6.61E-05	42.4111	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#17674 - 	CGI_10018781	superfamily	215683	344	392	0.00212836	37.9199	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#17674 - 	CGI_10018781	superfamily	219525	1325	1349	0.00343995	37.3986	cl06646	GCC2_GCC3 superfamily	C	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#17674 - 	CGI_10018781	superfamily	214531	290	321	0.00679151	36.4257	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#17674 - 	CGI_10018781	superfamily	214531	376	419	0.00864785	36.0405	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#17675 - 	CGI_10018782	superfamily	248338	117	283	9.51E-12	64.93	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#17676 - 	CGI_10018783	superfamily	243077	617	673	0.00672733	35.2881	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#17678 - 	CGI_10018786	superfamily	241638	204	337	2.99E-14	68.1636	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#17679 - 	CGI_10018787	superfamily	241638	192	318	6.97E-13	63.9264	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#17680 - 	CGI_10018788	superfamily	241638	185	331	1.06E-27	105.505	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#17682 - 	CGI_10018790	superfamily	245208	44	410	0	631.811	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#17682 - 	CGI_10018790	superfamily	245208	482	537	0.00328079	38.419	cl09933	ACAD superfamily	N	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#17683 - 	CGI_10018791	superfamily	220673	12	112	1.87E-21	83.8833	cl10960	Med11 superfamily	 - 	 - 	"Mediator complex protein; Mediator is a large, modular protein complex that is conserved from yeast to human and conveys regulatory signals from DNA-binding transcription factors to RNA polymerase II. Not only are the polypeptides conserved but the structural organisation is also largely conserved. One or two subunits are either fungal or vertebral specific but Med11 is one of the subunits that is conserved from fungi to humans. Med11 appears to be necessary for the full and successful assembly of the core head sub-region."
Q#17684 - 	CGI_10004467	superfamily	247941	147	319	5.53E-11	59.8337	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#17685 - 	CGI_10004468	superfamily	241563	63	95	2.14E-05	42.2744	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17686 - 	CGI_10004469	superfamily	216112	507	874	2.13E-37	144.747	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#17686 - 	CGI_10004469	superfamily	219408	101	209	0.0061231	38.5626	cl06454	DUF1510 superfamily	C	 - 	Protein of unknown function (DUF1510); This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Q#17687 - 	CGI_10004470	superfamily	242406	4	107	2.08E-12	59.5273	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#17692 - 	CGI_10006366	superfamily	243035	60	176	9.94E-31	109.632	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17693 - 	CGI_10006367	superfamily	243035	23	100	1.41E-21	91.2121	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17694 - 	CGI_10006368	superfamily	243035	18	146	9.65E-30	107.005	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17697 - 	CGI_10006371	superfamily	243061	929	997	1.75E-18	82.775	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#17699 - 	CGI_10006373	superfamily	242274	47	330	1.93E-114	337.007	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#17700 - 	CGI_10006374	superfamily	243058	341	433	5.48E-05	41.5312	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#17701 - 	CGI_10004962	superfamily	199011	465	539	5.66E-36	129.597	cl11064	BHD_3 superfamily	 - 	 - 	Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds to DNA.
Q#17701 - 	CGI_10004962	superfamily	245491	403	458	1.26E-18	80.8428	cl11063	BHD_2 superfamily	 - 	 - 	Rad4 beta-hairpin domain 2; This short domain is found in the Rad4 protein. This domain binds to DNA.
Q#17701 - 	CGI_10004962	superfamily	245490	349	400	3.49E-18	79.5765	cl11062	BHD_1 superfamily	 - 	 - 	Rad4 beta-hairpin domain 1; This short domain is found in the Rad4 protein. This domain binds to DNA.
Q#17701 - 	CGI_10004962	superfamily	217753	266	343	5.90E-15	72.4162	cl10615	Rad4 superfamily	N	 - 	Rad4 transglutaminase-like domain; Rad4 transglutaminase-like domain.  
Q#17701 - 	CGI_10004962	superfamily	247916	85	152	0.00311759	36.6098	cl17362	Transglut_core superfamily	C	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#17702 - 	CGI_10004963	superfamily	241896	163	325	2.40E-77	247.05	cl00483	UDG_like superfamily	 - 	 - 	"Uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDG) catalyzes the removal of uracil from DNA, which initiates the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. At least five UDG families have been characterized so far; these families share similar overall folds and common active site motifs. They demonstrate different substrate specificities, but often the function of one enzyme can be complemented by the other. Family 1 enzymes are active against uracil in both ssDNA and dsDNA, and recognize uracil explicitly in an extrahelical conformation via a combination of protein and bound-water interactions. Family 2 enzymes are mismatch specific and explicitly recognize the widowed guanine on the complementary strand, rather than the extrahelical scissile pyrimidine. This allows a broader specificity so that some Family 2 enzymes can excise uracil as well as 3, N(4)-ethenocytosine from mismatches with guanine. A Family 3 UDG from human was first characterized to remove Uracil from ssDNA, hence the name hSMUG (single-strand-selective monofunctional uracil-DNA glycosylase). However, subsequent research has shown that hSMUG1 and its rat ortholog can remove uracil and its oxidized pyrimidine derivatives from both, ssDNA and dsDNA. Enzymes in Families 4 and 5 are both thermostable. Family 4 enzymes specifically recognize uracil in a manner similar to human UDG (Family 1), rather than guanine in the complementary strand DNA, as does E. coli MUG (Family 2). These results suggest that the mechanism by which Family 4 UDGs remove uracils from DNA is similar to that of Family 1 enzyme. Although Family 5 enzymes are close relatives of Family 4, they show different substrate specificities."
Q#17703 - 	CGI_10004964	superfamily	248338	21	210	3.31E-13	66.856	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#17704 - 	CGI_10004965	superfamily	222058	166	230	3.66E-06	44.1449	cl16248	DUF4098 superfamily	 - 	 - 	Domain of unknown function (DUF4098); This domain is a C-terminal repeat found in many bacterial species.
Q#17705 - 	CGI_10004966	superfamily	241578	316	473	5.97E-27	110.733	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17705 - 	CGI_10004966	superfamily	245213	1916	1953	9.19E-10	57.2614	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1763	1800	2.05E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1840	1876	6.60E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	2228	2263	7.19E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1802	1837	4.54E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	2195	2225	8.42E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1350	1384	2.86E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	2080	2113	5.00E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1644	1679	6.26E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1269	1303	7.13E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1569	1605	8.36E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1879	1913	0.000367565	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1387	1420	0.000446468	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	1231	1266	0.0041255	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	245213	2117	2151	0.00555089	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17705 - 	CGI_10004966	superfamily	149481	3	269	4.11E-41	155.261	cl07163	CLCA_N superfamily	 - 	 - 	Calcium-activated chloride channel; The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells and has four or five putative transmembrane regions. Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors. The domain described here is found at the N-terminus of CLCAs.
Q#17705 - 	CGI_10004966	superfamily	150094	503	677	2.37E-25	106.69	cl09605	DUF1973 superfamily	 - 	 - 	Domain of unknown function (DUF1973); Members of his family of functionally uncharacterized domains are found in various eukaryotic calcium-dependent chloride channels.
Q#17708 - 	CGI_10001635	superfamily	247724	127	287	0.000360241	39.362	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#17708 - 	CGI_10001635	superfamily	242902	25	75	3.42E-10	56.8715	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#17710 - 	CGI_10001788	superfamily	248019	2	155	1.16E-20	91.485	cl17465	DAGK_cat superfamily	NC	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#17714 - 	CGI_10001440	superfamily	247744	2	150	5.28E-27	104.56	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#17714 - 	CGI_10001440	superfamily	241802	169	373	3.87E-72	234.272	cl00342	Trp-synth-beta_II superfamily	C	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#17715 - 	CGI_10001441	superfamily	241810	355	407	8.11E-24	92.9845	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#17715 - 	CGI_10001441	superfamily	220714	54	180	5.59E-64	203.254	cl11024	Kin17_mid superfamily	 - 	 - 	"Domain of Kin17 curved DNA-binding protein; Kin17_mid is the conserved central 169 residue region of a family of Kin17 proteins. Towards the N-terminal end there is a zinc-finger domain, and in human and mouse members there is a RecA-like domain further downstream. The Kin17 protein in humans forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle."
Q#17715 - 	CGI_10001441	superfamily	205121	28	52	0.00650241	34.402	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#17716 - 	CGI_10002232	superfamily	247792	505	549	1.04E-08	52.0628	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17717 - 	CGI_10002233	superfamily	245201	20	182	8.22E-46	153.461	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17718 - 	CGI_10002234	superfamily	246908	263	361	3.44E-19	82.7674	cl15255	SH2 superfamily	C	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#17718 - 	CGI_10002234	superfamily	241563	66	102	1.79E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17718 - 	CGI_10002234	superfamily	243138	158	224	0.00748284	36.397	cl02675	DZF superfamily	NC	 - 	DZF domain; The function of this domain is unknown. It is often found associated with pfam00098 or pfam00035. This domain has been predicted to belong to the nucleotidyltransferase superfamily.
Q#17719 - 	CGI_10002235	superfamily	248097	27	133	1.05E-08	48.8006	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17722 - 	CGI_10002610	superfamily	241609	204	272	2.11E-24	93.9819	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#17722 - 	CGI_10002610	superfamily	241609	125	190	4.08E-24	93.2115	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#17723 - 	CGI_10002632	superfamily	243119	53	93	0.00458193	34.727	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#17724 - 	CGI_10002633	superfamily	248097	49	178	2.39E-19	79.6166	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17725 - 	CGI_10002706	superfamily	241584	11	83	1.32E-07	49.0319	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17727 - 	CGI_10002708	superfamily	219261	243	401	1.90E-51	177.956	cl15654	DUF1308 superfamily	N	 - 	Protein of unknown function (DUF1308); This family consists of several hypothetical eukaryotic sequences of around 400 residues in length. The function of this family is unknown.
Q#17727 - 	CGI_10002708	superfamily	219261	1	138	6.38E-32	124.028	cl15654	DUF1308 superfamily	C	 - 	Protein of unknown function (DUF1308); This family consists of several hypothetical eukaryotic sequences of around 400 residues in length. The function of this family is unknown.
Q#17728 - 	CGI_10002709	superfamily	219261	147	179	2.98E-05	41.9802	cl15654	DUF1308 superfamily	N	 - 	Protein of unknown function (DUF1308); This family consists of several hypothetical eukaryotic sequences of around 400 residues in length. The function of this family is unknown.
Q#17730 - 	CGI_10019250	superfamily	243047	38	81	1.18E-22	91.5275	cl02464	ArfGap superfamily	C	 - 	"Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs."
Q#17731 - 	CGI_10019251	superfamily	245201	49	285	3.57E-61	202.082	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17732 - 	CGI_10019252	superfamily	247757	59	274	1.49E-92	275.498	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#17733 - 	CGI_10019253	superfamily	242868	128	204	0.00103725	37.757	cl02079	YtxH superfamily	N	 - 	YtxH-like protein; This family of proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved. Proteins is this family are functionally uncharacterized.
Q#17735 - 	CGI_10019255	superfamily	245814	135	210	6.10E-13	61.5807	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17735 - 	CGI_10019255	superfamily	245814	26	112	4.77E-05	39.7961	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17737 - 	CGI_10019257	superfamily	220695	117	173	0.00318208	37.5583	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#17738 - 	CGI_10019258	superfamily	220695	38	271	3.63E-07	50.2699	cl18571	7TM_GPCR_Srx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#17738 - 	CGI_10019258	superfamily	243031	401	504	2.86E-05	44.5968	cl02425	Osteopontin superfamily	C	 - 	Osteopontin; Osteopontin.  
Q#17739 - 	CGI_10019259	superfamily	241574	1038	1266	8.82E-105	334.169	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17739 - 	CGI_10019259	superfamily	241574	1329	1561	8.63E-77	255.588	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17739 - 	CGI_10019259	superfamily	241584	560	649	1.57E-15	74.8403	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17739 - 	CGI_10019259	superfamily	241584	660	749	2.41E-08	53.6543	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17739 - 	CGI_10019259	superfamily	241584	336	438	4.47E-05	43.6391	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17739 - 	CGI_10019259	superfamily	241609	62	123	1.95E-13	68.1735	cl00100	KR superfamily	C	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#17741 - 	CGI_10019261	superfamily	247723	191	276	7.62E-27	105.808	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17741 - 	CGI_10019261	superfamily	247723	103	180	4.83E-16	74.6144	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17741 - 	CGI_10019261	superfamily	247723	31	95	0.00753888	35.5348	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17742 - 	CGI_10019262	superfamily	245201	61	310	4.48E-58	197.374	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17745 - 	CGI_10019265	superfamily	192997	305	458	6.65E-38	140.024	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#17746 - 	CGI_10019266	superfamily	241596	39	76	7.53E-10	51.8311	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#17747 - 	CGI_10019267	superfamily	247856	48	106	5.54E-10	52.5501	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17747 - 	CGI_10019267	superfamily	247856	83	140	6.31E-07	44.4609	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17748 - 	CGI_10019268	superfamily	202009	64	108	8.20E-16	67.9076	cl09271	NAC superfamily	 - 	 - 	NAC domain; NAC domain.  
Q#17749 - 	CGI_10019269	superfamily	243034	121	222	8.81E-06	44.2932	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#17749 - 	CGI_10019269	superfamily	220793	394	431	6.14E-08	49.7733	cl11153	SHNi-TPR superfamily	 - 	 - 	SHNi-TPR; SHNi-TPR family members contain a reiterated sequence motif that is an interrupted form of TPR repeat.
Q#17750 - 	CGI_10019270	superfamily	245595	515	659	3.12E-78	260.007	cl11393	Peptidase_M14_like superfamily	N	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#17750 - 	CGI_10019270	superfamily	245595	178	288	6.01E-46	168.715	cl11393	Peptidase_M14_like superfamily	C	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#17751 - 	CGI_10019271	superfamily	248313	37	100	6.87E-05	41.1406	cl17759	EamA superfamily	N	 - 	EamA-like transporter family; This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.
Q#17753 - 	CGI_10019273	superfamily	219248	40	183	9.39E-40	145.159	cl06159	POP1 superfamily	 - 	 - 	Ribonucleases P/MRP protein subunit POP1; This family represents a conserved region approximately 150 residues long located towards the N-terminus of the POP1 subunit that is common to both the RNase MRP and RNase P ribonucleoproteins (EC:3.1.26.5). These RNA-containing enzymes generate mature tRNA molecules by cleaving their 5' ends.
Q#17753 - 	CGI_10019273	superfamily	219735	563	654	3.18E-32	121.235	cl06978	POPLD superfamily	 - 	 - 	POPLD (NUC188) domain; This domain is found in POP1-like nucleolar proteins.
Q#17754 - 	CGI_10019274	superfamily	245229	62	167	4.66E-41	136.149	cl10015	YjgF_YER057c_UK114_family superfamily	 - 	 - 	"YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site."
Q#17755 - 	CGI_10019275	superfamily	241739	52	341	5.04E-123	363.05	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#17755 - 	CGI_10019275	superfamily	241738	356	437	3.81E-10	56.829	cl00266	HGTP_anticodon superfamily	C	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#17756 - 	CGI_10019276	superfamily	244539	116	294	5.61E-45	163.892	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#17756 - 	CGI_10019276	superfamily	241584	368	452	0.00105668	39.0167	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#17756 - 	CGI_10019276	superfamily	150458	54	87	1.10E-07	50.3879	cl10765	Oxidored-like superfamily	 - 	 - 	"Oxidoreductase-like protein, N-terminal; Members of this family are found in the N terminal region of various oxidoreductase like proteins. Their exact function is, as yet, unknown."
Q#17758 - 	CGI_10019278	superfamily	248097	266	387	4.86E-28	109.277	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17758 - 	CGI_10019278	superfamily	248097	123	248	2.45E-26	104.655	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17758 - 	CGI_10019278	superfamily	248097	39	113	3.58E-11	61.127	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#17760 - 	CGI_10019280	superfamily	241691	72	283	1.82E-05	43.9266	cl00213	DNA_BRE_C superfamily	C	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#17762 - 	CGI_10019282	superfamily	241585	138	172	0.000197539	39.4244	cl00066	FU superfamily	C	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#17763 - 	CGI_10021414	superfamily	241686	325	387	3.31E-16	75.3349	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#17763 - 	CGI_10021414	superfamily	241686	213	273	1.26E-15	73.7941	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#17763 - 	CGI_10021414	superfamily	241686	134	196	8.38E-14	68.4013	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#17763 - 	CGI_10021414	superfamily	241686	44	104	3.15E-12	63.7789	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#17763 - 	CGI_10021414	superfamily	241686	400	463	1.87E-05	44.1337	cl00207	HMA superfamily	 - 	 - 	"Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions."
Q#17763 - 	CGI_10021414	superfamily	215733	611	841	1.67E-58	202.025	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#17763 - 	CGI_10021414	superfamily	226572	1039	1151	4.78E-08	52.9464	cl18761	COG4087 superfamily	N	 - 	Soluble P-type ATPase [General function prediction only]
Q#17764 - 	CGI_10021415	superfamily	216897	2	65	6.25E-24	86.9665	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#17766 - 	CGI_10021417	superfamily	248469	76	161	5.53E-05	41.2015	cl17915	HAD_like superfamily	C	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#17767 - 	CGI_10021418	superfamily	241670	144	324	8.72E-19	82.4059	cl00188	BPI superfamily	 - 	 - 	"BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide."
Q#17767 - 	CGI_10021418	superfamily	241670	20	120	1.68E-05	43.9204	cl00188	BPI superfamily	C	 - 	"BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide."
Q#17768 - 	CGI_10021419	superfamily	241670	31	186	6.66E-24	96.2248	cl00188	BPI superfamily	 - 	 - 	"BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide."
Q#17768 - 	CGI_10021419	superfamily	241670	213	375	2.87E-23	96.2731	cl00188	BPI superfamily	 - 	 - 	"BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide."
Q#17769 - 	CGI_10021420	superfamily	241670	1	131	2.14E-29	111.633	cl00188	BPI superfamily	N	 - 	"BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide."
Q#17769 - 	CGI_10021420	superfamily	241670	198	384	1.97E-26	105.518	cl00188	BPI superfamily	 - 	 - 	"BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide."
Q#17770 - 	CGI_10021421	superfamily	247743	161	298	6.04E-19	84.1199	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17770 - 	CGI_10021421	superfamily	192911	415	563	9.21E-79	247.754	cl15342	MgsA_C superfamily	 - 	 - 	"MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication. Additionally, MgsA may play a role in chromosomal segregation. This is consistent with a report that MgsA co-localises with the replisome and affects chromosome segregation. This domain represents the C terminal region of MgsA."
Q#17772 - 	CGI_10021423	superfamily	241578	4	94	1.23E-20	82.3394	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17773 - 	CGI_10021424	superfamily	245226	6	193	2.68E-22	94.9797	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#17773 - 	CGI_10021424	superfamily	247723	652	725	3.74E-17	77.2123	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17773 - 	CGI_10021424	superfamily	247723	225	304	1.06E-48	165.857	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17773 - 	CGI_10021424	superfamily	247723	308	405	9.80E-46	158.509	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17773 - 	CGI_10021424	superfamily	247723	457	541	1.71E-33	124.232	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#17774 - 	CGI_10021426	superfamily	216981	87	158	9.71E-07	45.2162	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#17776 - 	CGI_10021428	superfamily	247683	419	471	3.40E-20	84.2352	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17776 - 	CGI_10021428	superfamily	247725	13	131	2.79E-23	94.9163	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#17777 - 	CGI_10021429	superfamily	241642	24	78	4.65E-07	42.5145	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#17778 - 	CGI_10021430	superfamily	217294	8	217	1.27E-89	272.785	cl08381	GatB_N superfamily	 - 	 - 	GatB/GatE catalytic domain; This domain is found in the GatB and GatE proteins.
Q#17778 - 	CGI_10021430	superfamily	248248	218	330	5.42E-12	62.1365	cl17694	GatB_Yqey superfamily	N	 - 	"GatB domain; This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB, which transamidates Glu-tRNA to Gln-tRNA."
Q#17783 - 	CGI_10002990	superfamily	243092	21	302	1.12E-19	90.472	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17784 - 	CGI_10002991	superfamily	244859	1	251	1.74E-39	139.244	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#17792 - 	CGI_10003599	superfamily	220775	4377	4946	0	574.576	cl11120	FSA_C superfamily	 - 	 - 	Fragile site-associated protein C-terminus; This is the conserved C-terminal half of the protein KIAA1109 which is the fragile site-associated protein FSA. Genome-wide-association studies showed this protein to linked to the susceptibility to coeliac disease. The protein may also be associated with polycystic kidney disease.
Q#17793 - 	CGI_10003600	superfamily	243179	164	267	2.87E-12	61.7799	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#17795 - 	CGI_10003867	superfamily	216363	102	194	4.90E-21	84.4442	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#17800 - 	CGI_10011361	superfamily	247805	33	147	3.17E-12	59.6584	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#17803 - 	CGI_10011364	superfamily	247866	6	73	4.70E-05	39.358	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#17804 - 	CGI_10011365	superfamily	245201	155	221	2.85E-05	42.2238	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17806 - 	CGI_10011368	superfamily	243035	74	147	5.85E-11	56.0889	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17807 - 	CGI_10011369	superfamily	241610	17	69	1.51E-15	64.5786	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#17810 - 	CGI_10004193	superfamily	241574	3	217	1.04E-89	287.175	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17810 - 	CGI_10004193	superfamily	241574	557	663	1.80E-27	112.294	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17810 - 	CGI_10004193	superfamily	241574	242	451	1.19E-19	89.1821	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17810 - 	CGI_10004193	superfamily	241574	743	953	3.66E-12	66.0701	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#17811 - 	CGI_10004194	superfamily	248264	126	178	2.53E-15	69.1881	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#17811 - 	CGI_10004194	superfamily	222263	43	137	1.93E-05	40.3789	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#17813 - 	CGI_10007517	superfamily	247746	16	55	0.00587499	31.5831	cl17192	ATP-synt_B superfamily	NC	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#17816 - 	CGI_10007520	superfamily	242274	3	155	1.07E-11	58.963	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#17817 - 	CGI_10007521	superfamily	245364	26	109	2.10E-23	88.9496	cl10717	CactinC_cactus superfamily	N	 - 	"Cactus-binding C-terminus of cactin protein; CactinC_cactus is the C-terminal 200 residues of the cactin protein which are necessary for the association of cactin with IkappaB-cactus as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo. Most members of the family also have a Cactin_mid domain pfam10312 further upstream."
Q#17820 - 	CGI_10015384	superfamily	246676	315	472	8.77E-31	117.831	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#17820 - 	CGI_10015384	superfamily	246671	25	152	1.35E-19	85.1672	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#17820 - 	CGI_10015384	superfamily	246710	172	311	4.68E-17	78.6236	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#17821 - 	CGI_10015385	superfamily	216897	38	88	0.00123099	36.5053	cl03463	Gal_Lectin superfamily	C	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#17822 - 	CGI_10015386	superfamily	247637	40	200	4.03E-31	124.604	cl16912	MDR superfamily	C	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#17822 - 	CGI_10015386	superfamily	242289	375	570	2.27E-21	93.9607	cl01077	SIMPL superfamily	 - 	 - 	"Protein of unknown function (DUF541); Members of this family have so far been found in bacteria and mouse SwissProt or TrEMBL entries. However possible family members have also been identified in translated rat (Genbank:AW144450) and human (Genbank:AI478629) ESTs. A mouse family member has been named SIMPL (signalling molecule that associates with mouse pelle-like kinase). SIMPL appears to facilitate and/or regulate complex formation between IRAK/mPLK (IL-1 receptor-associated kinase) and IKK (inhibitor of kappa-B kinase) containing complexes, and thus regulate NF-kappa-B activity. Separate experiments demonstrate that a mouse family member (named LaXp180) binds the Listeria monocytogenes surface protein ActA, which is a virulence factor that induces actin polymerisation. It may also bind stathmin, a protein involved in signal transduction and in the regulation of microtubule dynamics. In bacteria its function is unknown, but it is thought to be located in the periplasm or outer membrane."
Q#17822 - 	CGI_10015386	superfamily	216897	602	652	0.00236421	37.2757	cl03463	Gal_Lectin superfamily	C	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#17823 - 	CGI_10015387	superfamily	148600	1	189	1.03E-38	132.548	cl06218	DUF1352 superfamily	 - 	 - 	Protein of unknown function (DUF1352); This family consists of several hypothetical eukaryotic proteins of around 190 residues in length. The function of this family is unknown.
Q#17824 - 	CGI_10015388	superfamily	247683	1022	1071	8.53E-26	102.493	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17824 - 	CGI_10015388	superfamily	247683	927	978	3.25E-25	100.903	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17824 - 	CGI_10015388	superfamily	247856	169	233	2.38E-23	95.7494	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17824 - 	CGI_10015388	superfamily	247683	820	875	7.13E-22	91.2654	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17824 - 	CGI_10015388	superfamily	247856	394	427	3.10E-06	46.0587	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#17824 - 	CGI_10015388	superfamily	218657	674	754	0.0067657	36.5138	cl09577	THOC7 superfamily	N	 - 	Tho complex subunit 7; The Tho complex is involved in transcription elongation and mRNA export from the nucleus.
Q#17828 - 	CGI_10015392	superfamily	217939	124	302	3.77E-88	268.679	cl04432	TIP41 superfamily	 - 	 - 	TIP41-like family; The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway.
Q#17828 - 	CGI_10015392	superfamily	217939	337	399	6.57E-26	103.043	cl04432	TIP41 superfamily	N	 - 	TIP41-like family; The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway.
Q#17831 - 	CGI_10015395	superfamily	144618	53	103	0.000973543	35.1516	cl03092	PTN_MK_C superfamily	 - 	 - 	"PTN/MK heparin-binding protein family, C-terminal domain; PTN/MK heparin-binding protein family, C-terminal domain.  "
Q#17831 - 	CGI_10015395	superfamily	144618	99	141	0.00302154	33.996	cl03092	PTN_MK_C superfamily	C	 - 	"PTN/MK heparin-binding protein family, C-terminal domain; PTN/MK heparin-binding protein family, C-terminal domain.  "
Q#17832 - 	CGI_10015396	superfamily	246669	66	185	1.81E-77	233.762	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#17832 - 	CGI_10015396	superfamily	243130	241	282	4.21E-13	62.1229	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#17833 - 	CGI_10015397	superfamily	217645	96	364	3.08E-81	255.732	cl04187	DUF303 superfamily	 - 	 - 	Domain of unknown function (DUF303); Distribution of this domain seems limited to prokaryotes and viruses.
Q#17835 - 	CGI_10015400	superfamily	241754	10	557	0	604.259	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#17835 - 	CGI_10015400	superfamily	241577	714	880	4.23E-19	86.5946	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#17836 - 	CGI_10015401	superfamily	246925	1258	1503	4.12E-18	86.2553	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#17837 - 	CGI_10015402	superfamily	242909	67	228	3.70E-70	214.424	cl02156	PTPLA superfamily	 - 	 - 	"Protein tyrosine phosphatase-like protein, PTPLA; This family includes the mammalian protein tyrosine phosphatase-like protein, PTPLA. A significant variation of PTPLA from other protein tyrosine phosphatases is the presence of proline instead of catalytic arginine at the active site. It is thought that PTPLA proteins have a role in the development, differentiation, and maintenance of a number of tissue types."
Q#17839 - 	CGI_10015404	superfamily	243035	44	118	0.00027731	37.5994	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17840 - 	CGI_10015405	superfamily	248098	45	76	2.45E-05	40.2961	cl17544	U-box superfamily	C	 - 	U-box domain; This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
Q#17842 - 	CGI_10015407	superfamily	241599	102	160	2.79E-22	88.4544	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#17843 - 	CGI_10015408	superfamily	243072	22	129	1.66E-19	82.4314	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#17843 - 	CGI_10015408	superfamily	201217	196	245	3.72E-06	43.6684	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#17843 - 	CGI_10015408	superfamily	201217	144	193	0.00126965	36.3496	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#17848 - 	CGI_10027044	superfamily	241782	221	567	6.35E-148	433.937	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#17849 - 	CGI_10027045	superfamily	245206	60	282	9.45E-93	277.982	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#17850 - 	CGI_10027046	superfamily	247044	8	119	1.80E-40	133.145	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#17851 - 	CGI_10027047	superfamily	247727	37	89	3.06E-07	48.9655	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#17852 - 	CGI_10027048	superfamily	241571	65	161	1.78E-13	65.5114	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#17852 - 	CGI_10027048	superfamily	241613	170	208	1.80E-07	47.2014	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#17856 - 	CGI_10027052	superfamily	128926	27	81	1.63E-21	81.526	cl02732	DM16 superfamily	 - 	 - 	"Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc; Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc.  "
Q#17858 - 	CGI_10027054	superfamily	237847	1	216	8.47E-68	209.763	cl17178	PRK14879 superfamily	 - 	 - 	serine/threonine protein kinase; Provisional
Q#17859 - 	CGI_10027055	superfamily	241832	11	85	7.12E-13	62.9482	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#17859 - 	CGI_10027055	superfamily	243175	165	275	5.08E-08	49.7551	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#17860 - 	CGI_10027056	superfamily	148567	42	122	1.46E-16	69.9143	cl06182	Rab5ip superfamily	 - 	 - 	Rab5-interacting protein (Rab5ip); This family consists of several Rab5-interacting protein (RIP5 or Rab5ip) sequences. The ras-related GTPase rab5 is rate-limiting for homotypic early endosome fusion. Rab5ip represents a novel rab5 interacting protein that may function on endocytic vesicles as a receptor for rab5-GDP and participate in the activation of rab5.
Q#17861 - 	CGI_10027057	superfamily	243092	96	436	2.32E-30	118.592	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17862 - 	CGI_10027058	superfamily	245599	149	368	1.68E-147	424.48	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#17862 - 	CGI_10027058	superfamily	207662	55	130	2.48E-52	173.144	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#17863 - 	CGI_10027059	superfamily	241782	58	279	1.56E-27	108.968	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#17864 - 	CGI_10027060	superfamily	221913	1584	1794	2.04E-56	196.607	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#17864 - 	CGI_10027060	superfamily	216112	668	1026	7.52E-39	149.754	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#17864 - 	CGI_10027060	superfamily	222258	1529	1573	3.15E-05	45.2516	cl18656	AAA_30 superfamily	NC	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#17864 - 	CGI_10027060	superfamily	222005	1353	1412	4.11E-05	43.88	cl18632	AAA_19 superfamily	C	 - 	Part of AAA domain; Part of AAA domain.  
Q#17866 - 	CGI_10027062	superfamily	115363	289	337	3.55E-11	58.1522	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#17868 - 	CGI_10027064	superfamily	115363	4	21	0.00427234	32.729	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#17869 - 	CGI_10027065	superfamily	115363	172	222	8.91E-12	60.0781	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#17871 - 	CGI_10027067	superfamily	241578	10	77	4.57E-07	48.9237	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#17872 - 	CGI_10027068	superfamily	115363	185	225	1.29E-06	45.4406	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#17872 - 	CGI_10027068	superfamily	207713	302	366	0.000481515	37.7046	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#17874 - 	CGI_10027070	superfamily	241563	13	44	0.00123243	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17875 - 	CGI_10027071	superfamily	247792	21	71	0.000156157	36.6548	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17879 - 	CGI_10027075	superfamily	247725	106	265	2.85E-86	268.356	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#17879 - 	CGI_10027075	superfamily	206020	304	364	1.98E-15	71.385	cl18286	Y_phosphatase_m superfamily	 - 	 - 	"Myotubularin Y_phosphatase-like; This short region is highly conserved and seems to be common to many myotubularin proteins with protein tyrosine pyrophosphate activity. As the family has a number of highly conserved residues such as histidine, cysteine, glutamine and aspartate, it is possible that this represents a catalytic core of the active enzymatic part of the proteins."
Q#17881 - 	CGI_10027077	superfamily	241758	10	373	7.65E-167	474.318	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#17882 - 	CGI_10027078	superfamily	205524	43	145	1.27E-20	85.9408	cl17723	Hydrolase_6 superfamily	 - 	 - 	Haloacid dehalogenase-like hydrolase; This family is part of the HAD superfamily.
Q#17883 - 	CGI_10027079	superfamily	247941	82	231	5.86E-17	75.0648	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#17884 - 	CGI_10027080	superfamily	247941	15	164	7.07E-15	68.1312	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#17885 - 	CGI_10027081	superfamily	243859	5	97	1.09E-18	75.059	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#17886 - 	CGI_10027082	superfamily	247746	8935	9062	5.54E-10	62.0358	cl17192	ATP-synt_B superfamily	 - 	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#17891 - 	CGI_10027087	superfamily	247900	56	550	1.08E-146	436.344	cl17346	Trehalase superfamily	 - 	 - 	Trehalase; Trehalase (EC:3.2.1.28) is known to recycle trehalose to glucose. Trehalose is a physiological hallmark of heat-shock response in yeast and protects of proteins and membranes against a variety of stresses. This family is found in conjunction with pfam07492 in fungi.
Q#17894 - 	CGI_10027090	superfamily	245814	157	237	0.00695018	35.4795	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#17897 - 	CGI_10027093	superfamily	243092	90	383	6.30E-21	92.7832	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17898 - 	CGI_10027094	superfamily	243092	355	670	5.43E-21	93.5536	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17899 - 	CGI_10027095	superfamily	203428	8	319	5.26E-94	299.757	cl05703	HSL_N superfamily	 - 	 - 	"Hormone-sensitive lipase (HSL) N-terminus; This family consists of several mammalian hormone-sensitive lipase (HSL) proteins (EC:3.1.1.-). Hormone-sensitive lipase, a key enzyme in fatty acid mobilisation, overall energy homeostasis, and possibly steroidogenesis, is acutely controlled through reversible phosphorylation by catecholamines and insulin."
Q#17899 - 	CGI_10027095	superfamily	220701	325	425	2.42E-05	45.9823	cl18572	DUF2424 superfamily	NC	 - 	Protein of unknown function (DUF2424); This is a family of proteins conserved in yeasts. The function is not known.
Q#17900 - 	CGI_10027096	superfamily	245201	267	467	5.53E-41	147.768	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17900 - 	CGI_10027096	superfamily	243113	231	259	4.81E-12	61.3574	cl02621	TGF_beta_GS superfamily	 - 	 - 	Transforming growth factor beta type I GS-motif; This motif is found in the transforming growth factor beta (TGF-beta) type I which regulates cell growth and differentiation. The name of the GS motif comes from its highly conserved GSGSGLP signature in the cytoplasmic juxtamembrane region immediately preceding the protein's kinase domain. Point mutations in the GS motif modify the signaling ability of the type I receptor.
Q#17900 - 	CGI_10027096	superfamily	245201	387	554	0.000160766	42.68	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17900 - 	CGI_10027096	superfamily	245309	73	151	0.0017409	37.1121	cl10471	LU superfamily	 - 	 - 	"Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins."
Q#17905 - 	CGI_10027101	superfamily	245213	117	148	3.73E-05	42.2386	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#17905 - 	CGI_10027101	superfamily	243092	637	913	2.78E-13	70.0564	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17905 - 	CGI_10027101	superfamily	246680	535	592	0.00232116	37.5508	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#17906 - 	CGI_10027102	superfamily	243091	199	237	1.38E-06	45.5608	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#17908 - 	CGI_10027104	superfamily	241550	1	22	3.19E-06	46.4181	cl00015	nt_trans superfamily	NC	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#17908 - 	CGI_10027104	superfamily	245839	150	202	0.00260001	36.3138	cl12020	Anticodon_Ia_like superfamily	NC	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#17909 - 	CGI_10027105	superfamily	219574	371	561	2.74E-29	116.227	cl06698	DC_STAMP superfamily	 - 	 - 	"DC-STAMP-like protein; This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family."
Q#17911 - 	CGI_10027107	superfamily	242889	230	325	1.55E-10	57.2278	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#17912 - 	CGI_10027108	superfamily	198738	653	743	1.81E-25	102.731	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#17912 - 	CGI_10027108	superfamily	243066	22	121	5.89E-12	64.1757	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#17912 - 	CGI_10027108	superfamily	248312	845	959	0.00207986	39.2589	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#17913 - 	CGI_10027109	superfamily	247057	603	654	9.26E-06	44.1525	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#17913 - 	CGI_10027109	superfamily	245596	18	206	1.19E-67	226.035	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#17913 - 	CGI_10027109	superfamily	247057	533	592	6.55E-06	44.9817	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#17916 - 	CGI_10027112	superfamily	241564	82	150	3.29E-21	82.6987	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#17919 - 	CGI_10027115	superfamily	245226	48	216	5.63E-26	99.6824	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#17921 - 	CGI_10027118	superfamily	247999	38	82	1.18E-09	49.5178	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#17922 - 	CGI_10027120	superfamily	246680	2	75	3.18E-05	37.6662	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#17925 - 	CGI_10027124	superfamily	216709	132	280	5.62E-72	224.463	cl03357	Nop superfamily	 - 	 - 	Putative snoRNA binding domain; This family consists of various Pre RNA processing ribonucleoproteins. The function of the aligned region is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Nop5p (Nop58p) from yeast is the protein component of a ribonucleoprotein protein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex. Nop56p and Nop5p interact with Nop1p and are required for ribosome biogenesis. Prp31p is required for pre-mRNA splicing in S. cerevisiae.
Q#17925 - 	CGI_10027124	superfamily	208568	37	88	2.19E-27	102.585	cl06890	NOSIC superfamily	 - 	 - 	NOSIC (NUC001) domain; This is the central domain in Nop56/SIK1-like proteins.
Q#17926 - 	CGI_10002384	superfamily	241609	18	85	2.81E-27	101.686	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#17926 - 	CGI_10002384	superfamily	241609	94	162	4.97E-21	84.7371	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#17927 - 	CGI_10002385	superfamily	241609	446	520	5.49E-28	109.005	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#17927 - 	CGI_10002385	superfamily	241609	528	606	4.96E-26	103.227	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#17927 - 	CGI_10002385	superfamily	216897	721	799	2.36E-26	103.915	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#17927 - 	CGI_10002385	superfamily	243093	272	353	3.56E-17	77.9558	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17927 - 	CGI_10002385	superfamily	243093	173	250	2.90E-16	75.2594	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17927 - 	CGI_10002385	superfamily	243093	73	151	3.10E-15	72.563	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17927 - 	CGI_10002385	superfamily	243093	1	57	3.16E-11	60.6218	cl02568	WSC superfamily	N	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17928 - 	CGI_10002386	superfamily	243093	152	230	1.60E-15	72.9482	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17928 - 	CGI_10002386	superfamily	243093	546	624	1.68E-15	72.9482	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17928 - 	CGI_10002386	superfamily	243093	53	131	2.10E-15	72.563	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17928 - 	CGI_10002386	superfamily	243093	639	717	2.13E-13	66.785	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17928 - 	CGI_10002386	superfamily	243093	345	432	2.75E-12	64.0285	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17928 - 	CGI_10002386	superfamily	243093	447	525	3.46E-12	63.3182	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17928 - 	CGI_10002386	superfamily	243093	246	324	1.54E-10	58.6958	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#17933 - 	CGI_10009400	superfamily	247725	441	568	8.71E-45	159.723	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#17933 - 	CGI_10009400	superfamily	243096	231	423	9.29E-35	132.807	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#17933 - 	CGI_10009400	superfamily	241559	28	120	1.18E-13	69.2619	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#17933 - 	CGI_10009400	superfamily	241566	573	622	3.85E-07	49.0276	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#17933 - 	CGI_10009400	superfamily	246908	737	885	4.52E-30	116.624	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#17933 - 	CGI_10009400	superfamily	247683	628	683	1.58E-10	58.6325	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#17935 - 	CGI_10009402	superfamily	243146	99	147	3.16E-07	47.2839	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17935 - 	CGI_10009402	superfamily	243146	238	276	2.61E-06	44.5251	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17935 - 	CGI_10009402	superfamily	243146	201	250	4.42E-05	41.1207	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17935 - 	CGI_10009402	superfamily	243146	138	192	7.72E-05	40.5093	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17935 - 	CGI_10009402	superfamily	243146	47	93	0.000846225	37.2687	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17936 - 	CGI_10009404	superfamily	243092	218	508	2.99E-35	138.622	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17936 - 	CGI_10009404	superfamily	243056	1071	1290	3.96E-63	217.174	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#17936 - 	CGI_10009404	superfamily	247725	548	635	2.55E-22	95.426	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#17937 - 	CGI_10009405	superfamily	241600	548	752	1.55E-74	242.531	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#17938 - 	CGI_10009406	superfamily	248458	24	139	2.66E-09	57.3237	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17938 - 	CGI_10009406	superfamily	248458	339	486	0.000296839	41.5305	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17940 - 	CGI_10018093	superfamily	241976	1	110	2.23E-28	101.45	cl00606	Archease superfamily	N	 - 	"Archease protein family (MTH1598/TM1083); This archease family of proteins, has two SHS2 domains, with one inserted into another. It is predicted to be an enzyme. It is predicted to act as a chaperone in DNA/RNA metabolism."
Q#17942 - 	CGI_10018095	superfamily	216686	137	323	6.56E-36	130.521	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#17943 - 	CGI_10018096	superfamily	241563	269	301	1.67E-05	43.0447	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17943 - 	CGI_10018096	superfamily	243176	20	210	1.35E-106	337.722	cl02777	chaperonin_like superfamily	C	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#17943 - 	CGI_10018096	superfamily	245010	308	402	0.000183824	40.6791	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#17943 - 	CGI_10018096	superfamily	241563	214	245	0.00974717	35.0055	cl00034	BBOX superfamily	C	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#17944 - 	CGI_10018097	superfamily	243092	3	293	3.97E-28	113.969	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17947 - 	CGI_10018100	superfamily	241687	32	122	4.18E-19	79.7929	cl00208	RNase_T2 superfamily	N	 - 	"Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far.  This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases).  Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen."
Q#17948 - 	CGI_10018101	superfamily	241687	28	67	5.50E-07	42.8137	cl00208	RNase_T2 superfamily	C	 - 	"Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far.  This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases).  Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen."
Q#17950 - 	CGI_10018105	superfamily	243035	20	131	4.51E-30	112.713	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#17950 - 	CGI_10018105	superfamily	246918	254	305	1.17E-12	62.9895	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17950 - 	CGI_10018105	superfamily	246918	140	192	2.32E-10	56.4411	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17950 - 	CGI_10018105	superfamily	246918	311	363	6.40E-10	55.2855	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17950 - 	CGI_10018105	superfamily	246918	197	249	8.51E-10	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#17951 - 	CGI_10018106	superfamily	217280	1	190	7.10E-43	148.508	cl14953	Fe_hyd_lg_C superfamily	N	 - 	"Iron only hydrogenase large subunit, C-terminal domain; Iron only hydrogenase large subunit, C-terminal domain.  "
Q#17951 - 	CGI_10018106	superfamily	243441	203	251	3.66E-09	51.0997	cl03503	Fe_hyd_SSU superfamily	 - 	 - 	Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.
Q#17952 - 	CGI_10018107	superfamily	243092	158	397	1.06E-30	119.362	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17952 - 	CGI_10018107	superfamily	221499	54	124	4.70E-13	64.5501	cl13671	CAF1C_H4-bd superfamily	 - 	 - 	Histone-binding protein RBBP4 or subunit C of CAF1 complex; The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an alpha helix which sits just upstream of the WD40 seven-bladed beta-propeller in the human RbAp46 protein. RbAp46 folds into the beta-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six.
Q#17957 - 	CGI_10018112	superfamily	245201	456	716	7.82E-167	484.43	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#17957 - 	CGI_10018112	superfamily	241570	295	409	8.90E-27	106.256	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#17957 - 	CGI_10018112	superfamily	241570	199	278	1.49E-17	79.6774	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#17957 - 	CGI_10018112	superfamily	213458	69	121	0.000197166	39.8588	cl17044	DD_cGKI superfamily	 - 	 - 	"Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I; Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a  soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing their targeting to different subcellular compartments and intracellular substrates."
Q#17957 - 	CGI_10018112	superfamily	245597	711	760	5.07E-10	56.5999	cl11395	Pkinase_C superfamily	 - 	 - 	Protein kinase C terminal domain; Protein kinase C terminal domain.  
Q#17959 - 	CGI_10018114	superfamily	241874	14	474	1.34E-164	480.478	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#17960 - 	CGI_10018115	superfamily	247707	304	527	1.84E-119	354.643	cl17107	PMM superfamily	 - 	 - 	Eukaryotic phosphomannomutase; This enzyme EC:5.4.2.8 is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.
Q#17961 - 	CGI_10018116	superfamily	198867	160	259	5.24E-25	99.7232	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#17961 - 	CGI_10018116	superfamily	243066	48	152	5.96E-25	99.6141	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#17961 - 	CGI_10018116	superfamily	243146	385	427	3.96E-08	50.5245	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17961 - 	CGI_10018116	superfamily	243146	350	393	6.50E-05	41.1207	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#17962 - 	CGI_10018117	superfamily	247792	320	370	1.86E-07	47.3744	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17964 - 	CGI_10018119	superfamily	246748	116	415	8.67E-133	390.98	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#17969 - 	CGI_10018124	superfamily	213107	54	85	0.0005712	33.7583	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#17971 - 	CGI_10018126	superfamily	243269	15	408	2.90E-76	247.566	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#17972 - 	CGI_10018127	superfamily	248458	113	375	5.69E-13	68.4945	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#17973 - 	CGI_10018128	superfamily	247743	153	238	1.70E-11	61.7783	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#17973 - 	CGI_10018128	superfamily	209247	366	453	3.24E-15	71.3207	cl11083	ClpB_D2-small superfamily	 - 	 - 	"C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighboring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724."
Q#17974 - 	CGI_10018129	superfamily	221175	1	118	1.09E-20	86.3455	cl13200	RNA_pol_3_Rpc31 superfamily	C	 - 	"DNA-directed RNA polymerase III subunit Rpc31; RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain."
Q#17975 - 	CGI_10018130	superfamily	241643	279	317	1.25E-06	44.7575	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#17975 - 	CGI_10018130	superfamily	241645	35	64	6.58E-07	46.0658	cl00155	UBQ superfamily	N	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#17977 - 	CGI_10003770	superfamily	247792	127	167	1.28E-05	39.7364	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#17977 - 	CGI_10003770	superfamily	148004	46	90	7.24E-08	46.5489	cl05589	Ifi-6-16 superfamily	NC	 - 	Interferon-induced 6-16 family; Interferon-induced 6-16 family.  
Q#17978 - 	CGI_10012657	superfamily	221377	257	300	6.94E-05	41.6855	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#17979 - 	CGI_10012659	superfamily	245847	166	208	3.94E-13	65.0661	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#17983 - 	CGI_10012663	superfamily	245384	75	165	1.58E-30	109.285	cl10767	AD superfamily	 - 	 - 	"Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. It is an anticodon-binding domain of a prolyl-tRNA synthetase, whose PDB structure is available under the identifier 1h4q."
Q#17983 - 	CGI_10012663	superfamily	241733	7	67	1.90E-23	89.7262	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#17984 - 	CGI_10006520	superfamily	242025	41	132	6.82E-26	95.7473	cl00682	Alba superfamily	 - 	 - 	Alba; Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.
Q#17985 - 	CGI_10006521	superfamily	242047	856	957	2.96E-29	113.835	cl00720	DUF296 superfamily	 - 	 - 	"Domain of unknown function found in archaea, bacteria, and plants; This domain is found in proteins that contain AT-hook motifs, which suggests a role in DNA-binding for the proteins as a whole. Three conserved histidine residues appear to form a zinc-binding site, and the domain has been observed to form homotrimers. It co-occurs with a thioredoxin-like domain in uncharacterized cyanobacterial proteins."
Q#17985 - 	CGI_10006521	superfamily	218535	704	838	3.16E-45	163.14	cl05037	Secretogranin_V superfamily	N	 - 	"Neuroendocrine protein 7B2 precursor (Secretogranin V); The neuroendocrine protein 7B2 has a critical role in the proteolytic conversion and activation of proPC2, the enzyme responsible for the proteolytic conversion of many peptide hormone precursors. The 7B2 protein acts as an intracellular binding protein for proPC2, facilitates its maturation, and is required for its enzymatic activity. Processing of many important peptide precursors does not occur in 7B2 nulls. 7B2 null mice exhibit a unique form of Cushing's disease with many atypical symptoms, such as hypoglycemia."
Q#17985 - 	CGI_10006521	superfamily	243092	389	608	1.15E-20	93.1684	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17985 - 	CGI_10006521	superfamily	243092	50	141	2.96E-08	55.0336	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17985 - 	CGI_10006521	superfamily	243092	350	418	2.27E-07	52.3372	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#17986 - 	CGI_10006522	superfamily	243158	767	801	1.12E-07	49.8648	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17986 - 	CGI_10006522	superfamily	243158	984	1016	1.87E-06	46.398	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17986 - 	CGI_10006522	superfamily	243158	803	838	4.61E-06	45.2424	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17986 - 	CGI_10006522	superfamily	243158	693	729	0.000304361	39.8496	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17986 - 	CGI_10006522	superfamily	243158	843	873	0.000311763	39.8496	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17986 - 	CGI_10006522	superfamily	243158	949	982	0.000338097	39.8496	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17986 - 	CGI_10006522	superfamily	243158	610	641	0.00124519	37.9236	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17986 - 	CGI_10006522	superfamily	243158	736	766	0.00141605	37.9236	cl02723	Sel1 superfamily	 - 	 - 	Sel1 repeat; This short repeat is found in the Sel1 protein. It is related to TPR repeats.
Q#17988 - 	CGI_10006524	superfamily	220695	57	175	9.64E-06	46.0327	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#17989 - 	CGI_10006525	superfamily	243767	11	122	5.87E-53	167.506	cl04466	P-mevalo_kinase superfamily	 - 	 - 	"Phosphomevalonate kinase; Phosphomevalonate kinase (EC:2.7.4.2) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. This family represents the animal type of the enzyme. The other is the ERG8 type, found in plants and fungi, and some bacteria (see pfam00288)."
Q#17990 - 	CGI_10006526	superfamily	247727	63	166	3.81E-05	42.0319	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#17992 - 	CGI_10006528	superfamily	220629	138	211	7.85E-06	43.2259	cl10891	Adaptin_binding superfamily	C	 - 	"Alpha and gamma adaptin binding protein p34; p34 is a protein involved in membrane trafficking. It is known to interact with both alpha and gamma adaptin. It has been speculated that p34 may play a chaperone role such as preventing the soluble adaptors from co-assembling with soluble clathrin, or helping to remove the adaptors from the coated vesicle. Another possible function is in aiding the recruitment of soluble adaptors onto the membrane."
Q#17993 - 	CGI_10006529	superfamily	219667	72	155	6.29E-33	119.635	cl06829	Swi3 superfamily	 - 	 - 	"Replication Fork Protection Component Swi3; Replication fork pausing is required to initiate a recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1 Swi3, together with Swi1, define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks. The Swi1-Swi3 complex is required for accurate replication, fork protection and replication checkpoint signalling"
Q#17999 - 	CGI_10003902	superfamily	241600	117	335	1.13E-89	270.266	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#17999 - 	CGI_10003902	superfamily	241619	37	85	0.000131269	39.4877	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#18000 - 	CGI_10005902	superfamily	245814	784	857	9.80E-07	48.2543	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	986	1059	1.24E-06	47.8691	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	672	747	1.35E-06	47.8691	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	1086	1161	2.62E-06	47.0987	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	1295	1366	5.53E-05	42.8615	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	886	961	7.22E-05	42.4763	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	1177	1260	1.64E-10	59.4412	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	544	630	4.60E-06	46.2651	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18000 - 	CGI_10005902	superfamily	245814	452	531	2.38E-05	44.2468	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18001 - 	CGI_10005903	superfamily	243092	197	506	1.03E-15	78.916	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18001 - 	CGI_10005903	superfamily	240521	1121	1180	0.000375071	43.8348	cl18940	Syo1_like superfamily	C	 - 	"Fungal symportin 1 (syo1) and similar proteins; This family of eukaryotic proteins includes Saccharomyces cerevisiae Ydl063c and Chaetomium thermophilum Syo1, which mediate the co-import of two ribosomal proteins, Rpl5 and Rpl11 (which both interact with 5S rRNA) into the nucleus. Import precedes their association with rRNA and subsequent ribosome assembly in the nucleolus. The primary structure of syo1 is a mixture of Armadillo- (ARM, N-terminal part of syo1) and HEAT-repeats (C-terminal part of syo1)."
Q#18002 - 	CGI_10005904	superfamily	247723	78	149	2.67E-24	96.8857	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#18002 - 	CGI_10005904	superfamily	247723	195	232	1.91E-05	43.0115	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#18004 - 	CGI_10005906	superfamily	242406	676	803	3.50E-23	98.0472	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#18004 - 	CGI_10005906	superfamily	245119	36	129	5.54E-14	70.1695	cl09653	Btz superfamily	 - 	 - 	"CASC3/Barentsz eIF4AIII binding; This domain is found on CASC3 (cancer susceptibility candidate gene 3 protein) which is also known as Barentsz (Btz). CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa. The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide."
Q#18004 - 	CGI_10005906	superfamily	245119	227	263	1.22E-06	48.2132	cl09653	Btz superfamily	N	 - 	"CASC3/Barentsz eIF4AIII binding; This domain is found on CASC3 (cancer susceptibility candidate gene 3 protein) which is also known as Barentsz (Btz). CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa. The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide."
Q#18005 - 	CGI_10005907	superfamily	247856	424	482	1.34E-11	60.6393	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18006 - 	CGI_10005249	superfamily	241623	3232	3519	1.83E-92	304.17	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#18006 - 	CGI_10005249	superfamily	202180	3563	3591	0.00720323	37.4432	cl03505	FATC superfamily	 - 	 - 	"FATC domain; The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability."
Q#18007 - 	CGI_10025183	superfamily	241749	26	170	2.20E-22	88.5969	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#18012 - 	CGI_10025188	superfamily	241862	38	329	2.32E-08	53.5442	cl00437	COG0428 superfamily	 - 	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#18013 - 	CGI_10025189	superfamily	241599	170	228	5.37E-21	84.2172	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#18016 - 	CGI_10025192	superfamily	243092	52	388	8.07E-47	166.741	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18016 - 	CGI_10025192	superfamily	243092	313	602	4.97E-18	83.5384	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18020 - 	CGI_10025196	superfamily	242611	329	362	0.00765644	35.964	cl01629	TPP_enzymes superfamily	C	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#18021 - 	CGI_10025197	superfamily	220695	57	146	2.31E-05	43.7215	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18022 - 	CGI_10025198	superfamily	243184	439	541	6.48E-40	142.333	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#18022 - 	CGI_10025198	superfamily	247724	111	335	1.30E-80	257.805	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18022 - 	CGI_10025198	superfamily	243185	345	435	1.04E-22	93.7706	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#18024 - 	CGI_10025200	superfamily	217255	726	929	2.46E-63	214.155	cl03746	DDHD superfamily	 - 	 - 	"DDHD domain; The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3). This suggests that this region is involved in functionally important interactions in other members of this family."
Q#18024 - 	CGI_10025200	superfamily	247057	610	656	1.10E-17	79.3785	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#18025 - 	CGI_10025201	superfamily	218565	121	441	2.63E-105	323.515	cl05086	DUF747 superfamily	 - 	 - 	Eukaryotic membrane protein family; This family is a family of eukaryotic membrane proteins. It was previously annotated as including a putative receptor for human cytomegalovirus gH but this has has since been disputed. Analysis of the mouse Tapt1 protein (transmembrane anterior posterior transformation 1) has shown it to be involved in patterning of the vertebrate axial skeleton.
Q#18028 - 	CGI_10025204	superfamily	246751	61	349	5.22E-114	335.367	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#18029 - 	CGI_10025205	superfamily	245201	429	693	9.71E-123	369.558	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18029 - 	CGI_10025205	superfamily	238012	183	217	0.00458605	35.793	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18030 - 	CGI_10025206	superfamily	209898	399	420	0.000162178	40.4015	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#18030 - 	CGI_10025206	superfamily	209898	424	444	0.000348042	39.6942	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#18030 - 	CGI_10025206	superfamily	209898	249	270	0.00299494	36.6126	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#18030 - 	CGI_10025206	superfamily	209898	342	363	0.00376913	36.5495	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#18030 - 	CGI_10025206	superfamily	209898	226	246	0.00395043	36.2274	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#18031 - 	CGI_10025207	superfamily	243035	1	117	2.38E-23	96.9201	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18031 - 	CGI_10025207	superfamily	215647	577	813	1.90E-34	132.347	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#18031 - 	CGI_10025207	superfamily	243086	518	564	3.16E-16	74.3337	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#18031 - 	CGI_10025207	superfamily	221370	300	501	5.74E-11	62.0037	cl13441	DUF3497 superfamily	 - 	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#18031 - 	CGI_10025207	superfamily	243029	239	291	3.14E-05	42.7229	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#18032 - 	CGI_10025208	superfamily	246676	586	804	1.08E-44	161.744	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#18032 - 	CGI_10025208	superfamily	246710	461	622	2.27E-35	134.092	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#18032 - 	CGI_10025208	superfamily	246671	37	177	5.09E-28	111.746	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#18032 - 	CGI_10025208	superfamily	246710	196	359	4.49E-24	101.35	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#18035 - 	CGI_10025211	superfamily	241750	1520	1786	1.96E-62	215.9	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#18036 - 	CGI_10025212	superfamily	241578	266	428	1.21E-41	148.594	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18036 - 	CGI_10025212	superfamily	241578	75	241	3.06E-41	147.76	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18036 - 	CGI_10025212	superfamily	241578	451	609	6.09E-32	124.034	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18037 - 	CGI_10025213	superfamily	226426	5	185	0.000382914	38.6959	cl18756	COG3911 superfamily	 - 	 - 	Predicted ATPase [General function prediction only]
Q#18041 - 	CGI_10025217	superfamily	241832	1	78	2.32E-48	150.721	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18042 - 	CGI_10025218	superfamily	247743	368	517	5.27E-05	42.5183	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#18043 - 	CGI_10025219	superfamily	248020	200	375	3.61E-12	66.334	cl17466	Sulfatase superfamily	N	 - 	Sulfatase; Sulfatase.  
Q#18044 - 	CGI_10025220	superfamily	244906	147	212	4.84E-22	91.1076	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#18044 - 	CGI_10025220	superfamily	246925	251	482	0.00127638	40.0314	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#18045 - 	CGI_10025221	superfamily	241594	550	908	6.11E-116	360.727	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#18045 - 	CGI_10025221	superfamily	216033	194	289	5.27E-08	51.5656	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#18049 - 	CGI_10025225	superfamily	248289	25	83	0.00472443	32.8732	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#18051 - 	CGI_10025227	superfamily	246681	218	339	8.65E-59	187.769	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#18051 - 	CGI_10025227	superfamily	244786	29	160	2.34E-37	132.005	cl07747	Aha1_N superfamily	 - 	 - 	"Activator of Hsp90 ATPase, N-terminal; Members of this family, which are predominantly found in the protein 'Activator of Hsp90 ATPase' adopt a secondary structure consisting of an N-terminal alpha-helix leading into a four-stranded meandering antiparallel beta-sheet, followed by a C-terminal alpha-helix. The two helices are packed together, with the beta-sheet curving around them. They bind to the molecular chaperone HSP82 and stimulate its ATPase activity."
Q#18054 - 	CGI_10025230	superfamily	248097	14	121	1.15E-14	65.3642	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18057 - 	CGI_10025234	superfamily	202095	541	625	1.24E-31	120.416	cl03409	RyR superfamily	 - 	 - 	RyR domain; This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
Q#18057 - 	CGI_10025234	superfamily	202095	427	516	7.62E-30	115.409	cl03409	RyR superfamily	 - 	 - 	RyR domain; This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
Q#18057 - 	CGI_10025234	superfamily	243094	1046	1117	6.80E-19	88.8187	cl02569	RasGAP superfamily	C	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#18060 - 	CGI_10005375	superfamily	241596	740	800	1.74E-12	64.5427	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#18060 - 	CGI_10005375	superfamily	241596	824	870	1.03E-06	47.5939	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#18060 - 	CGI_10005375	superfamily	241596	897	943	1.39E-06	47.2087	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#18061 - 	CGI_10005376	superfamily	245213	75	101	2.33E-07	47.6314	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18062 - 	CGI_10005377	superfamily	243051	356	512	1.55E-48	166.014	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#18062 - 	CGI_10005377	superfamily	245814	275	327	0.00298612	35.9279	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18064 - 	CGI_10010783	superfamily	207662	327	400	3.33E-38	136.421	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#18064 - 	CGI_10010783	superfamily	245599	428	664	2.66E-98	304.056	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#18065 - 	CGI_10010784	superfamily	243058	864	978	1.01E-14	72.3471	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18065 - 	CGI_10010784	superfamily	243058	656	770	6.41E-13	66.9543	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18065 - 	CGI_10010784	superfamily	243058	946	1061	7.57E-13	66.9543	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18065 - 	CGI_10010784	superfamily	243058	564	686	9.46E-11	60.7911	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18065 - 	CGI_10010784	superfamily	243058	738	893	4.62E-09	55.3983	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18065 - 	CGI_10010784	superfamily	243058	488	597	4.30E-07	49.6203	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18066 - 	CGI_10010785	superfamily	243179	104	205	1.06E-21	86.4042	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#18068 - 	CGI_10010787	superfamily	243040	35	152	1.04E-76	241.148	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#18071 - 	CGI_10010790	superfamily	222150	65	90	0.00293578	31.5934	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18073 - 	CGI_10010792	superfamily	241644	26	149	1.00E-57	178.935	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#18074 - 	CGI_10010590	superfamily	248097	86	186	1.25E-24	95.0246	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18076 - 	CGI_10010592	superfamily	245205	94	164	1.83E-08	50.3141	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#18079 - 	CGI_10010595	superfamily	245847	200	266	4.24E-13	64.5001	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18079 - 	CGI_10010595	superfamily	241619	33	100	0.00607204	34.0949	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#18080 - 	CGI_10010596	superfamily	243161	2	47	7.69E-07	41.6518	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#18083 - 	CGI_10026468	superfamily	241770	51	187	2.91E-18	77.8212	cl00309	PRTases_typeI superfamily	 - 	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#18084 - 	CGI_10026470	superfamily	248347	63	309	4.95E-18	84.4424	cl17793	Peptidase_C69 superfamily	C	 - 	Peptidase family C69; Peptidase family C69.  
Q#18088 - 	CGI_10026475	superfamily	248264	2	67	1.07E-09	51.469	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#18089 - 	CGI_10026476	superfamily	241642	214	272	2.35E-09	52.4978	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#18089 - 	CGI_10026476	superfamily	241634	40	171	1.79E-10	57.2942	cl00143	SynN superfamily	 - 	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#18090 - 	CGI_10026477	superfamily	245847	6	126	2.63E-23	89.5381	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18091 - 	CGI_10026478	superfamily	220348	16	117	6.20E-25	92.2848	cl09902	Ctf8 superfamily	 - 	 - 	Ctf8; Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.
Q#18092 - 	CGI_10026479	superfamily	219749	53	153	8.89E-43	149.043	cl07010	DUF1716 superfamily	 - 	 - 	Eukaryotic domain of unknown function (DUF1716); This domain is found in eukaryotic proteins. A human nuclear protein with this domain is thought to have a role in apoptosis.
Q#18093 - 	CGI_10026480	superfamily	245716	545	567	1.86E-05	43.3869	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#18094 - 	CGI_10026481	superfamily	247725	599	698	1.33E-09	56.9933	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18094 - 	CGI_10026481	superfamily	247725	356	450	3.13E-05	43.6913	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18096 - 	CGI_10026483	superfamily	222462	20	235	2.12E-37	142.358	cl16486	ELYS superfamily	 - 	 - 	Nuclear pore complex assembly; ELYS (embryonic large molecule derived from yolk sac) is conserved from fungi such Aspergillus nidulans and Schizosaccharomyces pombe to human. It is important for the assembly of the nuclear pore complex.
Q#18098 - 	CGI_10026485	superfamily	247725	1	58	2.62E-11	55.7638	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18099 - 	CGI_10026486	superfamily	241578	56	240	5.90E-98	292.697	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18099 - 	CGI_10026486	superfamily	244528	343	383	3.75E-12	60.8383	cl06838	C1_4 superfamily	 - 	 - 	"TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterized by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (pfam00130)."
Q#18100 - 	CGI_10026487	superfamily	246723	69	116	1.64E-18	80.425	cl14813	GluZincin superfamily	C	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#18101 - 	CGI_10026488	superfamily	246723	48	569	1.59E-166	490.663	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#18102 - 	CGI_10026489	superfamily	243035	132	244	1.32E-20	84.2085	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18102 - 	CGI_10026489	superfamily	241619	13	78	0.000567932	36.6789	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#18103 - 	CGI_10026490	superfamily	247684	8	121	4.91E-11	59.5247	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#18104 - 	CGI_10026491	superfamily	247684	16	213	2.01E-87	265.41	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#18105 - 	CGI_10026492	superfamily	207684	6	40	4.51E-08	46.6031	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#18106 - 	CGI_10026493	superfamily	248012	284	417	3.48E-14	68.8393	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#18107 - 	CGI_10026494	superfamily	241597	54	110	3.58E-12	63.0215	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#18109 - 	CGI_10026496	superfamily	247727	160	261	1.99E-09	54.3583	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#18110 - 	CGI_10026497	superfamily	244535	173	346	9.25E-07	49.6568	cl06858	DUF1704 superfamily	N	 - 	Domain of unknown function (DUF1704); This family contains many hypothetical proteins.
Q#18112 - 	CGI_10026499	superfamily	241622	126	210	4.53E-18	81.8442	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#18112 - 	CGI_10026499	superfamily	241622	43	114	8.35E-16	75.2958	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#18112 - 	CGI_10026499	superfamily	241622	225	309	3.63E-09	55.6507	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#18113 - 	CGI_10026500	superfamily	216686	21	211	4.27E-36	128.98	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#18114 - 	CGI_10026501	superfamily	241570	378	455	9.48E-12	62.7286	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#18115 - 	CGI_10026502	superfamily	241758	15	154	7.82E-29	104.374	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#18116 - 	CGI_10026503	superfamily	247724	62	255	2.29E-46	160.779	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18117 - 	CGI_10026504	superfamily	241754	1	338	1.25E-169	502.997	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#18117 - 	CGI_10026504	superfamily	221571	648	690	9.16E-13	64.4462	cl13810	KIF1B superfamily	 - 	 - 	"Kinesin protein 1B; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00225, pfam00498. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells."
Q#18117 - 	CGI_10026504	superfamily	241581	471	528	1.22E-05	44.1243	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#18118 - 	CGI_10026505	superfamily	221913	20	221	1.00E-54	176.962	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#18119 - 	CGI_10026506	superfamily	247805	675	796	0.00024685	41.1688	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18119 - 	CGI_10026506	superfamily	221913	841	1035	2.33E-43	157.317	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#18120 - 	CGI_10026507	superfamily	243074	394	440	8.62E-10	55.5905	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#18120 - 	CGI_10026507	superfamily	243092	467	503	9.36E-05	41.1438	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18120 - 	CGI_10026507	superfamily	243092	712	784	0.000290292	42.322	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18120 - 	CGI_10026507	superfamily	243092	265	349	0.00141147	40.0108	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18121 - 	CGI_10026508	superfamily	220710	1671	2115	6.19E-90	303.055	cl11019	Apt1 superfamily	 - 	 - 	"Golgi-body localisation protein domain; This is the C-terminus of a family of proteins conserved from plants to humans. The plant members are localised to the Golgi proteins and appear to regulate membrane trafficking, as they are required for rapid vesicle accumulation at the tip of the pollen tube. The C-terminus probably contains the Golgi localisation signal and it is well-conserved."
Q#18121 - 	CGI_10026508	superfamily	220707	996	1128	1.14E-32	126.974	cl11015	Fmp27_GFWDK superfamily	 - 	 - 	RNA pol II promoter Fmp27 protein domain; Fmp27_GFWDK is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic GFWDK sequence motifs. Some members are associated with domain Fmp27_SW (pfam10305) towards the N terminus.
Q#18121 - 	CGI_10026508	superfamily	220678	777	887	0.000571394	41.0545	cl10972	DUF2405 superfamily	 - 	 - 	Domain of unknown function (DUF2405); This is a conserved region of a family of proteins conserved in fungi. The function is unknown.
Q#18122 - 	CGI_10026509	superfamily	218994	1472	2006	7.60E-54	196.411	cl09408	Med13_C superfamily	 - 	 - 	"Mediator complex subunit 13 C-terminal; Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood."
Q#18123 - 	CGI_10026510	superfamily	241733	6	75	2.18E-45	144.201	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#18126 - 	CGI_10026514	superfamily	241836	49	76	0.00219222	34.7673	cl00393	Ribosomal_L20 superfamily	NC	 - 	"Ribosomal protein L20; The ribosomal protein family L20 contains members from eubacteria, as well as their mitochondrial and plastid homologs. L20 is an assembly protein, required for the first in-vitro reconstitution step of the 50S ribosomal subunit, but does not seem to be essential for ribosome activity. L20 has been shown to partially unfold in the absence of RNA, in regions corresponding to the RNA-binding sites. L20 represses the translation of its own mRNA via specific binding to two distinct mRNA sites, in a manner similar to the L20 interaction with 23S ribosomal RNA."
Q#18127 - 	CGI_10026515	superfamily	215895	181	471	0	581.419	cl02856	6PGD superfamily	 - 	 - 	"6-phosphogluconate dehydrogenase, C-terminal domain; This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each."
Q#18127 - 	CGI_10026515	superfamily	236582	7	295	5.90E-77	245.429	cl18895	PRK09599 superfamily	 - 	 - 	6-phosphogluconate dehydrogenase-like protein; Reviewed
Q#18128 - 	CGI_10026516	superfamily	215733	380	616	1.12E-29	119.592	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#18128 - 	CGI_10026516	superfamily	222006	733	777	7.98E-06	45.6762	cl16182	Hydrolase_like2 superfamily	N	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#18128 - 	CGI_10026516	superfamily	247756	948	1015	0.00380296	39.1401	cl17202	HAD superfamily	N	 - 	haloacid dehalogenase-like hydrolase; haloacid dehalogenase-like hydrolase.  
Q#18129 - 	CGI_10026517	superfamily	247684	1	124	7.92E-26	102.741	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#18130 - 	CGI_10026518	superfamily	241619	33	100	0.00280866	32.5541	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#18131 - 	CGI_10026519	superfamily	245847	22	87	8.19E-17	71.0485	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18132 - 	CGI_10026520	superfamily	247684	1	34	6.08E-05	41.1788	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#18133 - 	CGI_10026521	superfamily	241758	26	75	3.07E-14	63.1578	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#18134 - 	CGI_10026522	superfamily	241563	62	102	0.000561023	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18134 - 	CGI_10026522	superfamily	110440	484	508	0.00446848	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18135 - 	CGI_10026523	superfamily	241758	31	176	1.23E-21	86.2698	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#18136 - 	CGI_10026524	superfamily	241749	2	115	1.14E-24	97.4565	cl00280	globin_like superfamily	C	 - 	superfamily containing globins and truncated hemoglobins
Q#18137 - 	CGI_10026525	superfamily	241797	2	301	2.04E-131	382.117	cl00337	UbiA superfamily	 - 	 - 	4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]
Q#18139 - 	CGI_10026527	superfamily	245213	972	1009	1.01E-09	56.491	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	823	857	5.40E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	1149	1184	0.000255246	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	1261	1294	0.000283476	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	896	931	0.000388248	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	939	970	0.000613643	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	1298	1332	0.00063416	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	597	632	0.00151176	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	245213	1224	1257	0.00864802	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18139 - 	CGI_10026527	superfamily	220692	66	344	2.00E-11	65.6885	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#18140 - 	CGI_10026528	superfamily	243066	78	160	2.16E-34	127.284	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#18140 - 	CGI_10026528	superfamily	243066	415	497	2.16E-34	127.284	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#18140 - 	CGI_10026528	superfamily	219619	691	760	3.67E-10	57.6027	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#18145 - 	CGI_10026533	superfamily	242575	113	214	3.80E-32	114.216	cl01548	YccV-like superfamily	 - 	 - 	Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.
Q#18146 - 	CGI_10026534	superfamily	217804	175	219	0.00015238	38.0355	cl04337	INCENP_ARK-bind superfamily	N	 - 	"Inner centromere protein, ARK binding region; This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregation with cell division in yeast."
Q#18147 - 	CGI_10026535	superfamily	241633	703	831	4.03E-36	134.324	cl00140	SNc superfamily	 - 	 - 	"Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds."
Q#18147 - 	CGI_10026535	superfamily	241633	522	666	5.75E-31	119.687	cl00140	SNc superfamily	 - 	 - 	"Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds."
Q#18147 - 	CGI_10026535	superfamily	241633	197	337	2.02E-23	98.1153	cl00140	SNc superfamily	 - 	 - 	"Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds."
Q#18147 - 	CGI_10026535	superfamily	241633	373	477	2.34E-23	97.7301	cl00140	SNc superfamily	 - 	 - 	"Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds."
Q#18147 - 	CGI_10026535	superfamily	243098	903	940	2.20E-12	63.7711	cl02573	TUDOR superfamily	C	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#18147 - 	CGI_10026535	superfamily	247724	10	170	3.01E-67	223.438	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18150 - 	CGI_10026538	superfamily	241882	590	824	2.06E-13	71.5137	cl00465	yhhT superfamily	N	 - 	"Predicted permease, member of the PurR regulon [General function prediction only]"
Q#18151 - 	CGI_10026539	superfamily	243519	23	536	0	764.06	cl03757	phosphohexomutase superfamily	 - 	 - 	"The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model."
Q#18153 - 	CGI_10026542	superfamily	241622	118	185	8.32E-10	52.236	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#18154 - 	CGI_10026543	superfamily	243540	275	499	1.11E-27	110.03	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#18156 - 	CGI_10005838	superfamily	245213	74	109	2.85E-09	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18156 - 	CGI_10005838	superfamily	245213	112	147	2.95E-09	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18156 - 	CGI_10005838	superfamily	245213	36	71	3.13E-09	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18156 - 	CGI_10005838	superfamily	245847	151	219	2.72E-11	58.3369	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18158 - 	CGI_10008594	superfamily	241874	1	533	0	710.873	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#18159 - 	CGI_10008595	superfamily	241874	24	503	0	664.649	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#18159 - 	CGI_10008595	superfamily	241874	503	719	3.69E-90	294.857	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#18160 - 	CGI_10008596	superfamily	247792	50	93	3.93E-05	36.9741	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18161 - 	CGI_10008597	superfamily	248458	102	490	1.05E-24	104.318	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18163 - 	CGI_10008599	superfamily	248458	373	513	9.35E-05	43.4565	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18163 - 	CGI_10008599	superfamily	248458	115	200	0.00194221	39.2193	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18164 - 	CGI_10008600	superfamily	241802	19	300	4.57E-88	268.398	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#18165 - 	CGI_10008601	superfamily	241802	17	58	2.16E-15	67.7094	cl00342	Trp-synth-beta_II superfamily	C	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#18166 - 	CGI_10008602	superfamily	241802	12	246	2.67E-68	216.396	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#18168 - 	CGI_10008604	superfamily	248097	60	186	1.95E-24	93.4838	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18168 - 	CGI_10008604	superfamily	150420	14	84	0.00555129	34.7111	cl18042	Jnk-SapK_ap_N superfamily	N	 - 	JNK_SAPK-associated protein-1; This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end.
Q#18169 - 	CGI_10008605	superfamily	222150	527	551	2.94E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18169 - 	CGI_10008605	superfamily	246975	514	535	0.00726751	35.0153	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#18170 - 	CGI_10008606	superfamily	245456	183	454	2.36E-165	469.757	cl10970	AP_MHD_Cterm superfamily	 - 	 - 	"C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15."
Q#18170 - 	CGI_10008606	superfamily	242876	18	142	0.00204562	37.3337	cl02092	Clat_adaptor_s superfamily	 - 	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#18171 - 	CGI_10008607	superfamily	207919	26	126	1.20E-48	153.915	cl03348	Ribosomal_L22e superfamily	 - 	 - 	Ribosomal L22e protein family; Ribosomal L22e protein family.  
Q#18172 - 	CGI_10014390	superfamily	241563	39	77	5.60E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18172 - 	CGI_10014390	superfamily	110440	506	533	0.00354108	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18173 - 	CGI_10014391	superfamily	222070	26	106	0.00601381	33.4201	cl18634	DDE_3 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#18174 - 	CGI_10014392	superfamily	247683	391	443	5.43E-26	99.7245	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#18174 - 	CGI_10014392	superfamily	245835	61	171	1.13E-10	60.0874	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#18176 - 	CGI_10014394	superfamily	247724	58	127	3.31E-10	58.7121	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18179 - 	CGI_10014397	superfamily	217437	59	170	3.71E-27	102.025	cl03944	GILT superfamily	 - 	 - 	"Gamma interferon inducible lysosomal thiol reductase (GILT); This family includes the two characterized human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences. It also contains several other eukaryotic putative proteins with similarity to GILT. The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction."
Q#18185 - 	CGI_10014403	superfamily	241567	115	212	0.000123365	40.7614	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#18186 - 	CGI_10014404	superfamily	241567	271	468	1.26E-06	48.7507	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#18186 - 	CGI_10014404	superfamily	241567	568	646	0.00271687	38.4502	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#18188 - 	CGI_10014406	superfamily	222258	490	625	2.06E-14	73.3711	cl18656	AAA_30 superfamily	N	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#18188 - 	CGI_10014406	superfamily	222209	802	880	6.48E-06	45.8549	cl18648	UvrD_C_2 superfamily	N	 - 	Family description; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Q#18191 - 	CGI_10014409	superfamily	243088	28	116	6.67E-40	135.243	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#18192 - 	CGI_10014410	superfamily	247683	147	200	3.23E-19	83.275	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#18192 - 	CGI_10014410	superfamily	247683	838	890	2.04E-17	78.0619	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#18192 - 	CGI_10014410	superfamily	247683	758	808	3.21E-15	71.8987	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#18192 - 	CGI_10014410	superfamily	247683	77	129	3.04E-19	83.2378	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#18192 - 	CGI_10014410	superfamily	247683	290	314	0.000573468	38.9733	cl17036	SH3 superfamily	C	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#18193 - 	CGI_10014411	superfamily	247805	175	340	1.34E-09	55.8064	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18194 - 	CGI_10001090	superfamily	247856	33	84	9.22E-05	36.7569	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18197 - 	CGI_10008977	superfamily	241568	214	267	5.88E-10	56.3172	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#18197 - 	CGI_10008977	superfamily	245213	273	305	4.43E-08	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18197 - 	CGI_10008977	superfamily	241568	173	210	3.30E-07	48.228	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#18197 - 	CGI_10008977	superfamily	241863	525	702	3.83E-25	103.623	cl00438	Flavodoxin_2 superfamily	 - 	 - 	Flavodoxin-like fold; This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
Q#18197 - 	CGI_10008977	superfamily	111397	70	149	1.89E-17	78.537	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#18197 - 	CGI_10008977	superfamily	111397	306	387	1.53E-06	46.5655	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#18201 - 	CGI_10008981	superfamily	198877	361	439	4.23E-43	148.913	cl06957	BING4CT superfamily	 - 	 - 	BING4CT (NUC141) domain; This C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins.
Q#18201 - 	CGI_10008981	superfamily	243092	208	330	4.07E-09	56.5744	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18207 - 	CGI_10001142	superfamily	248067	120	233	3.12E-24	96.5083	cl17513	ABC1 superfamily	 - 	 - 	"ABC1 family; This family includes ABC1 from yeast and AarF from E. coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex and E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins."
Q#18209 - 	CGI_10001170	superfamily	245606	1	66	4.58E-36	126.439	cl11410	TPP_enzyme_PYR superfamily	N	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#18209 - 	CGI_10001170	superfamily	217227	89	209	1.13E-31	113.46	cl08363	Transketolase_C superfamily	 - 	 - 	"Transketolase, C-terminal domain; The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site."
Q#18211 - 	CGI_10004779	superfamily	245201	209	500	0	545.824	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18212 - 	CGI_10004780	superfamily	222150	344	367	4.13E-06	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18212 - 	CGI_10004780	superfamily	222150	314	341	0.000199413	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18213 - 	CGI_10004781	superfamily	222150	355	378	3.20E-06	43.9197	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18213 - 	CGI_10004781	superfamily	222150	325	352	0.000140723	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18213 - 	CGI_10004781	superfamily	197676	369	391	0.00831784	34.3638	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#18214 - 	CGI_10004782	superfamily	245531	248	300	9.45E-07	45.8178	cl11158	BEN superfamily	C	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#18218 - 	CGI_10012939	superfamily	244539	65	241	3.44E-27	106.62	cl06868	FNR_like superfamily	C	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#18218 - 	CGI_10012939	superfamily	247856	17	65	2.88E-05	41.3793	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18218 - 	CGI_10012939	superfamily	203841	167	344	3.97E-24	96.2528	cl17716	NAD_binding_6 superfamily	 - 	 - 	Ferric reductase NAD binding domain; Ferric reductase NAD binding domain.  
Q#18222 - 	CGI_10012943	superfamily	241563	62	102	0.0036005	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18224 - 	CGI_10012945	superfamily	243555	378	567	3.85E-09	56.2454	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#18226 - 	CGI_10012947	superfamily	245306	45	139	9.98E-19	76.8555	cl10465	Peptidase_S24_S26 superfamily	 - 	 - 	"The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases."
Q#18227 - 	CGI_10012948	superfamily	245226	57	170	3.05E-18	81.1767	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#18228 - 	CGI_10012949	superfamily	245864	32	419	5.35E-71	233.71	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#18230 - 	CGI_10012951	superfamily	148767	7	89	2.34E-20	79.4596	cl06404	CI-B14_5a superfamily	 - 	 - 	"NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a); This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) (EC:1.6.5.3). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane. The main function of the complex is the transport of electrons from NADH to ubiquinone, accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space."
Q#18231 - 	CGI_10012952	superfamily	245847	25	139	1.27E-06	45.2402	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18234 - 	CGI_10012955	superfamily	217293	76	245	1.36E-40	144.698	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#18234 - 	CGI_10012955	superfamily	202474	255	312	2.27E-15	73.8421	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#18235 - 	CGI_10004400	superfamily	222413	98	141	0.00804306	34.1678	cl16433	DDE_Tnp_1_7 superfamily	C	 - 	Transposase IS4; Transposase IS4.  
Q#18236 - 	CGI_10004402	superfamily	243066	12	123	1.31E-17	75.7317	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#18236 - 	CGI_10004402	superfamily	198867	135	222	8.59E-06	42.916	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#18240 - 	CGI_10021594	superfamily	243072	748	891	1.28E-27	110.166	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18240 - 	CGI_10021594	superfamily	241565	20	89	4.40E-09	54.6351	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#18241 - 	CGI_10021595	superfamily	241563	58	96	8.52E-07	46.3184	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18241 - 	CGI_10021595	superfamily	241563	13	42	0.000307325	38.8575	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18242 - 	CGI_10021596	superfamily	118308	47	138	1.18E-32	112.925	cl10755	Mitoc_L55 superfamily	N	 - 	Mitochondrial ribosomal protein L55; Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Q#18243 - 	CGI_10021597	superfamily	248100	159	215	7.32E-12	60.6308	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#18243 - 	CGI_10021597	superfamily	248100	300	357	1.53E-10	56.7788	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#18245 - 	CGI_10021599	superfamily	241748	130	366	4.79E-139	398.79	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#18246 - 	CGI_10021600	superfamily	245205	181	279	1.09E-10	57.9794	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#18249 - 	CGI_10021603	superfamily	247805	258	459	1.39E-91	290.54	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18249 - 	CGI_10021603	superfamily	247905	470	600	2.99E-28	111.561	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#18251 - 	CGI_10021605	superfamily	242414	42	120	1.58E-26	100.045	cl01285	Gar1 superfamily	C	 - 	"Gar1/Naf1 RNA binding region; Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex. In humans, Gar1 is also component of telomerase in vivo. Naf1 is an essentail protein that plays a role in ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis, and is homologous to Gar1."
Q#18252 - 	CGI_10021606	superfamily	247723	119	204	1.17E-49	167.138	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#18252 - 	CGI_10021606	superfamily	247723	27	106	8.11E-37	131.338	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#18252 - 	CGI_10021606	superfamily	247723	343	412	1.54E-34	124.612	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#18252 - 	CGI_10021606	superfamily	247723	460	543	2.61E-34	124.273	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#18255 - 	CGI_10021609	superfamily	220695	31	209	2.56E-06	46.8031	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18256 - 	CGI_10021610	superfamily	220695	28	175	2.63E-05	43.7215	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18257 - 	CGI_10021611	superfamily	241832	8	82	3.84E-16	67.5833	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18258 - 	CGI_10021612	superfamily	220695	52	224	3.44E-10	58.7442	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18259 - 	CGI_10021613	superfamily	220695	81	136	0.000251397	40.6399	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18260 - 	CGI_10021614	superfamily	220695	37	154	0.00152171	38.3287	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18261 - 	CGI_10021615	superfamily	243035	1	67	6.39E-16	66.8745	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18263 - 	CGI_10021617	superfamily	243092	427	670	1.68E-36	138.622	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18263 - 	CGI_10021617	superfamily	202808	1	75	1.22E-49	170.404	cl08405	TLE_N superfamily	C	 - 	Groucho/TLE N-terminal Q-rich domain; The N-terminal domain of the Grouch/TLE co-repressor proteins are involved in oligomerisation.
Q#18264 - 	CGI_10021618	superfamily	246722	931	1087	2.27E-42	153.318	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#18264 - 	CGI_10021618	superfamily	220722	74	196	1.78E-20	89.4009	cl11040	EST1 superfamily	 - 	 - 	Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerisation.
Q#18265 - 	CGI_10021619	superfamily	247042	1	428	0	558.486	cl15693	Sema superfamily	 - 	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#18265 - 	CGI_10021619	superfamily	243104	428	470	0.000148166	40.2292	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#18266 - 	CGI_10021620	superfamily	244363	11	142	8.73E-35	123.259	cl06336	Commd superfamily	 - 	 - 	"COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals."
Q#18267 - 	CGI_10021621	superfamily	245874	16	54	0.0034899	35.5217	cl12111	TNFR superfamily	 - 	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#18268 - 	CGI_10021622	superfamily	203031	32	88	2.21E-09	50.4044	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#18270 - 	CGI_10021624	superfamily	245874	163	204	0.00126857	36.6354	cl12111	TNFR superfamily	NC	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#18274 - 	CGI_10021628	superfamily	247684	10	430	1.72E-94	297.652	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#18275 - 	CGI_10021629	superfamily	241752	1	62	4.53E-21	80.0561	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#18277 - 	CGI_10000225	superfamily	247805	99	156	5.55E-12	58.888	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18282 - 	CGI_10012348	superfamily	245814	592	662	2.66E-06	49.0247	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	5276	5329	5.71E-06	47.8691	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	403	471	1.09E-05	47.0987	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1319	1385	2.00E-05	46.3283	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	3637	3706	3.13E-05	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	702	767	5.18E-05	45.1727	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1808	1865	7.59E-05	44.4023	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1411	1478	0.000155538	43.6319	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	3815	3882	0.000192767	43.2467	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	5177	5235	0.00035189	42.4763	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2932	2983	0.00037174	42.4763	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	997	1054	0.000531605	42.0911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	5367	5423	0.000842478	41.3207	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	3987	4045	0.0024946	39.7799	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	193	255	0.00269441	39.7799	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2326	2384	0.00970455	38.2391	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1674	1756	1.83E-08	55.5893	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2441	2515	4.52E-08	54.4337	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2037	2100	7.06E-08	53.5647	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	94	168	7.82E-08	53.6633	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	499	569	1.64E-07	52.8929	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	3723	3779	3.33E-07	51.2535	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	3137	3214	5.08E-07	51.3521	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4739	4809	5.31E-06	48.4267	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	792	863	6.96E-06	47.8853	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2130	2192	1.16E-05	46.6312	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1594	1651	1.43E-05	46.9941	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	5079	5135	1.89E-05	46.6193	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4251	4311	2.30E-05	45.8608	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4856	4913	2.56E-05	45.8608	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4154	4226	4.64E-05	45.1889	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1192	1274	6.12E-05	44.8037	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4452	4500	0.000112263	43.9348	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2783	2857	0.000140062	43.6481	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	3888	3972	0.00018106	43.3102	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1900	1948	0.00027007	42.7569	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4558	4633	0.000631836	41.7969	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	3527	3597	0.000664178	41.7221	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	902	959	0.000664361	41.6236	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4976	5034	0.00069819	41.6236	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	1107	1166	0.00103499	40.9583	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	297	364	0.00184555	40.4457	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2216	2289	0.00269429	39.6753	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2664	2726	0.00373917	39.3124	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	2558	2631	0.00412275	39.2901	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18282 - 	CGI_10012348	superfamily	245814	4667	4714	0.00456534	38.9272	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18284 - 	CGI_10012350	superfamily	243119	86	123	0.000744311	37.0382	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18285 - 	CGI_10012351	superfamily	241609	114	189	7.98E-25	96.2931	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#18285 - 	CGI_10012351	superfamily	241609	24	100	4.48E-19	80.8851	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#18285 - 	CGI_10012351	superfamily	245814	243	300	7.93E-06	43.2467	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18286 - 	CGI_10012352	superfamily	245814	402	471	3.48E-11	60.9659	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18286 - 	CGI_10012352	superfamily	241611	1018	1112	0.000449371	40.4496	cl00102	PTX superfamily	N	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#18286 - 	CGI_10012352	superfamily	243119	11	57	0.00663438	36.2577	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18287 - 	CGI_10012353	superfamily	243119	67	117	0.00118332	37.0382	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18288 - 	CGI_10012354	superfamily	222150	730	755	0.000970503	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18288 - 	CGI_10012354	superfamily	222150	790	815	0.00307308	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18288 - 	CGI_10012354	superfamily	197676	776	798	0.00560622	35.9045	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#18290 - 	CGI_10012356	superfamily	246921	306	351	6.58E-09	53.9185	cl15299	FG-GAP superfamily	C	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#18290 - 	CGI_10012356	superfamily	246921	373	417	5.02E-06	45.4441	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#18294 - 	CGI_10000839	superfamily	241563	65	102	3.25E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18297 - 	CGI_10002968	superfamily	243058	250	347	1.08E-07	50.0055	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18298 - 	CGI_10002969	superfamily	216363	3	108	1.33E-23	88.6813	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#18300 - 	CGI_10002971	superfamily	241563	68	104	2.34E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18300 - 	CGI_10002971	superfamily	241563	21	59	0.000502081	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18301 - 	CGI_10002972	superfamily	241563	71	104	0.000333753	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18301 - 	CGI_10002972	superfamily	241563	28	59	0.000398472	38.6144	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18305 - 	CGI_10009558	superfamily	246680	9	87	5.38E-14	64.5304	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#18307 - 	CGI_10009560	superfamily	243035	46	168	4.27E-27	105.394	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18311 - 	CGI_10009564	superfamily	214531	145	188	6.89E-08	49.1373	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18311 - 	CGI_10009564	superfamily	214531	190	231	4.56E-06	44.1297	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18312 - 	CGI_10009565	superfamily	219542	88	203	4.58E-34	126.202	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#18312 - 	CGI_10009565	superfamily	215896	310	401	3.42E-15	73.4832	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#18312 - 	CGI_10009565	superfamily	219541	592	628	3.83E-08	52.0855	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#18314 - 	CGI_10009567	superfamily	241568	2514	2550	0.000684434	40.1388	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#18314 - 	CGI_10009567	superfamily	214531	1790	1832	6.40E-09	54.9153	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18314 - 	CGI_10009567	superfamily	214531	816	856	1.78E-08	53.7597	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18314 - 	CGI_10009567	superfamily	214531	1305	1346	2.63E-07	50.2929	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18314 - 	CGI_10009567	superfamily	215683	1767	1807	4.29E-07	49.4759	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#18314 - 	CGI_10009567	superfamily	214531	171	213	8.21E-07	48.7521	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18314 - 	CGI_10009567	superfamily	214531	2019	2060	1.46E-06	47.9817	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18314 - 	CGI_10009567	superfamily	214531	1260	1302	3.09E-05	44.1297	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#18314 - 	CGI_10009567	superfamily	215683	791	830	0.000140129	42.1571	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#18315 - 	CGI_10001046	superfamily	247805	23	96	0.00485147	32.6944	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18317 - 	CGI_10000911	superfamily	216363	7	73	1.03E-08	47.465	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#18320 - 	CGI_10001152	superfamily	242542	26	188	8.38E-09	51.848	cl01505	YhhN superfamily	 - 	 - 	"YhhN-like protein; The members of this family are similar to the hypothetical protein yhhN expressed by E. coli. Many of the members of this family are annotated as being possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues."
Q#18321 - 	CGI_10001379	superfamily	243161	4	91	4.28E-20	82.4421	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#18324 - 	CGI_10001659	superfamily	241674	141	216	3.89E-32	119.238	cl00194	EF1B superfamily	 - 	 - 	"Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction."
Q#18324 - 	CGI_10001659	superfamily	204519	111	134	0.00192912	36.4563	cl11209	EF-1_beta_acid superfamily	 - 	 - 	Eukaryotic elongation factor 1 beta central acidic region; Eukaryotic elongation factor 1 beta central acidic region.  
Q#18326 - 	CGI_10001699	superfamily	218118	31	101	1.91E-17	72.2616	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#18328 - 	CGI_10002658	superfamily	220131	627	907	3.25E-64	220.611	cl11721	DUF1943 superfamily	 - 	 - 	"Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined."
Q#18328 - 	CGI_10002658	superfamily	219034	935	1028	2.04E-07	50.4126	cl05778	DUF1081 superfamily	 - 	 - 	Domain of Unknown Function (DUF1081); This region is found in Apolipophorin proteins.
Q#18329 - 	CGI_10002659	superfamily	245210	13	381	8.55E-83	261.213	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#18332 - 	CGI_10023840	superfamily	243035	45	166	2.82E-27	100.387	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18334 - 	CGI_10023842	superfamily	241563	61	99	0.000173403	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18335 - 	CGI_10023843	superfamily	248097	72	195	1.19E-16	72.683	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18335 - 	CGI_10023843	superfamily	248213	6	63	5.76E-05	39.0953	cl17659	DivIC superfamily	C	 - 	Septum formation initiator; DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil.
Q#18336 - 	CGI_10023844	superfamily	248097	24	133	4.06E-13	61.8974	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18337 - 	CGI_10023845	superfamily	248097	72	197	5.67E-15	68.0606	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18337 - 	CGI_10023845	superfamily	243100	33	63	0.0001272	37.9288	cl02576	B_zip1 superfamily	NC	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#18339 - 	CGI_10023847	superfamily	245604	1389	1454	9.76E-21	89.0123	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#18339 - 	CGI_10023847	superfamily	247809	904	1112	4.96E-82	269.171	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#18339 - 	CGI_10023847	superfamily	201133	790	897	4.38E-56	191.542	cl02837	CPSase_L_chain superfamily	 - 	 - 	"Carbamoyl-phosphate synthase L chain, N-terminal domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117."
Q#18339 - 	CGI_10023847	superfamily	244920	1124	1230	1.22E-37	138.7	cl08365	Biotin_carb_C superfamily	 - 	 - 	"Biotin carboxylase C-terminal domain; Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyzes the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain."
Q#18339 - 	CGI_10023847	superfamily	202474	626	673	0.00426459	39.1741	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#18340 - 	CGI_10023848	superfamily	245864	44	380	2.98E-53	184.789	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#18341 - 	CGI_10023849	superfamily	241868	5	138	3.76E-53	166.269	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#18342 - 	CGI_10023850	superfamily	241677	25	130	2.65E-57	178.219	cl00197	cyclophilin superfamily	C	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#18343 - 	CGI_10023851	superfamily	241677	85	237	7.68E-61	191.316	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#18344 - 	CGI_10023852	superfamily	247856	128	154	0.00988073	34.4457	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18347 - 	CGI_10023855	superfamily	247857	78	170	0.000703866	39.5344	cl17303	Esterase_713_like superfamily	NC	 - 	Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; This family contains proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible sequence homology to other esterase and lipase enzymes. It is active as a dimer and cleaves esters on halogenated cyclic compounds though its natural substrate is unknown. This enzyme is possibly exported from the cytosol to the periplasmic space. A large majority of sequences in this family have yet to be characterized.
Q#18348 - 	CGI_10023856	superfamily	245818	137	248	1.82E-33	124.592	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#18348 - 	CGI_10023856	superfamily	217750	305	365	1.53E-15	72.2266	cl04280	PAP_assoc superfamily	 - 	 - 	Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.
Q#18350 - 	CGI_10023858	superfamily	241594	67	139	5.38E-05	40.3664	cl00077	HECTc superfamily	N	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#18354 - 	CGI_10023862	superfamily	243072	58	183	4.34E-35	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18354 - 	CGI_10023862	superfamily	243072	124	249	2.00E-31	114.788	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18354 - 	CGI_10023862	superfamily	243072	223	287	7.24E-11	57.7786	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18354 - 	CGI_10023862	superfamily	243072	30	59	0.000190516	37.9188	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18355 - 	CGI_10023863	superfamily	241573	14	334	5.54E-121	363.961	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#18355 - 	CGI_10023863	superfamily	246669	482	606	6.33E-23	95.0379	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#18355 - 	CGI_10023863	superfamily	241653	347	457	8.07E-23	95.1247	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#18358 - 	CGI_10023866	superfamily	238012	171	197	0.00013629	39.2598	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18358 - 	CGI_10023866	superfamily	243061	205	302	9.17E-28	105.117	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#18358 - 	CGI_10023866	superfamily	243061	309	356	5.11E-13	64.2854	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#18360 - 	CGI_10023868	superfamily	243051	89	142	6.89E-09	50.8121	cl02479	MAM superfamily	NC	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#18361 - 	CGI_10023869	superfamily	241889	1	47	1.42E-11	56.8697	cl00474	PAP2_like superfamily	N	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#18362 - 	CGI_10023870	superfamily	241889	76	199	4.14E-22	88.8412	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#18363 - 	CGI_10023871	superfamily	241610	121	174	1.07E-07	47.2446	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#18364 - 	CGI_10023872	superfamily	247743	221	355	8.11E-08	50.2223	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#18364 - 	CGI_10023872	superfamily	244709	30	191	1.56E-60	196.297	cl07381	BCS1_N superfamily	 - 	 - 	BCS1 N terminal; This domain is found at the N terminal of the mitochondrial ATPase BSC1. It encodes the import and intramitochondrial sorting for the protein.
Q#18365 - 	CGI_10023873	superfamily	245201	86	232	1.49E-14	71.8841	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18365 - 	CGI_10023873	superfamily	245201	178	303	3.75E-07	50.1348	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18366 - 	CGI_10023874	superfamily	246925	137	444	1.37E-43	162.525	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#18366 - 	CGI_10023874	superfamily	247684	866	1224	1.83E-21	96.7621	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#18368 - 	CGI_10023876	superfamily	247805	298	439	1.95E-23	98.9487	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18368 - 	CGI_10023876	superfamily	247905	524	653	8.83E-12	64.1812	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#18368 - 	CGI_10023876	superfamily	243098	1089	1144	6.22E-10	57.2227	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#18368 - 	CGI_10023876	superfamily	243778	709	809	1.85E-17	79.9607	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#18369 - 	CGI_10023877	superfamily	191675	1	84	8.08E-13	61.1275	cl06196	OPA3 superfamily	N	 - 	"Optic atrophy 3 protein (OPA3); This family consists of several optic atrophy 3 (OPA3) proteins. OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity."
Q#18370 - 	CGI_10023878	superfamily	241559	1	97	2.80E-15	73.1139	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#18371 - 	CGI_10006959	superfamily	245847	136	208	1.06E-08	52.9442	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18371 - 	CGI_10006959	superfamily	241619	34	80	0.000103217	40.2581	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#18376 - 	CGI_10006965	superfamily	216901	299	483	4.60E-84	265.989	cl03466	Rap_GAP superfamily	 - 	 - 	Rap/ran-GAP; Rap/ran-GAP.  
Q#18379 - 	CGI_10006968	superfamily	243091	29	122	1.49E-06	48.6424	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#18379 - 	CGI_10006968	superfamily	246975	528	549	0.00283774	38.0969	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#18379 - 	CGI_10006968	superfamily	222150	513	536	0.00781531	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#18382 - 	CGI_10025975	superfamily	243161	10	56	0.00020522	37.759	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#18387 - 	CGI_10025981	superfamily	203213	1	21	0.00179968	33.2454	cl04999	HTH_psq superfamily	NC	 - 	"helix-turn-helix, Psq domain; This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence."
Q#18390 - 	CGI_10025984	superfamily	241574	1	113	1.33E-35	123.85	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18392 - 	CGI_10025987	superfamily	241644	1	94	1.48E-17	72.712	cl00154	UBCc superfamily	N	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#18393 - 	CGI_10025988	superfamily	243778	355	446	3.30E-31	116.169	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#18393 - 	CGI_10025988	superfamily	243082	34	159	6.64E-24	101.68	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#18394 - 	CGI_10025989	superfamily	220692	52	363	1.40E-10	60.6809	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#18396 - 	CGI_10025991	superfamily	216939	9	68	2.66E-08	47.6577	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#18396 - 	CGI_10025991	superfamily	216939	93	135	0.000195133	37.2573	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#18397 - 	CGI_10025992	superfamily	241564	193	261	1.39E-16	71.9131	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#18397 - 	CGI_10025992	superfamily	247792	4	62	1.13E-09	52.8332	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18398 - 	CGI_10025993	superfamily	245864	5	440	1.52E-72	237.947	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#18400 - 	CGI_10025995	superfamily	247725	176	305	7.47E-50	167.396	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18400 - 	CGI_10025995	superfamily	247792	389	427	7.00E-05	40.5068	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18400 - 	CGI_10025995	superfamily	220215	10	89	2.92E-18	79.1914	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#18400 - 	CGI_10025995	superfamily	215882	94	201	3.29E-14	68.8466	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#18401 - 	CGI_10025996	superfamily	219963	160	269	7.42E-16	70.7146	cl08487	GCV_T_C superfamily	 - 	 - 	"Glycine cleavage T-protein C-terminal barrel domain; This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyzes the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase."
Q#18402 - 	CGI_10025997	superfamily	240523	619	817	1.74E-76	251.387	cl18941	DAXX_histone_binding superfamily	 - 	 - 	"Histone binding domain of the death-domain associated protein (DAXX); DAXX is a nuclear protein that modulates transcription of various genes and is involved in cell death and/or the suppression of growth. DAXX is also a histone chaperone conserved in Metazoa that acts specifically on histone H3.3. This alignment models a functional domain of DAXX that interacts with the histone H3.3-H4 dimer, and in doing so competes with DNA binding and interactions between the histone chaperone ASF1/CIA and the H3-H4 dimer."
Q#18403 - 	CGI_10025998	superfamily	217293	27	232	2.81E-41	146.239	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#18405 - 	CGI_10026000	superfamily	241578	167	317	5.18E-31	115.852	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18406 - 	CGI_10026001	superfamily	241599	264	324	2.22E-16	73.8168	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#18406 - 	CGI_10026001	superfamily	217730	35	262	3.01E-97	294.807	cl04264	PBC superfamily	 - 	 - 	PBC domain; The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins.
Q#18407 - 	CGI_10026002	superfamily	248458	148	285	2.64E-21	94.3028	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18408 - 	CGI_10026003	superfamily	215733	221	464	2.42E-20	91.4726	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#18408 - 	CGI_10026003	superfamily	226572	783	836	0.000167587	41.7756	cl18761	COG4087 superfamily	NC	 - 	Soluble P-type ATPase [General function prediction only]
Q#18408 - 	CGI_10026003	superfamily	222006	535	610	0.000794265	39.1278	cl16182	Hydrolase_like2 superfamily	 - 	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#18409 - 	CGI_10026004	superfamily	155755	1	113	8.79E-18	73.3254	cl03922	V-ATPase_G superfamily	 - 	 - 	"Vacuolar (H+)-ATPase G subunit; This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialised cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation."
Q#18410 - 	CGI_10026005	superfamily	218721	12	337	9.92E-39	144.951	cl05344	TROVE superfamily	 - 	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#18413 - 	CGI_10026008	superfamily	241599	67	125	3.79E-23	95.0028	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#18415 - 	CGI_10026010	superfamily	219852	871	1313	2.71E-09	60.867	cl15656	Sfi1 superfamily	 - 	 - 	Sfi1 spindle body protein; This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organising centres.
Q#18415 - 	CGI_10026010	superfamily	219852	1540	2054	1.08E-08	58.941	cl15656	Sfi1 superfamily	 - 	 - 	Sfi1 spindle body protein; This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organising centres.
Q#18416 - 	CGI_10026011	superfamily	247905	1003	1125	6.66E-29	115.028	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#18416 - 	CGI_10026011	superfamily	247805	700	858	4.62E-20	89.704	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18416 - 	CGI_10026011	superfamily	248013	576	624	1.03E-05	45.3327	cl17459	CHROMO superfamily	 - 	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#18416 - 	CGI_10026011	superfamily	248013	478	514	3.17E-05	44.1771	cl17459	CHROMO superfamily	N	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#18416 - 	CGI_10026011	superfamily	219716	1730	1902	3.93E-101	324.147	cl06903	CHDCT2 superfamily	 - 	 - 	CHDCT2 (NUC038) domain; The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases.
Q#18416 - 	CGI_10026011	superfamily	219039	1333	1466	2.75E-66	223.698	cl05788	DUF1086 superfamily	 - 	 - 	"Domain of Unknown Function (DUF1086); This family consists of several eukaryotic domains of unknown function which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with pfam00176, pfam00271, pfam06465, pfam00385 and pfam00628."
Q#18416 - 	CGI_10026011	superfamily	148208	1245	1297	4.32E-18	81.8243	cl05792	DUF1087 superfamily	 - 	 - 	"Domain of Unknown Function (DUF1087); Members of this family are found in various chromatin remodelling factors and transposases. Their exact function is, as yet, unknown."
Q#18416 - 	CGI_10026011	superfamily	116680	111	160	7.42E-17	77.8834	cl06902	CHDNT superfamily	 - 	 - 	CHDNT (NUC034) domain; The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases.
Q#18416 - 	CGI_10026011	superfamily	247999	385	430	1.30E-15	74.4491	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#18416 - 	CGI_10026011	superfamily	247999	327	369	3.16E-14	70.2119	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#18417 - 	CGI_10026012	superfamily	148593	15	184	3.56E-102	294.353	cl06212	TRAP-gamma superfamily	 - 	 - 	"Translocon-associated protein, gamma subunit (TRAP-gamma); This family consists of several eukaryotic translocon-associated protein, gamma subunit (TRAP-gamma) sequences. The translocation site (translocon), at which nascent polypeptides pass through the endoplasmic reticulum membrane, contains a component previously called 'signal sequence receptor' that is now renamed as 'translocon-associated protein' (TRAP). The TRAP complex is comprised of four membrane proteins alpha, beta, gamma and delta which are present in a stoichiometric relation, and are genuine neighbors in intact microsomes. The gamma subunit is predicted to span the membrane four times."
Q#18418 - 	CGI_10026013	superfamily	220692	12	233	6.51E-05	42.1913	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#18420 - 	CGI_10026015	superfamily	198858	1	178	1.73E-25	97.2271	cl05741	AGTRAP superfamily	 - 	 - 	"Angiotensin II, type I receptor-associated protein (AGTRAP); This family consists of several angiotensin II, type I receptor-associated protein (AGTRAP) sequences. AGTRAP is known to interact specifically with the carboxyl-terminal cytoplasmic region of the angiotensin II type 1 (AT(1)) receptor to regulate different aspects of AT(1) receptor physiology. The function of this family is unclear."
Q#18421 - 	CGI_10026016	superfamily	204041	22	172	1.29E-47	155.047	cl07367	GLTP superfamily	 - 	 - 	Glycolipid transfer protein (GLTP); GLTP is a cytosolic protein that catalyzes the intermembrane transfer of glycolipids.
Q#18424 - 	CGI_10026019	superfamily	241563	62	98	1.06E-05	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18424 - 	CGI_10026019	superfamily	110440	662	688	0.000220893	39.6985	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18424 - 	CGI_10026019	superfamily	241563	8	53	0.000328085	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18424 - 	CGI_10026019	superfamily	110440	703	730	0.00564259	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18425 - 	CGI_10026020	superfamily	243092	12	169	2.15E-17	76.99	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18427 - 	CGI_10014527	superfamily	241574	253	406	1.59E-44	158.903	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18427 - 	CGI_10014527	superfamily	241574	451	625	6.23E-19	86.1005	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18427 - 	CGI_10014527	superfamily	245847	29	97	0.000139895	40.9488	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18429 - 	CGI_10014529	superfamily	145792	193	218	0.00206569	34.5439	cl10597	Antistasin superfamily	 - 	 - 	Antistasin family; Members of this family are inhibitors of trypsin family proteases. This domain is highly disulphide bonded. The domain is also found in some large extracellular proteins in multiple copies.
Q#18432 - 	CGI_10014532	superfamily	247724	248	408	4.99E-05	42.4436	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18432 - 	CGI_10014532	superfamily	242902	41	190	1.28E-14	70.7386	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#18433 - 	CGI_10014533	superfamily	247724	109	227	0.00226455	37.9104	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18434 - 	CGI_10014534	superfamily	247724	31	197	0.000558938	38.9768	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18439 - 	CGI_10014539	superfamily	246723	2	340	2.96E-168	480.523	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#18441 - 	CGI_10014541	superfamily	241754	12	718	0	1056.81	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#18441 - 	CGI_10014541	superfamily	218855	826	1023	1.05E-34	132.811	cl10652	Myosin_TH1 superfamily	 - 	 - 	Myosin tail; Myosin tail.  
Q#18444 - 	CGI_10001810	superfamily	241584	25	73	0.00047885	34.0091	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18447 - 	CGI_10002069	superfamily	243065	310	464	3.26E-09	55.9109	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#18454 - 	CGI_10004766	superfamily	248020	526	762	1.77E-29	120.262	cl17466	Sulfatase superfamily	N	 - 	Sulfatase; Sulfatase.  
Q#18454 - 	CGI_10004766	superfamily	248020	27	90	6.70E-11	63.2524	cl17466	Sulfatase superfamily	C	 - 	Sulfatase; Sulfatase.  
Q#18455 - 	CGI_10004767	superfamily	216807	126	214	8.14E-28	105.04	cl18379	DUF106 superfamily	N	 - 	Integral membrane protein DUF106; This archaebacterial protein family has no known function. Members are predicted to be integral membrane proteins.
Q#18456 - 	CGI_10004768	superfamily	245819	778	955	1.96E-63	214.75	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#18456 - 	CGI_10004768	superfamily	245201	473	706	3.68E-28	114.641	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18456 - 	CGI_10004768	superfamily	219526	724	765	5.62E-06	47.6139	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#18457 - 	CGI_10004769	superfamily	241886	9	295	2.92E-93	284.837	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#18457 - 	CGI_10004769	superfamily	247792	352	406	0.00105085	36.6548	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18458 - 	CGI_10004770	superfamily	243179	104	207	3.94E-27	103.196	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#18458 - 	CGI_10004770	superfamily	241622	241	311	4.13E-12	61.0434	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#18459 - 	CGI_10004771	superfamily	247856	577	638	2.22E-06	45.6165	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18459 - 	CGI_10004771	superfamily	207712	88	193	3.44E-33	123.191	cl02728	DUF1126 superfamily	 - 	 - 	Repeat of unknown function (DUF1126); This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.
Q#18459 - 	CGI_10004771	superfamily	207712	413	517	1.93E-31	118.183	cl02728	DUF1126 superfamily	 - 	 - 	Repeat of unknown function (DUF1126); This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.
Q#18459 - 	CGI_10004771	superfamily	207712	236	352	6.71E-30	113.946	cl02728	DUF1126 superfamily	 - 	 - 	Repeat of unknown function (DUF1126); This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.
Q#18460 - 	CGI_10004772	superfamily	241622	52	134	1.25E-19	83.385	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#18460 - 	CGI_10004772	superfamily	247725	264	353	0.000766684	37.9133	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18461 - 	CGI_10004773	superfamily	246597	47	113	2.32E-29	109.625	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#18461 - 	CGI_10004773	superfamily	246597	195	261	5.67E-28	105.773	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#18465 - 	CGI_10026268	superfamily	242406	61	165	9.44E-11	56.0605	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#18466 - 	CGI_10026269	superfamily	245814	119	190	1.38E-12	64.0475	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18467 - 	CGI_10026270	superfamily	248458	23	199	2.63E-13	69.6501	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18467 - 	CGI_10026270	superfamily	248458	267	440	9.40E-06	46.1529	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18468 - 	CGI_10026271	superfamily	248458	195	340	6.91E-07	49.2345	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18469 - 	CGI_10026272	superfamily	248458	262	439	2.04E-09	57.7089	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18469 - 	CGI_10026272	superfamily	248458	11	183	0.00627981	37.2933	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18470 - 	CGI_10026273	superfamily	248458	12	188	3.76E-13	69.2649	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18471 - 	CGI_10026274	superfamily	247743	178	344	9.51E-22	90.6683	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#18472 - 	CGI_10026275	superfamily	246713	29	185	8.87E-42	145.077	cl14786	ENDO3c superfamily	 - 	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#18472 - 	CGI_10026275	superfamily	246713	232	327	2.71E-26	102.705	cl14786	ENDO3c superfamily	N	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#18473 - 	CGI_10026276	superfamily	246713	58	214	5.46E-44	147.773	cl14786	ENDO3c superfamily	 - 	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#18475 - 	CGI_10026278	superfamily	241770	153	310	4.02E-07	47.3904	cl00309	PRTases_typeI superfamily	 - 	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#18475 - 	CGI_10026278	superfamily	222383	11	126	3.93E-47	157.573	cl16402	Pribosyltran_N superfamily	 - 	 - 	"N-terminal domain of ribose phosphate pyrophosphokinase; This family is frequently found N-terminal to the Pribosyltran, pfam00156."
Q#18476 - 	CGI_10026279	superfamily	247724	12	182	1.77E-112	324.581	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18476 - 	CGI_10026279	superfamily	243073	190	232	1.71E-15	68.3566	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#18477 - 	CGI_10026280	superfamily	245201	56	343	0	553.896	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18479 - 	CGI_10026282	superfamily	241868	203	315	1.60E-36	130.118	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#18479 - 	CGI_10026282	superfamily	247976	51	115	5.54E-27	103.419	cl17422	RF-1 superfamily	C	 - 	"RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis."
Q#18480 - 	CGI_10026283	superfamily	191640	25	127	3.71E-24	92.7185	cl06121	DUF1279 superfamily	 - 	 - 	Protein of unknown function (DUF1279); This family represents the C-terminus (approx. 120 residues) of a number of eukaryotic proteins of unknown function.
Q#18481 - 	CGI_10026284	superfamily	247727	84	202	0.000100338	40.1059	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#18482 - 	CGI_10026285	superfamily	245206	11	237	2.28E-58	188.663	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#18485 - 	CGI_10026288	superfamily	246937	110	190	2.34E-11	57.5835	cl15368	RNase_Ire1_like superfamily	N	 - 	"RNase domain (also known as the kinase extension nuclease domain) of Ire1 and RNase L; This RNase domain is found in the multi-functional protein Ire1; Ire1 also contains a type I transmembrane serine/threonine protein kinase (STK) domain, and a Luminal dimerization domain. Ire1 is essential for the endoplasmic reticulum (ER) unfolded protein response (UPR). The UPR is activated when protein misfolding is detected in the ER in order to reduce the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1 acts as an ER stress sensor; IRE1 dimerizes through its N-terminal luminal domain and forms oligomers, promoting trans-autophosphorylation by its cytosolic kinase domain which stimulates its endoribonuclease (RNase) activity and results in the cleavage of its mRNA substrate, Hac1 in yeast and Xbp1 in metazoans, thus promoting a splicing event that enables translation into a transcription factor which activates the UPR. This RNase domain is also found in Ribonuclease L (RNase L), sometimes referred to as the 2-5A-dependent RNase. RNase L is a highly regulated, latent endoribonuclease widely expressed in most mammalian tissues. It is involved in the mediation of the antiviral and pro-apoptotic activities of the interferon-inducible 2-5A system; the interferon (IFN)-inducible 2'-5'-oligoadenylate synthetase (OAS)/RNase L pathway blocks infections by certain types of viruses through cleavage of viral and cellular single-stranded RNA. RNase L has been shown to have an impact on the pathogenesis of prostate cancer; the RNase L gene, RNASEL, has been identified as a strong candidate for the hereditary prostate cancer 1 (HPC1) allele."
Q#18485 - 	CGI_10026288	superfamily	245201	22	61	0.000967558	37.8487	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18486 - 	CGI_10026289	superfamily	245201	1208	1351	2.51E-13	69.9581	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18488 - 	CGI_10026291	superfamily	243072	81	203	1.10E-23	92.8318	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18490 - 	CGI_10026293	superfamily	198757	98	193	1.99E-41	144.774	cl02658	TAFH superfamily	 - 	 - 	"NHR1 homology to TAF; This corresponds to the region NHR1 that is conserved between the product of the nervy gene in Drosophila and the human mtg8b protein, which is hypothesised to be a transcription factor."
Q#18490 - 	CGI_10026293	superfamily	149750	320	366	8.80E-15	69.896	cl07409	NHR2 superfamily	N	 - 	NHR2 domain like; The NHR2 (Nervy homology 2) domain is found in the ETO protein where it mediates oligomerisation and protein-protein interactions. It forms an alpha-helical tetramer.
Q#18491 - 	CGI_10026294	superfamily	244881	337	656	6.30E-74	244.795	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#18491 - 	CGI_10026294	superfamily	215788	162	254	1.55E-20	88.0051	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#18491 - 	CGI_10026294	superfamily	203720	766	808	0.000155836	40.9946	cl08457	A2M_recep superfamily	C	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#18492 - 	CGI_10026295	superfamily	220692	85	343	1.91E-06	47.5841	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#18494 - 	CGI_10026297	superfamily	220695	49	193	0.000834217	39.4843	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18496 - 	CGI_10026299	superfamily	242206	140	261	5.64E-60	188.152	cl00938	Rieske superfamily	 - 	 - 	"Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis."
Q#18496 - 	CGI_10026299	superfamily	217287	68	128	2.55E-10	54.6779	cl03782	UCR_TM superfamily	 - 	 - 	Ubiquinol cytochrome reductase transmembrane region; Each subunit of the cytochrome bc1 complex provides a single helix (this family) to make up the transmembrane region of the complex.
Q#18498 - 	CGI_10026301	superfamily	218942	1	394	2.90E-126	374.734	cl12330	NPR2 superfamily	 - 	 - 	Nitrogen permease regulator 2; This family of regulators are involved in post-translational control of nitrogen permease.
Q#18499 - 	CGI_10026302	superfamily	243100	248	296	8.77E-06	42.2919	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#18500 - 	CGI_10026303	superfamily	243100	182	232	1.35E-10	54.9273	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#18501 - 	CGI_10026304	superfamily	243100	233	285	1.84E-14	66.4833	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#18502 - 	CGI_10026305	superfamily	243100	29	82	1.43E-07	44.1417	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#18503 - 	CGI_10026306	superfamily	241704	91	241	2.35E-39	138.275	cl00227	PEBP superfamily	 - 	 - 	"PhosphatidylEthanolamine-Binding Protein (PEBP) domain; PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer)."
Q#18504 - 	CGI_10026308	superfamily	246908	226	325	2.67E-57	184.656	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#18504 - 	CGI_10026308	superfamily	243073	348	388	6.95E-20	82.0803	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#18505 - 	CGI_10026309	superfamily	215859	124	278	4.13E-05	42.5887	cl18347	Peptidase_S9 superfamily	N	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#18506 - 	CGI_10026310	superfamily	220692	75	370	8.66E-10	58.3697	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#18508 - 	CGI_10026312	superfamily	241782	45	406	6.34E-84	263.433	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#18511 - 	CGI_10026315	superfamily	220665	2	493	3.59E-142	420.679	cl10950	Tmemb_161AB superfamily	 - 	 - 	Predicted transmembrane protein 161AB; Transmemb_161AB is a family of conserved proteins found from worms to humans. Members are putative transmembrane proteins but otherwise the function is not known.
Q#18512 - 	CGI_10026316	superfamily	241564	32	97	8.76E-28	103.885	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#18512 - 	CGI_10026316	superfamily	247792	310	355	1.49E-10	56.234	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18513 - 	CGI_10026317	superfamily	247057	234	264	0.00336255	34.7624	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#18517 - 	CGI_10026321	superfamily	204632	223	312	0.000447815	40.6181	cl12901	DUF3166 superfamily	 - 	 - 	Protein of unknown function (DUF3166); This eukaryotic family of proteins has no known function.
Q#18518 - 	CGI_10026322	superfamily	241832	1	179	7.12E-42	141.563	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18519 - 	CGI_10026323	superfamily	241750	9	430	0	540.328	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#18521 - 	CGI_10026325	superfamily	241884	119	349	2.42E-97	291.484	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#18522 - 	CGI_10026326	superfamily	247905	88	219	2.45E-29	113.102	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#18522 - 	CGI_10026326	superfamily	247805	21	76	6.46E-22	94.0885	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18522 - 	CGI_10026326	superfamily	222474	251	314	7.36E-22	90.1749	cl16500	DUF4217 superfamily	 - 	 - 	Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many helicase proteins.
Q#18523 - 	CGI_10026327	superfamily	217293	36	244	1.09E-60	199.011	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#18523 - 	CGI_10026327	superfamily	202474	252	455	2.81E-07	49.9597	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#18525 - 	CGI_10004278	superfamily	241600	694	902	2.24E-83	268.725	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18525 - 	CGI_10004278	superfamily	243092	32	301	1.36E-53	188.313	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18525 - 	CGI_10004278	superfamily	221242	370	669	1.20E-44	164.246	cl13285	DUF3337 superfamily	 - 	 - 	Domain of unknown function (DUF3337); This family of proteins are functionally uncharacterized. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length.
Q#18526 - 	CGI_10004279	superfamily	248264	1	110	0.000308566	36.4462	cl17710	DDE_4 superfamily	NC	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#18527 - 	CGI_10004280	superfamily	241600	120	256	1.04E-49	164.336	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18529 - 	CGI_10004282	superfamily	241600	145	357	1.42E-74	232.131	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18530 - 	CGI_10004283	superfamily	241600	133	243	1.25E-29	111.215	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18534 - 	CGI_10022832	superfamily	245601	318	496	2.51E-28	110.49	cl11399	HP superfamily	 - 	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#18535 - 	CGI_10022833	superfamily	216981	115	228	5.81E-19	80.2693	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#18537 - 	CGI_10022835	superfamily	241600	102	321	2.76E-91	273.732	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18538 - 	CGI_10022836	superfamily	241600	101	320	1.82E-89	269.11	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18540 - 	CGI_10022838	superfamily	241600	163	382	3.49E-82	252.546	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18541 - 	CGI_10022839	superfamily	241600	19	64	1.71E-14	63.7987	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18543 - 	CGI_10022841	superfamily	242902	27	126	1.04E-15	69.9682	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#18544 - 	CGI_10022842	superfamily	243119	97	145	2.27E-09	49.7396	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18544 - 	CGI_10022842	superfamily	243119	36	78	7.29E-05	37.4133	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18547 - 	CGI_10022845	superfamily	248054	26	77	4.46E-05	41.3036	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#18548 - 	CGI_10022846	superfamily	238191	94	208	7.34E-09	55.8012	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#18550 - 	CGI_10022848	superfamily	248289	707	764	3.44E-15	72.0715	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#18550 - 	CGI_10022848	superfamily	244382	427	547	6.32E-13	66.9539	cl06473	CHRD superfamily	 - 	 - 	"CHRD domain; CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin and Drosophila SOG.."
Q#18550 - 	CGI_10022848	superfamily	244382	569	672	8.18E-07	48.4643	cl06473	CHRD superfamily	 - 	 - 	"CHRD domain; CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin and Drosophila SOG.."
Q#18550 - 	CGI_10022848	superfamily	248289	780	843	1.12E-05	44.3371	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#18550 - 	CGI_10022848	superfamily	244382	189	298	5.36E-05	42.6863	cl06473	CHRD superfamily	 - 	 - 	"CHRD domain; CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin and Drosophila SOG.."
Q#18551 - 	CGI_10022849	superfamily	243238	41	337	2.32E-93	298.027	cl02915	Voltage_gated_ClC superfamily	C	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#18551 - 	CGI_10022849	superfamily	243238	438	557	2.11E-42	158.585	cl02915	Voltage_gated_ClC superfamily	N	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#18553 - 	CGI_10022851	superfamily	246936	37	75	2.16E-14	63.8105	cl15354	CBS_pair superfamily	N	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#18554 - 	CGI_10022852	superfamily	220419	93	257	1.79E-18	82.9666	cl17022	DUF2351 superfamily	NC	 - 	Uncharacterized conserved protein (DUF2351); Members of this family of proteins have no known function.
Q#18555 - 	CGI_10022853	superfamily	216574	82	219	6.47E-42	145.813	cl14794	FAD_binding_4 superfamily	 - 	 - 	"FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan."
Q#18556 - 	CGI_10022854	superfamily	222269	106	293	1.30E-20	88.5346	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#18557 - 	CGI_10022855	superfamily	248100	134	194	2.82E-11	57.164	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#18557 - 	CGI_10022855	superfamily	248100	68	128	2.90E-10	54.4676	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#18558 - 	CGI_10022856	superfamily	247677	1376	1508	9.78E-44	157.446	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#18558 - 	CGI_10022856	superfamily	243128	712	939	8.32E-43	157.106	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#18558 - 	CGI_10022856	superfamily	243129	1180	1291	4.21E-25	103.102	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#18558 - 	CGI_10022856	superfamily	247677	1488	1534	0.0097964	37.5777	cl17013	W2 superfamily	N	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#18559 - 	CGI_10022857	superfamily	245610	20	305	5.31E-122	362.717	cl11424	nitrilase superfamily	 - 	 - 	"Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy."
Q#18561 - 	CGI_10022859	superfamily	241886	64	418	2.85E-78	246.702	cl00470	Aldo_ket_red superfamily	 - 	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#18562 - 	CGI_10022860	superfamily	241913	329	431	1.46E-34	124.668	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#18562 - 	CGI_10022860	superfamily	241913	32	126	1.25E-33	121.959	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#18562 - 	CGI_10022860	superfamily	241913	203	254	9.15E-12	61.0975	cl00509	hot_dog superfamily	N	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#18569 - 	CGI_10022867	superfamily	199168	219	241	0.00783984	33.8644	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#18571 - 	CGI_10022869	superfamily	218140	291	835	4.01E-143	434.719	cl04579	Anoctamin superfamily	 - 	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#18573 - 	CGI_10022871	superfamily	248458	120	252	4.22E-13	68.8797	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18576 - 	CGI_10022874	superfamily	247912	25	369	5.40E-44	159.589	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#18576 - 	CGI_10022874	superfamily	221337	425	483	1.25E-06	46.5411	cl13401	DUF3471 superfamily	C	 - 	"Domain of unknown function (DUF3471); This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144."
Q#18577 - 	CGI_10004039	superfamily	244757	29	58	0.00164408	32.8329	cl07585	YopR_core superfamily	N	 - 	"YopR Core; The YopR core domain, predominantly found in the Yersinia pestis virulence factor YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle. Little is known about this domain, though it may contribute to the virulence of the protein YopR."
Q#18579 - 	CGI_10004041	superfamily	245531	64	116	0.000298552	36.6003	cl11158	BEN superfamily	C	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#18583 - 	CGI_10006206	superfamily	248312	50	196	1.20E-05	42.7257	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#18585 - 	CGI_10006208	superfamily	248312	17	195	0.000212958	39.2589	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#18587 - 	CGI_10006210	superfamily	221612	55	197	7.36E-14	70.936	cl13889	DUF3715 superfamily	 - 	 - 	"Protein of unknown function (DUF3715); This domain family is found in eukaryotes, and is approximately 170 amino acids in length."
Q#18588 - 	CGI_10006211	superfamily	245303	63	439	0	539.454	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#18588 - 	CGI_10006211	superfamily	243119	712	756	9.16E-06	44.732	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18588 - 	CGI_10006211	superfamily	243119	660	692	1.14E-05	44.3468	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18588 - 	CGI_10006211	superfamily	243119	466	498	1.14E-05	44.3468	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18588 - 	CGI_10006211	superfamily	243119	518	562	1.18E-05	44.3468	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#18590 - 	CGI_10006213	superfamily	243078	15	155	5.59E-72	227.305	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#18590 - 	CGI_10006213	superfamily	190532	194	285	1.06E-26	103.487	cl03906	GAT superfamily	 - 	 - 	"GAT domain; The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins."
Q#18592 - 	CGI_10006215	superfamily	242940	38	160	2.18E-49	161.531	cl02228	ATP12 superfamily	 - 	 - 	"ATP12 chaperone protein; Mitochondrial F1-ATPase is an oligomeric enzyme composed of five distinct subunit polypeptides. The alpha and beta subunits make up the bulk of protein mass of F1. In Saccharomyces cerevisiae both subunits are synthesised as precursors with amino-terminal targeting signals that are removed upon translocation of the proteins to the matrix compartment. These proteins include examples from eukaryotes and bacteria and may have chaperone activity, being involved in F1 ATPase complex assembly."
Q#18593 - 	CGI_10006216	superfamily	242890	22	192	5.10E-85	251.436	cl02113	Vac_ImportDeg superfamily	 - 	 - 	"Vacuolar import and degradation protein; Members of this family are involved in the negative regulation of gluconeogenesis. They are required for both proteosome-dependent and vacuolar catabolite degradation of fructose-1,6-bisphosphatase (FBPase), where they probably regulate FBPase targeting from the FBPase-containing vesicles to the vacuole."
Q#18594 - 	CGI_10006217	superfamily	206221	59	131	9.28E-30	110.067	cl16570	Requiem_N superfamily	 - 	 - 	"N-terminal domain of DPF2/REQ; This putative domain has been detected on the human DPF2 protein and was subsequently targeted for structure determination by the Joint Center for Structural Genomics (JCSG). Possibly, the C-terminus extends by 30 amino acids and forms a separate domain. DPF2 interacts with estrogen related receptor alpha (Err-alpha), an orphan receptor which acts as a regulator in energy metabolism. It was also identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodeling factor."
Q#18594 - 	CGI_10006217	superfamily	247999	331	373	2.07E-06	44.7888	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#18596 - 	CGI_10022023	superfamily	220695	73	193	0.0029086	36.4027	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18600 - 	CGI_10022027	superfamily	245604	3	75	1.08E-19	82.0671	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#18600 - 	CGI_10022027	superfamily	215782	177	388	4.16E-93	280.976	cl18344	2-oxoacid_dh superfamily	 - 	 - 	2-oxoacid dehydrogenases acyltransferase (catalytic domain); These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain.
Q#18601 - 	CGI_10022028	superfamily	245206	50	295	9.44E-68	214.638	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#18602 - 	CGI_10022029	superfamily	241583	5	208	2.50E-44	157.921	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#18602 - 	CGI_10022029	superfamily	245321	216	302	6.52E-10	56.0947	cl10507	Disintegrin superfamily	 - 	 - 	Disintegrin; Disintegrin.  
Q#18603 - 	CGI_10022030	superfamily	245206	27	302	3.29E-135	387.978	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#18604 - 	CGI_10022031	superfamily	245321	27	118	2.06E-10	59.1763	cl10507	Disintegrin superfamily	 - 	 - 	Disintegrin; Disintegrin.  
Q#18604 - 	CGI_10022031	superfamily	241563	847	886	0.000340746	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18605 - 	CGI_10022032	superfamily	247757	333	917	0	904.219	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#18605 - 	CGI_10022032	superfamily	247780	118	290	7.67E-88	279.44	cl17226	NAD_bind_amino_acid_DH superfamily	 - 	 - 	"NAD(P) binding domain of amino acid dehydrogenase-like proteins; Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel  domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts."
Q#18605 - 	CGI_10022032	superfamily	201431	3	123	1.70E-35	131.861	cl08290	THF_DHG_CYH superfamily	 - 	 - 	"Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain.  "
Q#18606 - 	CGI_10022033	superfamily	243034	132	231	9.82E-10	56.6196	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#18606 - 	CGI_10022033	superfamily	243058	632	730	0.000468988	39.22	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18606 - 	CGI_10022033	superfamily	243058	588	662	0.00306046	36.9088	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18607 - 	CGI_10022034	superfamily	247757	102	274	6.50E-68	217.797	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#18607 - 	CGI_10022034	superfamily	202493	326	431	8.76E-31	114.907	cl03814	SRP_SPB superfamily	 - 	 - 	Signal peptide binding domain; Signal peptide binding domain.  
Q#18607 - 	CGI_10022034	superfamily	243520	10	86	7.23E-14	67.1911	cl03758	SRP54_N superfamily	 - 	 - 	"SRP54-type protein, helical bundle domain; SRP54-type protein, helical bundle domain.  "
Q#18608 - 	CGI_10022035	superfamily	243066	6	98	4.81E-25	100.32	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#18609 - 	CGI_10022036	superfamily	243992	10	65	8.18E-07	41.4054	cl05087	Complex1_LYR_1 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#18610 - 	CGI_10022037	superfamily	241578	136	251	5.03E-22	90.4286	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18610 - 	CGI_10022037	superfamily	245213	89	125	1.20E-08	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18610 - 	CGI_10022037	superfamily	245213	10	47	2.94E-06	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18610 - 	CGI_10022037	superfamily	245213	50	86	3.10E-06	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18611 - 	CGI_10022038	superfamily	241763	11	222	1.54E-95	280.664	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#18612 - 	CGI_10022039	superfamily	241763	729	940	2.67E-101	317.258	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#18612 - 	CGI_10022039	superfamily	220393	13	297	1.33E-68	230.725	cl10751	Tmem26 superfamily	 - 	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#18612 - 	CGI_10022039	superfamily	220393	431	612	1.45E-39	149.063	cl10751	Tmem26 superfamily	N	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#18612 - 	CGI_10022039	superfamily	244586	643	701	1.66E-14	69.9651	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#18614 - 	CGI_10022041	superfamily	222269	236	491	8.42E-24	100.091	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#18615 - 	CGI_10022042	superfamily	247725	2670	2783	4.20E-44	159.673	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18615 - 	CGI_10022042	superfamily	247683	2146	2201	7.43E-21	90.0775	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#18615 - 	CGI_10022042	superfamily	241754	79	716	0	846.526	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#18615 - 	CGI_10022042	superfamily	243052	2315	2469	5.38E-41	151.359	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#18615 - 	CGI_10022042	superfamily	243052	990	1136	4.45E-31	122.469	cl02480	MyTH4 superfamily	 - 	 - 	"MyTH4 domain; Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins."
Q#18615 - 	CGI_10022042	superfamily	215882	2582	2692	4.60E-06	47.6606	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#18616 - 	CGI_10022043	superfamily	245227	1	403	0	546.827	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#18617 - 	CGI_10022044	superfamily	248390	15	205	3.02E-52	168.424	cl17836	NT5C superfamily	 - 	 - 	"5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known."
Q#18618 - 	CGI_10022045	superfamily	149077	545	657	5.25E-32	121.192	cl06719	TMC superfamily	 - 	 - 	"TMC domain; These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters."
Q#18619 - 	CGI_10022046	superfamily	241574	76	254	6.26E-75	234.402	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18619 - 	CGI_10022046	superfamily	241574	273	359	1.51E-07	50.2769	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18622 - 	CGI_10022049	superfamily	241574	27	167	1.21E-53	182.786	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18622 - 	CGI_10022049	superfamily	241574	241	436	6.78E-14	69.9221	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18623 - 	CGI_10022050	superfamily	242493	210	432	7.15E-16	76.5568	cl01417	Nuc-transf superfamily	 - 	 - 	Predicted nucleotidyltransferase; Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Q#18623 - 	CGI_10022050	superfamily	217926	7	168	6.79E-12	62.963	cl04418	YTH superfamily	 - 	 - 	"YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily."
Q#18625 - 	CGI_10022052	superfamily	241613	221	255	2.74E-10	54.135	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#18627 - 	CGI_10022054	superfamily	248097	8	120	8.72E-17	71.1422	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18628 - 	CGI_10022055	superfamily	220695	82	196	0.0001168	41.0251	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18629 - 	CGI_10022056	superfamily	246597	30	324	1.82E-88	274.563	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#18631 - 	CGI_10003680	superfamily	199156	138	153	0.000404377	36.6524	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#18631 - 	CGI_10003680	superfamily	199156	100	114	0.00464236	33.5817	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#18637 - 	CGI_10004461	superfamily	241758	27	124	1.22E-13	62.7726	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#18638 - 	CGI_10004462	superfamily	241563	167	205	3.55E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18638 - 	CGI_10004462	superfamily	110440	629	656	0.00898975	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18639 - 	CGI_10004463	superfamily	241563	71	109	0.000167256	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18639 - 	CGI_10004463	superfamily	191851	115	222	0.000972371	39.1503	cl06708	DUF1640 superfamily	 - 	 - 	Protein of unknown function (DUF1640); This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Q#18639 - 	CGI_10004463	superfamily	110440	492	518	0.00581179	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18643 - 	CGI_10018841	superfamily	247725	3	121	2.01E-62	201.218	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18644 - 	CGI_10018842	superfamily	198896	1579	1595	1.58E-06	47.5758	cl07394	Ca_chan_IQ superfamily	C	 - 	"Voltage gated calcium channel IQ domain; Voltage gated calcium channels control cellular calcium entry in response to changes in membrane potential. The isoleucine-glutamine (IQ) motif in the voltage gated calcium channel IQ domain interacts with hydrophobic pockets of Ca2+/calmodulin. The interaction regulates two self-regulatory calcium dependent feedback mechanism, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF)."
Q#18645 - 	CGI_10018843	superfamily	241644	33	122	3.46E-21	88.4133	cl00154	UBCc superfamily	C	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#18646 - 	CGI_10018844	superfamily	243134	28	148	3.19E-36	127.38	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#18646 - 	CGI_10018844	superfamily	243134	165	284	6.92E-32	115.824	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#18647 - 	CGI_10018845	superfamily	243134	29	149	2.93E-36	127.38	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#18647 - 	CGI_10018845	superfamily	243134	166	285	6.47E-32	115.824	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#18648 - 	CGI_10018846	superfamily	248097	54	177	2.39E-23	90.4022	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18650 - 	CGI_10018848	superfamily	248458	91	235	1.11E-15	77.3541	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18650 - 	CGI_10018848	superfamily	248458	389	567	7.26E-12	65.7981	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18651 - 	CGI_10018849	superfamily	248458	68	246	3.24E-20	91.2213	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18651 - 	CGI_10018849	superfamily	248458	424	599	1.61E-12	68.1093	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18652 - 	CGI_10018850	superfamily	248458	399	574	1.60E-17	83.1321	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18652 - 	CGI_10018850	superfamily	248458	36	214	1.83E-16	79.6653	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18653 - 	CGI_10018851	superfamily	248458	38	212	7.81E-21	93.1472	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18653 - 	CGI_10018851	superfamily	248458	491	629	1.50E-10	61.9461	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18654 - 	CGI_10018852	superfamily	243072	69	195	1.21E-36	134.819	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18654 - 	CGI_10018852	superfamily	247057	607	667	1.44E-30	115.669	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#18655 - 	CGI_10018853	superfamily	241795	1437	1571	2.60E-21	92.9171	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#18655 - 	CGI_10018853	superfamily	241795	1634	1760	4.55E-08	53.3236	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#18655 - 	CGI_10018853	superfamily	241795	885	973	1.54E-06	48.3991	cl00335	NDPk superfamily	 - 	 - 	"Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved."
Q#18656 - 	CGI_10018854	superfamily	241584	997	1093	3.96E-16	76.7663	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18656 - 	CGI_10018854	superfamily	241584	1101	1194	5.72E-13	67.5215	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18656 - 	CGI_10018854	superfamily	241584	1386	1476	9.20E-13	67.1363	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18656 - 	CGI_10018854	superfamily	241584	896	989	1.23E-12	66.7511	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18656 - 	CGI_10018854	superfamily	245814	336	402	1.73E-09	57.1139	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	245814	246	312	2.23E-09	56.7287	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	241584	1199	1288	8.06E-09	55.5803	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18656 - 	CGI_10018854	superfamily	245814	428	498	2.53E-08	53.6471	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	241584	1484	1573	2.53E-06	47.8763	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18656 - 	CGI_10018854	superfamily	245814	614	674	4.68E-06	46.7135	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	245814	709	793	3.02E-14	71.1135	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	245814	521	583	1.15E-09	57.4167	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	245814	811	899	3.32E-09	56.5771	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	245814	1312	1383	3.43E-09	56.0999	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	245814	25	113	3.50E-07	50.6194	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18656 - 	CGI_10018854	superfamily	245814	159	219	1.23E-05	45.513	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18657 - 	CGI_10018855	superfamily	247725	494	597	2.74E-39	139.354	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18659 - 	CGI_10018857	superfamily	245213	398	432	3.99E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	361	395	0.000204431	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	250	284	0.000241392	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	213	248	0.000404457	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	472	506	0.000456298	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	435	469	0.00070832	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	509	544	0.00109876	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	288	321	0.00179222	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	245213	324	359	0.00206959	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18659 - 	CGI_10018857	superfamily	243124	64	205	7.73E-36	131.01	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#18661 - 	CGI_10018859	superfamily	245201	54	338	3.95E-86	266.116	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18663 - 	CGI_10018861	superfamily	247792	17	64	5.13E-11	57.8408	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18663 - 	CGI_10018861	superfamily	110440	327	354	9.38E-06	42.7801	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18663 - 	CGI_10018861	superfamily	110440	280	306	0.00743213	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18664 - 	CGI_10018862	superfamily	241781	154	256	1.87E-52	169.716	cl00320	tRNA_bindingDomain superfamily	 - 	 - 	"The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs.  Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases.  The molecular chaperones Trbp111 and CsaA also contain this domain.  CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties.  In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. An EMAP-II-like cytokine is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain. For homodimeric members of this group which include CsaA, Trbp111 and Escherichia coli MetRS this domain acts as a dimerization domain."
Q#18665 - 	CGI_10018863	superfamily	241743	66	215	1.80E-39	135.008	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#18666 - 	CGI_10018864	superfamily	241743	278	427	1.85E-34	126.534	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#18666 - 	CGI_10018864	superfamily	241743	68	213	1.51E-26	104.192	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#18667 - 	CGI_10002979	superfamily	245225	374	661	4.81E-59	203.648	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#18667 - 	CGI_10002979	superfamily	242197	18	84	0.00190102	37.3444	cl00928	dsDNA_bind superfamily	N	 - 	Double-stranded DNA-binding domain; This domain is believed to bind double-stranded DNA of 20 bases length.
Q#18668 - 	CGI_10002980	superfamily	247856	31	68	1.31E-05	38.6829	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18669 - 	CGI_10002981	superfamily	247856	42	113	9.90E-10	52.9353	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18669 - 	CGI_10002981	superfamily	247856	178	248	2.19E-09	52.1649	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18669 - 	CGI_10002981	superfamily	247856	4	67	0.00274791	34.8309	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#18670 - 	CGI_10002982	superfamily	242323	54	159	3.32E-15	68.3039	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#18672 - 	CGI_10009945	superfamily	222070	75	185	3.11E-08	49.2133	cl18634	DDE_3 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#18674 - 	CGI_10009948	superfamily	241563	61	100	2.10E-05	42.2744	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18677 - 	CGI_10009951	superfamily	244895	85	429	7.64E-96	298.306	cl08294	Peptidase_M17 superfamily	N	 - 	"Cytosol aminopeptidase family, N-terminal and catalytic domains.  Family M17 contains zinc- and manganese-dependent exopeptidases ( EC  3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants."
Q#18678 - 	CGI_10009952	superfamily	241583	144	305	2.67E-48	168.904	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#18678 - 	CGI_10009952	superfamily	247097	365	401	0.00700143	35.4329	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#18679 - 	CGI_10009953	superfamily	245847	2	91	5.56E-08	46.0106	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18680 - 	CGI_10009954	superfamily	241629	37	142	1.79E-30	108.309	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#18681 - 	CGI_10001400	superfamily	245201	1	175	3.28E-115	343.853	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18681 - 	CGI_10001400	superfamily	243035	207	299	1.21E-13	67.4003	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18681 - 	CGI_10001400	superfamily	243035	371	461	1.75E-13	66.6308	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18685 - 	CGI_10009996	superfamily	241750	9	72	7.10E-13	60.665	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#18692 - 	CGI_10010003	superfamily	247677	204	397	1.71E-92	284.105	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#18693 - 	CGI_10010004	superfamily	243035	97	217	2.47E-25	96.5349	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18697 - 	CGI_10007672	superfamily	245864	5	86	1.56E-18	79.6298	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#18698 - 	CGI_10007673	superfamily	245864	20	416	2.15E-45	164.759	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#18699 - 	CGI_10007674	superfamily	245864	120	428	1.25E-43	160.136	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#18700 - 	CGI_10007675	superfamily	247727	259	323	0.000147012	40.1111	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#18700 - 	CGI_10007675	superfamily	247637	111	189	0.00613326	37.2299	cl16912	MDR superfamily	N	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#18701 - 	CGI_10007676	superfamily	241563	60	102	7.58E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18701 - 	CGI_10007676	superfamily	110440	421	447	9.90E-05	40.0837	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18702 - 	CGI_10007678	superfamily	241563	62	98	0.00117132	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18702 - 	CGI_10007678	superfamily	110440	429	456	0.00189788	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18702 - 	CGI_10007678	superfamily	247740	199	270	0.00487268	37.186	cl17186	TIM_phosphate_binding superfamily	C	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#18703 - 	CGI_10007679	superfamily	221433	1886	1994	3.30E-29	116.244	cl13553	DUF3585 superfamily	 - 	 - 	Protein of unknown function (DUF3585); This domain is found in eukaryotes. This domain is typically between 135 and 149 amino acids in length and is found associated with pfam00307.
Q#18703 - 	CGI_10007679	superfamily	243050	663	720	1.86E-25	102.759	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#18703 - 	CGI_10007679	superfamily	248054	66	103	0.0012877	39.3776	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#18704 - 	CGI_10007680	superfamily	110440	135	161	0.00537201	33.1501	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18705 - 	CGI_10007681	superfamily	241563	40	75	0.000134323	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18705 - 	CGI_10007681	superfamily	110440	463	489	0.00284661	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18705 - 	CGI_10007681	superfamily	110440	504	531	0.00945211	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#18706 - 	CGI_10005830	superfamily	248264	171	311	3.67E-36	128.894	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#18706 - 	CGI_10005830	superfamily	222263	83	182	1.43E-06	45.3865	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#18708 - 	CGI_10005832	superfamily	207666	7	61	0.000406194	38.0103	cl02605	SCAN superfamily	N	 - 	"SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix."
Q#18711 - 	CGI_10003762	superfamily	247809	628	797	1.03E-21	94.2651	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#18712 - 	CGI_10003763	superfamily	202805	56	92	4.48E-16	67.5978	cl18232	Sec61_beta superfamily	 - 	 - 	"Sec61beta family; This family consists of homologues of Sec61beta - a component of the Sec61/SecYEG protein secretory system. The domain is found in eukaryotes and archaea and is possibly homologous to the bacterial SecG. It consists of a single putative transmembrane helix, preceded by a short stretch containing various charged residues; this arrangement may help determine orientation in the cell membrane."
Q#18713 - 	CGI_10003764	superfamily	245814	31	110	0.00331574	34.0181	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18714 - 	CGI_10003765	superfamily	241832	23	114	2.09E-39	128.83	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18715 - 	CGI_10003766	superfamily	246680	189	269	4.38E-14	65.462	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#18715 - 	CGI_10003766	superfamily	245874	20	83	7.20E-10	54.3546	cl12111	TNFR superfamily	C	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#18716 - 	CGI_10003767	superfamily	241567	150	414	5.70E-87	267.159	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#18717 - 	CGI_10003768	superfamily	246680	7	83	4.10E-13	59.9354	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#18718 - 	CGI_10001245	superfamily	243033	225	356	7.22E-25	97.7741	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#18718 - 	CGI_10001245	superfamily	243033	67	162	1.68E-15	71.9657	cl02428	Ependymin superfamily	C	 - 	Ependymin; Ependymin.  
Q#18719 - 	CGI_10005681	superfamily	218118	94	133	2.80E-08	47.2237	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#18723 - 	CGI_10005685	superfamily	218118	73	113	2.41E-07	44.1421	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#18724 - 	CGI_10005686	superfamily	218118	66	98	2.50E-05	39.9049	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#18725 - 	CGI_10005687	superfamily	218118	69	108	1.76E-06	41.4457	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#18727 - 	CGI_10005058	superfamily	216378	1	362	1.06E-142	413.54	cl03133	IDO superfamily	 - 	 - 	"Indoleamine 2,3-dioxygenase; Indoleamine 2,3-dioxygenase.  "
Q#18729 - 	CGI_10005060	superfamily	216686	2	63	3.17E-14	64.6517	cl18377	Galactosyl_T superfamily	N	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#18731 - 	CGI_10005062	superfamily	246669	59	184	2.82E-54	175.523	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#18731 - 	CGI_10005062	superfamily	246669	194	327	5.96E-45	151.719	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#18732 - 	CGI_10005063	superfamily	243072	91	214	4.81E-26	100.151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18732 - 	CGI_10005063	superfamily	243073	252	291	2.23E-08	49.3909	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#18734 - 	CGI_10005065	superfamily	241596	148	191	2.08E-11	56.0683	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#18735 - 	CGI_10012412	superfamily	241563	61	100	9.75E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18736 - 	CGI_10012413	superfamily	243058	268	381	8.12E-09	53.8575	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18736 - 	CGI_10012413	superfamily	243058	351	469	0.000163241	40.7608	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#18736 - 	CGI_10012413	superfamily	241645	1	75	0.000658567	38.3126	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#18737 - 	CGI_10012414	superfamily	247924	126	204	7.01E-22	86.9937	cl17370	PEMT superfamily	 - 	 - 	Phospholipid methyltransferase; The S. cerevisiae phospholipid methyltransferase (EC:2.1.1.16) has a broad substrate specificity of unsaturated phospholipids.
Q#18738 - 	CGI_10012415	superfamily	241600	14	188	7.71E-50	162.795	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#18740 - 	CGI_10012417	superfamily	220397	73	182	1.88E-20	89.8748	cl10759	NDUF_B5 superfamily	N	 - 	"NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit; Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol."
Q#18741 - 	CGI_10012418	superfamily	241762	31	91	3.21E-19	78.5244	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#18743 - 	CGI_10012420	superfamily	193607	516	647	1.43E-69	224.373	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#18743 - 	CGI_10012420	superfamily	247792	469	509	4.92E-11	58.9964	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18743 - 	CGI_10012420	superfamily	241554	56	220	2.84E-46	162.055	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#18743 - 	CGI_10012420	superfamily	241554	333	435	3.65E-06	46.3737	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#18744 - 	CGI_10002412	superfamily	245201	1	275	0	577.831	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18745 - 	CGI_10002413	superfamily	217062	251	489	1.94E-36	138.171	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#18745 - 	CGI_10002413	superfamily	221621	524	699	2.85E-31	120.505	cl13906	Xylo_C superfamily	 - 	 - 	"Xylosyltransferase C terminal; This domain family is found in eukaryotes, and is typically between 169 and 183 amino acids in length. The family is found in association with pfam02485. There is a single completely conserved residue G that may be functionally important. Xylosyltransferases are enzymes involved in the biosynthesis of the glycosaminoglycan linker region in proteoglycans."
Q#18745 - 	CGI_10002413	superfamily	243093	126	204	1.31E-20	87.9709	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#18746 - 	CGI_10002414	superfamily	147445	4	182	3.39E-20	85.8035	cl05014	UPF0193 superfamily	 - 	 - 	Uncharacterized protein family (UPF0193); This family of proteins is functionally uncharacterized.
Q#18747 - 	CGI_10002415	superfamily	221683	72	161	8.63E-10	56.1231	cl15002	UPF0489 superfamily	 - 	 - 	UPF0489 domain; This family is probably an enzyme which is related to the Arginase family.
Q#18748 - 	CGI_10002416	superfamily	241984	61	151	2.04E-44	147.702	cl00615	Membrane-FADS-like superfamily	C	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#18749 - 	CGI_10002417	superfamily	241984	17	113	4.98E-32	113.034	cl00615	Membrane-FADS-like superfamily	N	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#18750 - 	CGI_10002418	superfamily	241984	17	113	4.98E-32	113.034	cl00615	Membrane-FADS-like superfamily	N	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#18762 - 	CGI_10022297	superfamily	115363	212	236	0.000290236	37.7366	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#18762 - 	CGI_10022297	superfamily	115363	240	260	0.000323627	37.7366	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#18762 - 	CGI_10022297	superfamily	241578	29	55	0.00305479	36.5973	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18763 - 	CGI_10022298	superfamily	241578	18	140	1.29E-05	44.0938	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18763 - 	CGI_10022298	superfamily	115363	264	326	1.46E-13	65.8561	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#18764 - 	CGI_10022299	superfamily	241578	24	125	2.51E-05	42.553	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18764 - 	CGI_10022299	superfamily	115363	212	259	2.76E-12	61.2337	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#18765 - 	CGI_10022300	superfamily	241578	51	227	1.17E-07	50.257	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18765 - 	CGI_10022300	superfamily	115363	300	337	1.22E-08	51.989	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#18765 - 	CGI_10022300	superfamily	207713	516	556	0.00190556	36.9137	cl02729	WWE superfamily	C	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#18765 - 	CGI_10022300	superfamily	115363	380	392	0.00375588	35.8106	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#18766 - 	CGI_10022301	superfamily	248458	122	234	0.00283134	38.8341	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#18766 - 	CGI_10022301	superfamily	241607	394	432	1.76E-08	51.5362	cl00097	KAZAL_FS superfamily	N	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#18768 - 	CGI_10022303	superfamily	243072	167	293	6.15E-21	87.8242	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18768 - 	CGI_10022303	superfamily	243072	70	221	2.62E-12	63.5566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18770 - 	CGI_10022305	superfamily	215821	45	137	1.08E-45	146.231	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#18771 - 	CGI_10022306	superfamily	241733	25	114	2.23E-50	156.722	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#18774 - 	CGI_10022309	superfamily	247736	108	175	2.13E-05	40.7221	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#18775 - 	CGI_10022310	superfamily	243092	371	716	1.08E-32	130.918	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18775 - 	CGI_10022310	superfamily	243092	127	537	3.81E-24	105.11	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18775 - 	CGI_10022310	superfamily	243092	69	159	3.24E-10	61.9672	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18779 - 	CGI_10022314	superfamily	247858	1	92	7.26E-26	95.9178	cl17304	2OG-FeII_Oxy_3 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#18783 - 	CGI_10022318	superfamily	241570	115	220	2.73E-18	81.2182	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#18783 - 	CGI_10022318	superfamily	241570	242	301	0.00767754	35.3794	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#18784 - 	CGI_10022319	superfamily	247724	17	269	3.28E-110	321.313	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18785 - 	CGI_10022320	superfamily	241571	29	151	7.40E-07	48.9479	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#18785 - 	CGI_10022320	superfamily	245814	321	397	9.22E-07	47.8691	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18786 - 	CGI_10022321	superfamily	241629	66	201	1.49E-34	123.014	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#18787 - 	CGI_10022322	superfamily	238191	30	523	2.16E-96	319.278	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#18787 - 	CGI_10022322	superfamily	248012	902	1001	2.15E-18	83.0108	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#18796 - 	CGI_10022331	superfamily	245864	34	441	5.00E-95	297.268	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#18797 - 	CGI_10022332	superfamily	243051	237	327	4.53E-22	90.1297	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#18797 - 	CGI_10022332	superfamily	241583	37	221	3.84E-32	119.213	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#18799 - 	CGI_10022334	superfamily	222429	6	82	6.58E-15	71.1176	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#18803 - 	CGI_10004883	superfamily	247724	32	56	0.000143407	36.16	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18804 - 	CGI_10004884	superfamily	241688	46	352	5.31E-80	247.465	cl00210	Isoprenoid_Biosyn_C1 superfamily	 - 	 - 	"Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD."
Q#18805 - 	CGI_10004885	superfamily	216977	110	291	2.94E-20	85.7497	cl03541	MAM33 superfamily	 - 	 - 	Mitochondrial glycoprotein; This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion interactions.
Q#18806 - 	CGI_10004886	superfamily	217394	9	475	6.42E-114	346.665	cl08387	Alg6_Alg8 superfamily	 - 	 - 	"ALG6, ALG8 glycosyltransferase family; N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue, and Alg8 transfers the second one. In the human alg6 gene, a C->T transition, which causes Ala333 to be replaced with Val, has been identified as the cause of a congenital disorder of glycosylation, designated as type Ic OMIM:603147."
Q#18807 - 	CGI_10004887	superfamily	247724	6	167	1.93E-45	149.35	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18809 - 	CGI_10004889	superfamily	243072	739	859	4.33E-27	108.24	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18809 - 	CGI_10004889	superfamily	243072	430	557	1.19E-17	80.8906	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18809 - 	CGI_10004889	superfamily	243072	68	181	2.83E-14	71.2606	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18809 - 	CGI_10004889	superfamily	243072	362	483	3.40E-12	65.0974	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18809 - 	CGI_10004889	superfamily	243072	133	247	6.39E-12	63.9418	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18811 - 	CGI_10019179	superfamily	192535	247	283	0.00149966	37.9606	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18814 - 	CGI_10019182	superfamily	241574	1	58	7.24E-17	76.4705	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18815 - 	CGI_10019183	superfamily	243066	4	93	2.22E-24	96.0828	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#18815 - 	CGI_10019183	superfamily	219619	315	391	1.99E-11	59.9139	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#18816 - 	CGI_10019184	superfamily	243035	161	231	4.13E-16	71.4969	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18818 - 	CGI_10019186	superfamily	245213	45	80	3.03E-11	54.9502	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18818 - 	CGI_10019186	superfamily	245847	86	152	1.30E-12	61.0333	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#18819 - 	CGI_10019187	superfamily	247905	1	34	3.62E-06	40.6581	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#18821 - 	CGI_10019189	superfamily	216939	1	26	7.94E-05	35.7165	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#18826 - 	CGI_10019194	superfamily	241574	346	602	4.48E-89	283.323	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18826 - 	CGI_10019194	superfamily	241574	740	808	2.45E-09	57.2105	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#18827 - 	CGI_10019195	superfamily	248293	46	94	0.00205706	32.711	cl17739	MADF_DNA_bdg superfamily	C	 - 	Alcohol dehydrogenase transcription factor Myb/SANT-like; The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains.
Q#18829 - 	CGI_10019197	superfamily	245226	285	333	6.40E-06	44.2137	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#18832 - 	CGI_10019200	superfamily	203031	193	251	3.73E-08	50.0192	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#18832 - 	CGI_10019200	superfamily	247999	16	55	0.000422898	38.2404	cl17445	PHD superfamily	N	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#18833 - 	CGI_10009736	superfamily	245814	63	142	1.81E-10	54.4337	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18834 - 	CGI_10009737	superfamily	248289	34	89	0.00121954	34.0288	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#18837 - 	CGI_10009740	superfamily	243062	282	366	1.29E-18	79.6272	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#18838 - 	CGI_10009741	superfamily	241570	242	348	1.44E-19	85.4553	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#18839 - 	CGI_10009742	superfamily	243072	29	153	1.74E-29	113.247	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18839 - 	CGI_10009742	superfamily	245201	384	491	6.62E-06	46.0757	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18840 - 	CGI_10009743	superfamily	241571	536	643	0.00384582	36.9844	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#18841 - 	CGI_10009744	superfamily	241563	1	32	0.00139003	32.6444	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#18842 - 	CGI_10009745	superfamily	215647	144	406	3.49E-64	215.165	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#18842 - 	CGI_10009745	superfamily	243029	61	127	9.26E-24	96.2657	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#18844 - 	CGI_10006923	superfamily	219542	71	170	1.37E-06	48.0068	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#18846 - 	CGI_10006925	superfamily	245814	18	49	0.00606889	31.4994	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18847 - 	CGI_10006926	superfamily	241638	36	163	5.68E-16	70.0896	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#18852 - 	CGI_10006931	superfamily	220647	12	49	0.000339779	38.4628	cl18565	L_HGMIC_fpl superfamily	C	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#18853 - 	CGI_10016903	superfamily	243035	20	134	4.34E-15	66.8745	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18855 - 	CGI_10016905	superfamily	245595	1	158	1.14E-43	150.217	cl11393	Peptidase_M14_like superfamily	N	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#18856 - 	CGI_10016906	superfamily	151798	53	182	9.00E-56	178.02	cl12893	Spy1 superfamily	 - 	 - 	"Cell cycle regulatory protein; Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27. Spy1 is also known as Ringo protein A."
Q#18858 - 	CGI_10016908	superfamily	247724	32	192	2.79E-55	176.699	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18859 - 	CGI_10016909	superfamily	203011	111	197	2.74E-18	81.0993	cl04515	SWIRM superfamily	 - 	 - 	SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
Q#18859 - 	CGI_10016909	superfamily	248054	224	273	2.93E-07	48.6224	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#18860 - 	CGI_10016910	superfamily	245202	12	74	4.02E-25	93.0269	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#18863 - 	CGI_10016913	superfamily	184428	15	156	3.98E-30	112.353	cl14742	PRK13971 superfamily	C	 - 	hydroxyproline-2-epimerase; Provisional
Q#18864 - 	CGI_10016914	superfamily	184428	2	326	8.91E-64	207.112	cl14742	PRK13971 superfamily	 - 	 - 	hydroxyproline-2-epimerase; Provisional
Q#18865 - 	CGI_10016915	superfamily	184428	6	138	1.40E-14	68.0551	cl14742	PRK13971 superfamily	N	 - 	hydroxyproline-2-epimerase; Provisional
Q#18867 - 	CGI_10016917	superfamily	216653	166	286	6.03E-19	80.7191	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#18868 - 	CGI_10016918	superfamily	207627	386	476	2.02E-37	133.529	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#18868 - 	CGI_10016918	superfamily	216653	81	240	1.06E-21	91.5046	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#18868 - 	CGI_10016918	superfamily	207627	515	580	7.60E-17	76.5243	cl02522	Calx-beta superfamily	C	 - 	Calx-beta domain; Calx-beta domain.  
Q#18870 - 	CGI_10016920	superfamily	219458	868	1012	2.38E-46	163.908	cl06529	DRIM superfamily	 - 	 - 	"Down-regulated in metastasis; These eukaryotic proteins include DRIM (Down-Regulated In Metastasis), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells. It is believed to be involved in processing of non-coding RNA."
Q#18871 - 	CGI_10016921	superfamily	243114	3	70	9.65E-09	48.9457	cl02622	Pre-SET superfamily	 - 	 - 	Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.
Q#18871 - 	CGI_10016921	superfamily	243091	79	107	5.81E-05	39.2399	cl02566	SET superfamily	C	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#18872 - 	CGI_10016922	superfamily	243072	855	980	7.54E-36	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18872 - 	CGI_10016922	superfamily	243072	789	914	5.14E-35	130.967	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18877 - 	CGI_10016927	superfamily	247866	16	207	6.54E-26	101.76	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#18878 - 	CGI_10016928	superfamily	247866	88	223	6.11E-26	106.768	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#18878 - 	CGI_10016928	superfamily	244539	178	290	0.00626572	38.0716	cl06868	FNR_like superfamily	C	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#18879 - 	CGI_10016929	superfamily	152695	240	439	7.53E-34	126.756	cl13667	PIP49_C superfamily	 - 	 - 	Pancreatitis induced protein 49 C terminal; This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 344 to 431 amino acids in length. This protein has a single completely conserved residue C that may be functionally important. PIP49 is a putative transmembrane protein which is induced to express during pancreatitis.
Q#18880 - 	CGI_10016930	superfamily	244265	98	302	5.83E-113	328.556	cl05973	FAM20_C_like superfamily	 - 	 - 	"C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins; Drosophila Fj is a Golgi kinase that phosphorylates Ser or Thr residues within extracellular cadherin domains of a transmembrane receptor Fat and its ligand, Dachsous (Ds). The Fat signaling pathway regulates growth, gene expression, and planar cell polarity (PCP). Defects from mutation in the Drosophila fj gene include loss of the intermediate leg joint, and a PCP defect in the eye. Fjx1, the murine homologue of Fj, has been shown to be involved in both the Fat and Hippo signaling pathways, these two pathways intersect at multiple points. The Hippo pathway is important in organ size control and in cancer. FAM20B is a xylose kinase that may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. This domain has homology to a kinase-active site, mutation of three conserved Asp residues at the Drosophila Fj putative active site abolished its ability to phosphorylate Ft and Ds cadherin domains. FAM20A may participate in enamel development and gingival homeostasis, FAM20B in proteoglycan production, and FAM20C in bone development. FAM20C, also called Dentin Matrix Protein 4, is abundant in the dentin matrix, and may participate in the differentiation of mesenchymal precursor cells into functional odontoblast-like cells. Mutations in FAM20C are associated with lethal Osteosclerotic Bone Dysplasia (Raine Syndrome), and mutations in FAM20A with Amelogenesis imperfecta (AI) and Gingival Hyperplasia Syndrome. This model includes the FAM20_C domain family, previously known as DUF1193; FAM20_C appears to be homologous to the catalytic domain of the phosphoinositide 3-kinase (PI3K)-like family."
Q#18881 - 	CGI_10016931	superfamily	202668	454	558	6.81E-25	101.587	cl04110	BK_channel_a superfamily	 - 	 - 	Calcium-activated BK potassium channel alpha subunit; Calcium-activated BK potassium channel alpha subunit.  
Q#18881 - 	CGI_10016931	superfamily	219619	236	302	1.62E-10	59.1435	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#18882 - 	CGI_10014835	superfamily	248345	123	238	2.17E-34	122.383	cl17791	SAC3_GANP superfamily	 - 	 - 	"SAC3/GANP/Nin1/mts3/eIF-3 p25 family; This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits."
Q#18883 - 	CGI_10014836	superfamily	220645	5	326	5.80E-116	344.513	cl10924	DUF2465 superfamily	 - 	 - 	Protein of unknown function (DUF2465); FAM98A and B proteins are found from worms to humans but their function is unknown. This entry is of a family of proteins that is rich in glycines.
Q#18885 - 	CGI_10014838	superfamily	246918	462	516	2.51E-05	42.7778	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#18885 - 	CGI_10014838	superfamily	246918	639	690	0.00124197	37.5663	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#18886 - 	CGI_10014839	superfamily	245814	112	202	0.00153162	35.1575	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18889 - 	CGI_10014842	superfamily	248012	22	157	3.07E-27	100.476	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#18893 - 	CGI_10014846	superfamily	241555	1023	1284	3.07E-92	297.604	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#18893 - 	CGI_10014846	superfamily	245231	662	937	1.24E-85	280.191	cl10019	PurM-like superfamily	 - 	 - 	"AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain."
Q#18893 - 	CGI_10014846	superfamily	245231	255	553	1.40E-80	267.801	cl10019	PurM-like superfamily	 - 	 - 	"AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain."
Q#18894 - 	CGI_10014847	superfamily	241832	384	468	0.0010876	37.9229	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18894 - 	CGI_10014847	superfamily	247805	131	324	1.34E-53	183.455	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18894 - 	CGI_10014847	superfamily	218246	462	615	8.09E-27	106.649	cl12301	OST3_OST6 superfamily	 - 	 - 	"OST3 / OST6 family; The proteins in this family are part of a complex of eight ER proteins that transfers core oligosaccharide from dolichol carrier to Asn-X-Ser/Thr motifs. This family includes both OST3 and OST6, each of which contains four predicted transmembrane helices. Disruption of OST3 and OST6 leads to a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation."
Q#18896 - 	CGI_10014849	superfamily	219621	30	152	1.13E-19	81.2535	cl06777	Rrp15p superfamily	 - 	 - 	Rrp15p; Rrp15p is required for the formation of 60S ribosomal subunits.
Q#18897 - 	CGI_10014850	superfamily	247907	1755	1914	9.57E-17	81.6956	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#18897 - 	CGI_10014850	superfamily	247907	1503	1717	1.39E-15	78.2288	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#18897 - 	CGI_10014850	superfamily	238012	722	770	1.11E-14	72.7722	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	238012	770	820	2.88E-12	65.8386	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	238012	616	668	8.25E-11	61.6014	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	241584	1232	1340	1.01E-09	59.4323	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	4574	4659	1.16E-09	59.4323	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	238012	988	1037	2.14E-09	57.7494	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	241584	3639	3711	4.17E-09	57.5063	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	238012	874	921	5.91E-09	56.2086	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	241584	4192	4293	1.76E-08	55.9655	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	4003	4097	2.07E-08	55.5803	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	238012	670	720	3.13E-08	54.2826	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	238012	945	987	3.14E-08	54.2826	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	241584	2670	2766	5.68E-08	54.4247	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	1045	1126	6.80E-08	54.0395	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	238012	821	873	8.07E-08	53.127	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	241584	4479	4569	1.95E-07	52.4987	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	1351	1443	2.52E-07	52.4987	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	3066	3145	3.23E-07	52.1135	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2483	2576	9.92E-07	50.5727	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2289	2363	1.17E-06	50.1875	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	1128	1210	4.59E-06	48.6467	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2771	2856	5.35E-06	48.2615	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2106	2190	6.38E-06	47.8763	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	3921	3988	1.18E-05	47.1059	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	4867	4963	1.39E-05	47.1059	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	238012	493	541	2.42E-05	45.8082	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	241584	4685	4765	2.82E-05	45.9503	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2197	2284	9.31E-05	44.4095	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	4108	4177	0.00036549	42.4835	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2970	3055	0.000406915	42.4835	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2870	2959	0.000674186	41.7131	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	3816	3881	0.00165252	40.5575	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	238012	550	603	0.00337863	39.2598	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#18897 - 	CGI_10014850	superfamily	241584	4399	4463	0.00452664	39.0167	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	241584	2585	2667	0.00577211	38.6315	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#18897 - 	CGI_10014850	superfamily	243198	298	492	2.71E-21	97.4308	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#18897 - 	CGI_10014850	superfamily	241611	132	272	1.58E-12	69.3396	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#18898 - 	CGI_10014851	superfamily	219619	118	193	3.86E-08	48.358	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#18898 - 	CGI_10014851	superfamily	219619	40	78	0.00152402	35.2612	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#18899 - 	CGI_10014852	superfamily	247725	506	652	1.92E-72	240.695	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#18899 - 	CGI_10014852	superfamily	243096	348	524	2.45E-45	164.008	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#18900 - 	CGI_10016882	superfamily	248369	104	229	8.39E-05	41.2646	cl17815	Yip1 superfamily	 - 	 - 	Yip1 domain; The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterized by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases.
Q#18901 - 	CGI_10016883	superfamily	218653	1	194	4.82E-67	206.006	cl05265	DUF775 superfamily	 - 	 - 	Protein of unknown function (DUF775); This family consists of several eukaryotic proteins of unknown function.
Q#18904 - 	CGI_10016886	superfamily	245814	177	263	2.81E-06	43.8616	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18905 - 	CGI_10016887	superfamily	241642	22	83	0.000190622	35.5809	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#18909 - 	CGI_10016891	superfamily	245814	350	420	1.66E-05	42.4763	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18909 - 	CGI_10016891	superfamily	245814	232	312	7.08E-05	40.78	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18910 - 	CGI_10016892	superfamily	243161	3	49	0.000192268	35.833	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#18911 - 	CGI_10016893	superfamily	241564	82	150	3.19E-21	82.6987	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#18920 - 	CGI_10011642	superfamily	248019	157	283	2.05E-17	76.9393	cl17465	DAGK_cat superfamily	 - 	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#18920 - 	CGI_10011642	superfamily	248019	16	235	8.86E-10	58.3579	cl17465	DAGK_cat superfamily	C	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#18921 - 	CGI_10011643	superfamily	241607	80	112	7.65E-05	38.7902	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#18921 - 	CGI_10011643	superfamily	241607	158	184	0.00249545	34.1678	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#18922 - 	CGI_10011644	superfamily	248338	104	381	1.92E-58	200.905	cl17784	Peptidase_C48 superfamily	N	 - 	"Ulp1 protease family, C-terminal catalytic domain; This domain contains the catalytic triad Cys-His-Asn."
Q#18923 - 	CGI_10011645	superfamily	220695	51	175	0.00112827	39.4843	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#18925 - 	CGI_10011647	superfamily	244882	100	378	4.48E-30	118.518	cl08270	Peptidase_S10 superfamily	N	 - 	Serine carboxypeptidase; Serine carboxypeptidase.  
Q#18925 - 	CGI_10011647	superfamily	244882	30	97	1.26E-12	67.2866	cl08270	Peptidase_S10 superfamily	C	 - 	Serine carboxypeptidase; Serine carboxypeptidase.  
Q#18926 - 	CGI_10011648	superfamily	245201	1318	1552	2.01E-38	145.457	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18926 - 	CGI_10011648	superfamily	243072	41	132	4.06E-09	56.623	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#18926 - 	CGI_10011648	superfamily	247724	662	814	5.92E-15	75.0651	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#18926 - 	CGI_10011648	superfamily	246925	420	548	0.0020527	41.187	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#18927 - 	CGI_10011649	superfamily	243034	2042	2162	2.48E-06	48.1452	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#18927 - 	CGI_10011649	superfamily	243034	1862	1969	7.91E-05	43.5228	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#18927 - 	CGI_10011649	superfamily	243034	1767	1886	8.21E-05	43.5228	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#18927 - 	CGI_10011649	superfamily	243034	2136	2250	0.000255259	41.982	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#18929 - 	CGI_10011651	superfamily	241617	7	81	2.10E-20	82.4205	cl00110	MBD superfamily	 - 	 - 	"MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin.  MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family."
Q#18929 - 	CGI_10011651	superfamily	222512	149	244	2.65E-30	109.692	cl16567	MBD_C superfamily	 - 	 - 	"C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2 and MBD3, the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex, an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics."
Q#18930 - 	CGI_10011652	superfamily	241832	364	467	4.22E-51	170.815	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18930 - 	CGI_10011652	superfamily	241832	234	344	3.56E-42	146.713	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18930 - 	CGI_10011652	superfamily	241832	20	120	3.03E-39	138.127	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18930 - 	CGI_10011652	superfamily	241832	128	230	8.01E-32	117.429	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#18931 - 	CGI_10001214	superfamily	248097	89	211	1.18E-17	75.7646	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18932 - 	CGI_10001215	superfamily	248097	4	43	9.67E-10	50.3414	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18933 - 	CGI_10001216	superfamily	248097	44	166	5.63E-22	86.5502	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#18945 - 	CGI_10005071	superfamily	217473	138	361	1.32E-31	124.4	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#18947 - 	CGI_10010344	superfamily	226749	212	549	5.61E-34	131.54	cl18777	COG4299 superfamily	 - 	 - 	Uncharacterized protein conserved in bacteria [Function unknown]
Q#18949 - 	CGI_10010346	superfamily	243035	214	328	6.04E-28	105.78	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18949 - 	CGI_10010346	superfamily	243035	16	106	7.06E-20	83.0529	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18949 - 	CGI_10010346	superfamily	243035	115	204	1.81E-16	73.8081	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#18952 - 	CGI_10010349	superfamily	241749	23	167	9.50E-28	102.464	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#18955 - 	CGI_10008023	superfamily	247905	59	180	2.90E-17	80.7448	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#18956 - 	CGI_10008024	superfamily	245819	644	818	4.20E-65	216.676	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#18956 - 	CGI_10008024	superfamily	245201	324	501	5.12E-38	142.376	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#18956 - 	CGI_10008024	superfamily	219526	588	629	9.65E-09	55.3179	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#18957 - 	CGI_10006053	superfamily	247745	37	379	0	568.82	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#18957 - 	CGI_10006053	superfamily	245003	373	458	2.25E-26	101.89	cl08536	Alpha-mann_mid superfamily	 - 	 - 	"Alpha mannosidase, middle domain; Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase."
Q#18959 - 	CGI_10006055	superfamily	241691	1	53	0.00150363	35.1804	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#18961 - 	CGI_10006057	superfamily	245819	343	498	6.08E-50	175.845	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#18961 - 	CGI_10006057	superfamily	245819	924	1108	7.70E-44	158.511	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#18961 - 	CGI_10006057	superfamily	218992	545	627	5.94E-18	81.3068	cl05691	DUF1053 superfamily	 - 	 - 	Domain of Unknown Function (DUF1053); This domain is found in Adenylate cyclases.
Q#18962 - 	CGI_10002585	superfamily	247068	693	761	2.26E-07	49.6194	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#18962 - 	CGI_10002585	superfamily	247068	513	575	5.49E-05	42.3006	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#18962 - 	CGI_10002585	superfamily	247068	603	676	0.000328422	40.0255	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#18963 - 	CGI_10002586	superfamily	243092	10	330	4.47E-69	219.899	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#18964 - 	CGI_10002587	superfamily	246925	55	196	0.00052423	39.261	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#18968 - 	CGI_10005226	superfamily	241886	5	236	9.66E-57	185.07	cl00470	Aldo_ket_red superfamily	N	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#18969 - 	CGI_10005227	superfamily	247805	36	217	1.96E-12	63.1252	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#18970 - 	CGI_10005228	superfamily	247905	223	298	3.45E-12	66.1072	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#18971 - 	CGI_10005229	superfamily	241564	54	123	1.90E-22	85.0099	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#18973 - 	CGI_10005231	superfamily	243161	7	91	3.25E-09	49.3558	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#18974 - 	CGI_10005232	superfamily	248281	50	82	0.000235549	37.2595	cl17727	GT1 superfamily	C	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#18976 - 	CGI_10005234	superfamily	246975	10	33	0.000430665	37.6175	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#18978 - 	CGI_10002724	superfamily	220701	181	354	2.08E-06	48.2935	cl18572	DUF2424 superfamily	N	 - 	Protein of unknown function (DUF2424); This is a family of proteins conserved in yeasts. The function is not known.
Q#18979 - 	CGI_10002725	superfamily	248312	2	113	0.00397486	35.0217	cl17758	PMP22_Claudin superfamily	N	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#18980 - 	CGI_10002726	superfamily	192780	80	155	5.52E-18	76.528	cl13103	Med28 superfamily	C	 - 	"Mediator complex subunit 28; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours."
Q#18984 - 	CGI_10007721	superfamily	222429	80	122	0.000961386	36.4497	cl18676	Myb_DNA-bind_5 superfamily	N	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#18985 - 	CGI_10007722	superfamily	189857	1	69	5.88E-16	67.6602	cl07832	Caveolin superfamily	N	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#18986 - 	CGI_10007723	superfamily	241577	124	288	5.34E-81	244.731	cl00056	MH2 superfamily	 - 	 - 	"C-terminal Mad Homology 2 (MH2) domain; The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected  in colorectal and other human cancers."
Q#18987 - 	CGI_10007724	superfamily	219574	434	592	1.31E-24	101.974	cl06698	DC_STAMP superfamily	 - 	 - 	"DC-STAMP-like protein; This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family."
Q#18988 - 	CGI_10007725	superfamily	245814	410	474	2.26E-10	57.1139	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#18989 - 	CGI_10007726	superfamily	245596	77	435	6.63E-162	463.339	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#18992 - 	CGI_10002944	superfamily	222429	3	78	7.20E-20	78.8216	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#18993 - 	CGI_10012790	superfamily	247792	13	65	6.54E-06	42.4328	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#18995 - 	CGI_10012792	superfamily	241578	23	201	8.43E-12	61.813	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#18997 - 	CGI_10012794	superfamily	220215	56	87	0.00101976	34.123	cl09630	FERM_N superfamily	N	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#18999 - 	CGI_10012796	superfamily	241571	479	584	3.90E-13	68.593	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#18999 - 	CGI_10012796	superfamily	245213	812	845	3.18E-08	52.2538	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18999 - 	CGI_10012796	superfamily	245213	928	970	0.00124319	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18999 - 	CGI_10012796	superfamily	245213	891	924	0.00442894	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#18999 - 	CGI_10012796	superfamily	219525	1285	1332	3.22E-06	46.6433	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#18999 - 	CGI_10012796	superfamily	219525	57	96	1.09E-05	45.1026	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#19001 - 	CGI_10012798	superfamily	245814	31	113	4.22E-12	58.2856	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19002 - 	CGI_10012799	superfamily	241862	46	279	9.07E-13	66.6409	cl00437	COG0428 superfamily	 - 	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#19004 - 	CGI_10002773	superfamily	242274	6	165	8.01E-06	43.555	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#19005 - 	CGI_10008388	superfamily	245596	310	631	4.40E-26	108.955	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#19006 - 	CGI_10008389	superfamily	241563	537	573	5.16E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19006 - 	CGI_10008389	superfamily	241563	67	98	0.000118303	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19007 - 	CGI_10008390	superfamily	241758	14	63	1.22E-14	63.543	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#19009 - 	CGI_10008392	superfamily	245815	64	516	0	795.099	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#19009 - 	CGI_10008392	superfamily	245815	561	699	7.36E-78	258.131	cl11961	ALDH-SF superfamily	N	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#19010 - 	CGI_10008393	superfamily	247068	979	1077	7.84E-27	107.399	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	668	765	1.42E-24	100.851	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	1087	1188	5.48E-22	93.5321	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	876	970	3.75E-21	91.2209	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	573	659	1.39E-20	89.2949	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	778	855	1.70E-16	77.7389	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	373	451	5.36E-12	64.2569	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	205	267	1.26E-10	60.4049	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	90	186	2.31E-09	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	1210	1283	7.86E-09	55.0122	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	279	364	8.83E-08	51.9306	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19010 - 	CGI_10008393	superfamily	247068	487	562	3.42E-05	43.8414	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19011 - 	CGI_10008394	superfamily	243161	3	59	1.66E-11	58.1745	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#19016 - 	CGI_10003097	superfamily	241546	87	211	2.35E-28	111.984	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#19017 - 	CGI_10017962	superfamily	245201	156	252	2.03E-15	71.4989	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19018 - 	CGI_10017963	superfamily	245201	5	98	3.90E-16	76.7682	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19019 - 	CGI_10017964	superfamily	245220	134	193	5.67E-19	78.2154	cl09957	zf-UBP superfamily	 - 	 - 	Zn-finger in ubiquitin-hydrolases and other protein; Zn-finger in ubiquitin-hydrolases and other protein.  
Q#19021 - 	CGI_10017966	superfamily	247675	109	465	2.96E-171	502.996	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#19021 - 	CGI_10017966	superfamily	247675	547	853	4.04E-133	404.798	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#19023 - 	CGI_10017968	superfamily	243082	1013	1185	1.04E-56	197.51	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#19023 - 	CGI_10017968	superfamily	241659	196	291	8.93E-15	71.8491	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#19023 - 	CGI_10017968	superfamily	243082	394	577	1.31E-23	103.221	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#19023 - 	CGI_10017968	superfamily	241659	39	97	0.00453241	36.881	cl00175	alpha-crystallin-Hsps_p23-like superfamily	C	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#19028 - 	CGI_10017973	superfamily	247724	43	225	4.28E-49	166.557	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19030 - 	CGI_10017975	superfamily	245847	150	264	0.0016836	36.7658	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#19032 - 	CGI_10017977	superfamily	243034	89	158	6.28E-09	53.9232	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#19033 - 	CGI_10017978	superfamily	242406	3	120	1.60E-20	83.7949	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#19035 - 	CGI_10017980	superfamily	245595	95	388	3.11E-131	381.484	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#19035 - 	CGI_10017980	superfamily	216944	30	79	4.40E-09	52.9699	cl03496	Propep_M14 superfamily	N	 - 	"Carboxypeptidase activation peptide; Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme."
Q#19037 - 	CGI_10017982	superfamily	247097	290	325	0.00325269	35.5046	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#19037 - 	CGI_10017982	superfamily	247097	371	407	0.00901983	34.349	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#19038 - 	CGI_10017983	superfamily	215827	8	172	2.07E-30	119.11	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#19040 - 	CGI_10017985	superfamily	241613	115	148	1.21E-10	53.7498	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#19041 - 	CGI_10017986	superfamily	241613	340	370	1.64E-08	50.6682	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#19041 - 	CGI_10017986	superfamily	241613	163	194	8.39E-05	39.8826	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#19041 - 	CGI_10017986	superfamily	241571	258	331	0.00129762	37.0067	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#19043 - 	CGI_10017988	superfamily	241619	48	101	3.52E-05	39.4844	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#19044 - 	CGI_10017990	superfamily	241564	78	138	7.64E-19	75.7651	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#19053 - 	CGI_10008147	superfamily	216363	2	57	2.35E-06	40.5314	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#19055 - 	CGI_10003809	superfamily	241584	415	526	1.80E-07	49.4171	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#19055 - 	CGI_10003809	superfamily	247792	48	92	6.08E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19055 - 	CGI_10003809	superfamily	128778	254	373	0.00018706	40.3259	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#19055 - 	CGI_10003809	superfamily	241563	210	242	0.000960426	37.652	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19056 - 	CGI_10003810	superfamily	241874	10	562	0	564.497	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#19058 - 	CGI_10003961	superfamily	216423	11	210	5.12E-71	227.504	cl18367	Glyco_hydro_35 superfamily	N	 - 	Glycosyl hydrolases family 35; Glycosyl hydrolases family 35.  
Q#19059 - 	CGI_10003962	superfamily	110440	425	451	0.00503257	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19060 - 	CGI_10003963	superfamily	241597	395	464	6.36E-21	86.5833	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#19060 - 	CGI_10003963	superfamily	207687	195	329	1.49E-16	75.5996	cl02647	AXH superfamily	 - 	 - 	Ataxin-1 and HBP1 module (AXH); AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1). ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression.
Q#19062 - 	CGI_10014216	superfamily	246680	293	362	2.02E-07	49.1224	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#19063 - 	CGI_10014217	superfamily	247684	16	108	3.56E-18	77.7027	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19064 - 	CGI_10014218	superfamily	227036	112	341	4.66E-12	65.7122	cl18794	COG4692 superfamily	C	 - 	Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]
Q#19065 - 	CGI_10014219	superfamily	215647	418	616	8.50E-32	123.873	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#19065 - 	CGI_10014219	superfamily	243029	332	395	7.89E-15	70.4573	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#19066 - 	CGI_10014220	superfamily	245206	3	320	1.72E-62	205.921	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#19068 - 	CGI_10014222	superfamily	245610	6	233	5.73E-94	278.927	cl11424	nitrilase superfamily	 - 	 - 	"Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy."
Q#19071 - 	CGI_10014225	superfamily	248281	113	186	1.72E-05	41.4871	cl17727	GT1 superfamily	 - 	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#19072 - 	CGI_10014226	superfamily	241886	5	227	3.66E-62	205.486	cl00470	Aldo_ket_red superfamily	C	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#19072 - 	CGI_10014226	superfamily	241886	247	433	2.36E-35	132.683	cl00470	Aldo_ket_red superfamily	N	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#19074 - 	CGI_10014228	superfamily	243100	50	99	0.00397625	34.8472	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#19078 - 	CGI_10014232	superfamily	220776	1	279	1.37E-10	59.6555	cl11123	Hap2_elong superfamily	 - 	 - 	"Histone acetylation protein 2; Hap2 is one of three histone acetyltransferases proteins that, in yeasts, are found associated with elongating forms of RNA polymerase II (Elongator). The Haps can be isolated in two forms, as a six-subunit complex with Elongator and as a complex of the three proteins on their own. The role of the Hap complex in transcription is still speculative, being possibly to keep the HAT activity of free Elongator in check, allowing histone acetylation only in the presence of a transcribing polymerase, or the interaction with Haps might render Elongator susceptible to modifications thereby altering its activity."
Q#19080 - 	CGI_10014234	superfamily	247684	2	73	2.85E-18	77.7027	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19081 - 	CGI_10014235	superfamily	247684	1	171	4.00E-35	128.164	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19082 - 	CGI_10014236	superfamily	247905	102	190	2.62E-13	67.2628	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#19083 - 	CGI_10015801	superfamily	245226	80	251	2.46E-24	96.986	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#19086 - 	CGI_10015804	superfamily	247725	6	125	3.11E-74	244.014	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19086 - 	CGI_10015804	superfamily	220787	1351	1549	4.56E-24	103.01	cl11143	NARG2_C superfamily	 - 	 - 	"NMDA receptor-regulated gene protein 2; The transition of neuronal cells from pre-cursor to mature state is regulated by the N-methyl-d-aspartate (NMDA) receptor, a glutamate-gated ion channel that is permeable to Ca2+. NMDA receptors probably mediate this activity by permitting expression of NARG2. NARG2 is transiently expressed, being a regulatory protein that is present in the nucleus of dividing cells and then down-regulated as progenitors exit the cell cycle and begin to differentiate. NARG2 contains repeats of (S/T)PXX, (11 in mouse, six in human), a putative DNA-binding motif that is found in many gene-regulatory proteins including Kruppel, Hunchback and Antennapedi."
Q#19089 - 	CGI_10015807	superfamily	241832	5	73	4.29E-28	102.242	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19089 - 	CGI_10015807	superfamily	243175	135	188	5.91E-08	48.0026	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#19090 - 	CGI_10015808	superfamily	241832	4	73	6.02E-31	110.716	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19090 - 	CGI_10015808	superfamily	243175	84	197	3.87E-08	49.1582	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#19090 - 	CGI_10015808	superfamily	243175	195	249	0.0036154	35.3711	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#19091 - 	CGI_10015809	superfamily	241832	4	73	2.06E-28	102.242	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19091 - 	CGI_10015809	superfamily	243175	84	161	7.53E-05	38.7579	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#19092 - 	CGI_10015810	superfamily	214781	146	262	8.12E-15	71.6044	cl02747	NRF superfamily	 - 	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#19092 - 	CGI_10015810	superfamily	226446	496	730	0.000961388	40.5797	cl18757	COG3936 superfamily	N	 - 	Protein involved in polysaccharide intercellular adhesin (PIA) synthesis/biofilm formation [Carbohydrate transport and metabolism]
Q#19094 - 	CGI_10015812	superfamily	248022	12	366	6.11E-33	127.394	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#19098 - 	CGI_10015816	superfamily	205121	868	892	3.48E-06	45.1876	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#19098 - 	CGI_10015816	superfamily	197732	630	664	1.58E-05	43.3951	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#19098 - 	CGI_10015816	superfamily	205121	730	753	6.39E-05	41.7208	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#19098 - 	CGI_10015816	superfamily	205121	780	804	0.00083316	38.254	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#19099 - 	CGI_10015817	superfamily	241742	512	682	3.01E-72	237.211	cl00271	PI3Ka superfamily	 - 	 - 	"Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture."
Q#19099 - 	CGI_10015817	superfamily	241623	685	1046	3.46E-154	464.968	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#19099 - 	CGI_10015817	superfamily	246669	324	479	5.68E-67	222.359	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19099 - 	CGI_10015817	superfamily	198687	29	106	5.93E-27	106.59	cl02483	PI3K_p85B superfamily	 - 	 - 	"PI3-kinase family, p85-binding domain; PI3-kinase family, p85-binding domain.  "
Q#19099 - 	CGI_10015817	superfamily	207610	175	291	1.17E-12	66.1981	cl02484	PI3K_rbd superfamily	 - 	 - 	"PI3-kinase family, ras-binding domain; Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding pfam00788 domains (unpublished observation)."
Q#19100 - 	CGI_10015818	superfamily	247057	837	904	1.37E-43	153.874	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#19100 - 	CGI_10015818	superfamily	247057	924	989	2.22E-42	150.316	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#19100 - 	CGI_10015818	superfamily	247057	1009	1081	7.57E-39	140.531	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#19100 - 	CGI_10015818	superfamily	243054	204	383	0.000211946	42.4328	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#19101 - 	CGI_10015819	superfamily	201526	67	125	2.16E-09	50.9997	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#19103 - 	CGI_10015821	superfamily	247939	346	398	0.000179496	39.7914	cl17385	DUF442 superfamily	N	 - 	Putative phosphatase (DUF442); Although this domain is uncharacterized it seems likely that it performs a phosphatase function.
Q#19103 - 	CGI_10015821	superfamily	247939	62	198	0.00151839	37.3464	cl17385	DUF442 superfamily	 - 	 - 	Putative phosphatase (DUF442); Although this domain is uncharacterized it seems likely that it performs a phosphatase function.
Q#19104 - 	CGI_10015822	superfamily	205166	14	43	0.00839391	33.8755	cl18265	DUF3850 superfamily	C	 - 	"Domain of Unknown Function with PDB structure (DUF3850); The search results from NCBI sequence alignment indicates a conserved domain belonging to ASCH superfamily. Dali searching results show that the protein is a structurally similar to the PUA domain, suggesting it may be involved in RNA recognition. It has been reported that the deletion of PUA genes results in impaired growth (RluD) and competitive disadvantage (TruB) in Escherichia coli. Suggestions have been put forward that, apart from their usual catalytic role, certain PUS enzymes (e.g. TruB) may also act as chaperones for RNA folding. The interface interaction indicates that the biomolecule of protein NP_809782.1 should be a dimer."
Q#19105 - 	CGI_10015823	superfamily	247724	1	108	2.47E-20	82.2392	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19107 - 	CGI_10015825	superfamily	247743	333	478	0.00128546	38.6663	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#19108 - 	CGI_10015826	superfamily	248458	31	351	1.07E-22	100.081	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19108 - 	CGI_10015826	superfamily	248458	555	786	2.58E-19	89.6805	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19109 - 	CGI_10015827	superfamily	248458	108	404	2.57E-10	60.7905	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19110 - 	CGI_10015828	superfamily	247725	1344	1483	2.96E-44	158.927	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19110 - 	CGI_10015828	superfamily	243096	1137	1322	6.00E-32	125.103	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#19110 - 	CGI_10015828	superfamily	247683	1496	1550	8.30E-29	112.044	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#19112 - 	CGI_10015830	superfamily	243035	35	158	7.79E-28	104.239	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19113 - 	CGI_10015831	superfamily	247725	714	821	3.71E-47	164.062	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19116 - 	CGI_10003213	superfamily	110440	141	161	0.00549754	32.3797	cl03211	NHL superfamily	C	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19117 - 	CGI_10015453	superfamily	247856	76	125	0.000383836	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19121 - 	CGI_10015457	superfamily	247792	46	90	8.80E-15	67.4708	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19122 - 	CGI_10015458	superfamily	247727	296	401	5.07E-18	79.7814	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19122 - 	CGI_10015458	superfamily	247727	62	160	1.49E-11	61.2918	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19123 - 	CGI_10015459	superfamily	241565	521	600	6.00E-07	48.0867	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#19123 - 	CGI_10015459	superfamily	247908	156	291	4.88E-40	145.446	cl17354	NIF superfamily	 - 	 - 	NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.
Q#19124 - 	CGI_10015460	superfamily	241644	15	141	2.82E-23	89.6607	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#19126 - 	CGI_10015462	superfamily	245864	69	497	2.41E-111	341.951	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#19127 - 	CGI_10015463	superfamily	242849	7	79	1.54E-31	108.83	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#19128 - 	CGI_10015464	superfamily	243072	112	217	6.40E-31	114.788	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19128 - 	CGI_10015464	superfamily	243072	33	163	4.35E-24	95.5282	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19128 - 	CGI_10015464	superfamily	243073	334	373	4.76E-05	40.536	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#19129 - 	CGI_10015465	superfamily	201894	28	345	2.63E-98	299.659	cl03288	Glyco_hydro_56 superfamily	 - 	 - 	Hyaluronidase; Hyaluronidase.  
Q#19130 - 	CGI_10015466	superfamily	201894	56	373	5.10E-93	295.036	cl03288	Glyco_hydro_56 superfamily	 - 	 - 	Hyaluronidase; Hyaluronidase.  
Q#19130 - 	CGI_10015466	superfamily	242240	520	673	9.08E-53	181.721	cl00997	DUF297 superfamily	 - 	 - 	TM1410 hypothetical-related protein; TM1410 hypothetical-related protein.  
Q#19131 - 	CGI_10015467	superfamily	242240	37	211	1.36E-49	164.772	cl00997	DUF297 superfamily	 - 	 - 	TM1410 hypothetical-related protein; TM1410 hypothetical-related protein.  
Q#19132 - 	CGI_10015468	superfamily	241680	15	229	1.89E-68	214.425	cl00200	MIP superfamily	 - 	 - 	"Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms."
Q#19133 - 	CGI_10015469	superfamily	245819	838	997	9.13E-55	188.557	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#19133 - 	CGI_10015469	superfamily	245225	25	401	5.83E-75	253.324	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#19133 - 	CGI_10015469	superfamily	245201	507	761	1.58E-42	156.928	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19133 - 	CGI_10015469	superfamily	219526	769	824	2.60E-06	47.9991	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#19134 - 	CGI_10015470	superfamily	243035	23	138	7.97E-19	78.0453	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19135 - 	CGI_10003663	superfamily	209898	13	35	0.000598477	35.0718	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#19135 - 	CGI_10003663	superfamily	209898	57	78	0.00138363	34.2383	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#19136 - 	CGI_10003664	superfamily	203213	485	521	2.36E-07	48.2682	cl04999	HTH_psq superfamily	 - 	 - 	"helix-turn-helix, Psq domain; This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence."
Q#19136 - 	CGI_10003664	superfamily	203213	187	218	6.63E-07	47.1126	cl04999	HTH_psq superfamily	C	 - 	"helix-turn-helix, Psq domain; This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence."
Q#19137 - 	CGI_10003665	superfamily	241646	1102	1147	8.14E-11	59.7711	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#19137 - 	CGI_10003665	superfamily	241646	674	722	3.97E-10	57.8451	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#19137 - 	CGI_10003665	superfamily	241646	853	901	4.98E-10	57.4599	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#19137 - 	CGI_10003665	superfamily	243060	571	640	1.14E-09	57.3888	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#19137 - 	CGI_10003665	superfamily	243060	999	1068	1.14E-09	57.3888	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#19137 - 	CGI_10003665	superfamily	243060	183	284	1.39E-08	53.922	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#19137 - 	CGI_10003665	superfamily	243060	786	819	0.00639977	36.588	cl02507	SEA superfamily	NC	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#19139 - 	CGI_10003667	superfamily	241733	8	68	2.79E-34	115.306	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#19140 - 	CGI_10003668	superfamily	241733	4	77	9.34E-43	137.648	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#19142 - 	CGI_10002963	superfamily	243035	33	152	1.05E-23	90.7569	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19145 - 	CGI_10002966	superfamily	248097	2	113	1.09E-11	56.8898	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19148 - 	CGI_10003284	superfamily	245847	143	217	5.33E-05	41.334	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#19149 - 	CGI_10013796	superfamily	247727	36	138	5.90E-09	50.5063	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19150 - 	CGI_10013797	superfamily	247727	98	200	4.15E-08	49.3507	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19151 - 	CGI_10013798	superfamily	245201	1	256	5.12E-139	396.424	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19152 - 	CGI_10013799	superfamily	243058	356	462	3.41E-07	49.6203	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#19153 - 	CGI_10013800	superfamily	241629	23	147	1.52E-29	110.302	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#19154 - 	CGI_10013801	superfamily	243074	31	77	6.21E-14	66.7613	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19156 - 	CGI_10013803	superfamily	245208	22	511	0	593.537	cl09933	ACAD superfamily	N	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#19158 - 	CGI_10013805	superfamily	245208	42	463	0	533.06	cl09933	ACAD superfamily	C	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#19158 - 	CGI_10013805	superfamily	201956	451	537	5.50E-24	99.2062	cl08333	ACOX superfamily	N	 - 	Acyl-CoA oxidase; This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA.
Q#19159 - 	CGI_10013806	superfamily	218499	28	393	1.88E-134	393.714	cl04986	ALG3 superfamily	 - 	 - 	"ALG3 protein; The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl pyrophosphate. Whereas early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9GlcNAc2-PP-Dol on the lumenal side use Dol-P-Man. ALG3 gene encodes the Dol-P-Man:Man5GlcNAc2-PP-Dol mannosyltransferase."
Q#19160 - 	CGI_10013807	superfamily	245231	443	740	2.70E-164	486.212	cl10019	PurM-like superfamily	 - 	 - 	"AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain."
Q#19160 - 	CGI_10013807	superfamily	241838	772	956	1.08E-93	296.221	cl00395	FMT_core superfamily	 - 	 - 	"Formyltransferase, catalytic core domain; Formyltransferase, catalytic core domain. The proteins of this superfamily contain a formyltransferase domain that hydrolyzes the removal of a formyl group from its substrate as part of a multistep transfer mechanism, and this alignment model represents the catalytic core of the formyltransferase domain.  This family includes the following known members; Glycinamide Ribonucleotide Transformylase (GART), Formyl-FH4 Hydrolase, Methionyl-tRNA Formyltransferase, ArnA, and 10-Formyltetrahydrofolate Dehydrogenase (FDH).  Glycinamide Ribonucleotide Transformylase  (GART) catalyzes the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Methionyl-tRNA Formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA, which plays important role in translation initiation. ArnA is required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. 10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. Members of this family are multidomain proteins. The formyltransferase domain is located at the N-terminus of FDH, Methionyl-tRNA Formyltransferase and ArnA, and at the C-terminus of Formyl-FH4 Hydrolase.  Prokaryotic Glycinamide Ribonucleotide Transformylase (GART) is a single domain protein while eukaryotic GART is a trifunctional protein that catalyzes the second, third and fifth steps in de novo purine biosynthesis."
Q#19160 - 	CGI_10013807	superfamily	247809	104	269	4.24E-83	267.97	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#19160 - 	CGI_10013807	superfamily	217251	4	103	7.84E-43	152.215	cl03744	GARS_N superfamily	 - 	 - 	"Phosphoribosylglycinamide synthetase, N domain; Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam00289)."
Q#19160 - 	CGI_10013807	superfamily	217250	304	399	1.30E-19	85.6554	cl03743	GARS_C superfamily	 - 	 - 	"Phosphoribosylglycinamide synthetase, C domain; Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the C-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02787)."
Q#19161 - 	CGI_10013808	superfamily	217725	65	333	9.29E-60	195.795	cl18425	FGE-sulfatase superfamily	 - 	 - 	"Formylglycine-generating sulfatase enzyme; This domain is found in eukaryotic proteins required for post-translational sulphatase modification (SUMF1). These proteins are associated with the rare disorder multiple sulphatase deficiency (MSD). The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase. Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases. FGE is localised to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesised sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilised by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidized cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases."
Q#19164 - 	CGI_10013811	superfamily	219566	32	107	5.32E-17	72.6655	cl06691	DUF1620 superfamily	N	 - 	Protein of unknown function (DUF1620); These sequences are mainly derived from predicted eukaryotic proteins. The region in question lies towards the C-terminus of these large proteins and is approximately 300 amino acid residues long.
Q#19165 - 	CGI_10017040	superfamily	245201	36	97	2.91E-07	46.2393	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19166 - 	CGI_10017041	superfamily	247683	499	559	4.10E-37	133.988	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#19166 - 	CGI_10017041	superfamily	247744	654	770	1.75E-25	103.381	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#19166 - 	CGI_10017041	superfamily	241622	382	462	8.18E-21	88.3926	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19166 - 	CGI_10017041	superfamily	241622	164	242	2.75E-20	86.8518	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19166 - 	CGI_10017041	superfamily	243136	2	64	8.04E-28	108.026	cl02672	L27 superfamily	 - 	 - 	L27 domain; The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.
Q#19167 - 	CGI_10017042	superfamily	247684	111	268	2.71E-12	64.5323	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19167 - 	CGI_10017042	superfamily	202746	250	487	3.87E-85	264.927	cl08402	Hexokinase_2 superfamily	 - 	 - 	Hexokinase; Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains.
Q#19168 - 	CGI_10017043	superfamily	145949	87	199	9.93E-24	94.3121	cl03870	Nucleoplasmin superfamily	C	 - 	Nucleoplasmin; Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays.
Q#19170 - 	CGI_10017045	superfamily	241579	37	85	0.00828024	33.6508	cl00060	FGF superfamily	N	 - 	"Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate embryogenesis, and has neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate one of four cell surface FGF receptors. Upon binding to FGF, the receptors dimerize and their intracellular tyrosine kinase domains become active. FGFs have internal pseudo-threefold symmetry (beta-trefoil topology)."
Q#19176 - 	CGI_10017052	superfamily	241749	1	90	9.18E-13	59.7069	cl00280	globin_like superfamily	N	 - 	superfamily containing globins and truncated hemoglobins
Q#19177 - 	CGI_10017053	superfamily	247724	118	270	2.39E-22	90.9782	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19180 - 	CGI_10017056	superfamily	247856	55	103	6.60E-15	64.4913	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19181 - 	CGI_10017057	superfamily	246680	30	90	7.26E-15	64.6494	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#19182 - 	CGI_10012829	superfamily	243088	14	132	9.26E-53	177.167	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#19182 - 	CGI_10012829	superfamily	245201	185	394	9.59E-10	57.6317	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19183 - 	CGI_10012830	superfamily	218118	761	826	7.57E-06	44.9125	cl04552	CD225 superfamily	N	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#19184 - 	CGI_10012831	superfamily	191163	21	186	3.68E-20	90.1763	cl04888	DUF667 superfamily	 - 	 - 	"Protein of unknown function (DUF667); This family of proteins are highly conserved in eukaryotes. Some proteins in the family are annotated as transcription factors. However, there is currently no support for this in the literature."
Q#19185 - 	CGI_10012832	superfamily	248097	86	224	1.37E-20	83.8538	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19186 - 	CGI_10012833	superfamily	204122	32	69	3.91E-07	42.5271	cl07623	TMA7 superfamily	N	 - 	Translation machinery associated TMA7; TMA7 plays a role in protein translation. Deletions of the TMA7 gene results in altered protein synthesis rates.
Q#19187 - 	CGI_10012834	superfamily	241563	66	102	0.00457871	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19191 - 	CGI_10012838	superfamily	217725	73	350	2.95E-79	251.649	cl18425	FGE-sulfatase superfamily	 - 	 - 	"Formylglycine-generating sulfatase enzyme; This domain is found in eukaryotic proteins required for post-translational sulphatase modification (SUMF1). These proteins are associated with the rare disorder multiple sulphatase deficiency (MSD). The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase. Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases. FGE is localised to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesised sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilised by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidized cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases."
Q#19192 - 	CGI_10012839	superfamily	247727	68	173	1.84E-09	54.3583	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19192 - 	CGI_10012839	superfamily	247727	260	341	1.77E-08	51.6619	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19192 - 	CGI_10012839	superfamily	219506	332	380	0.00467234	35.3284	cl18513	Eco57I superfamily	C	 - 	Eco57I restriction-modification methylase; Homologues of the Escherichia coli Eco57I restriction-modification methylase are found in several phylogenetically diverse bacteria. The structure of TaqI has been solved.
Q#19193 - 	CGI_10012840	superfamily	245213	41	77	8.33E-06	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19194 - 	CGI_10012841	superfamily	245213	447	484	3.18E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19194 - 	CGI_10012841	superfamily	245213	333	368	4.93E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19194 - 	CGI_10012841	superfamily	245213	295	331	0.000171876	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19194 - 	CGI_10012841	superfamily	245213	371	407	0.000603014	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19194 - 	CGI_10012841	superfamily	245213	763	792	0.00467544	36.0754	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19194 - 	CGI_10012841	superfamily	245213	652	681	0.00587773	35.6902	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19195 - 	CGI_10012842	superfamily	216363	74	182	5.44E-11	55.9394	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#19197 - 	CGI_10012844	superfamily	248097	9	130	9.82E-20	79.2314	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19199 - 	CGI_10012846	superfamily	245205	61	161	2.09E-32	115.311	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#19199 - 	CGI_10012846	superfamily	241739	165	198	2.84E-09	54.1183	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#19200 - 	CGI_10014753	superfamily	247750	7	393	0	560.77	cl17196	E1_enzyme_family superfamily	 - 	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#19200 - 	CGI_10014753	superfamily	247750	420	525	6.67E-20	90.8268	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#19201 - 	CGI_10014754	superfamily	217881	33	90	8.36E-18	76.8214	cl04390	Abhydro_lipase superfamily	 - 	 - 	Partial alpha/beta-hydrolase lipase region; This family corresponds to a N-terminal part of an alpha/beta hydrolase domain.
Q#19202 - 	CGI_10014755	superfamily	243035	24	138	6.35E-20	82.6677	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19203 - 	CGI_10014756	superfamily	247743	356	512	1.35E-12	66.4007	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#19203 - 	CGI_10014756	superfamily	191262	629	833	1.61E-96	302.6	cl18170	Lon_C superfamily	 - 	 - 	"Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops."
Q#19204 - 	CGI_10014757	superfamily	199166	261	433	4.77E-12	64.656	cl15308	AMN1 superfamily	N	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#19204 - 	CGI_10014757	superfamily	243074	18	50	0.00140843	37.1009	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19204 - 	CGI_10014757	superfamily	199166	492	567	0.00424731	37.692	cl15308	AMN1 superfamily	NC	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#19205 - 	CGI_10014758	superfamily	243092	9	236	9.22E-16	74.2936	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19206 - 	CGI_10014759	superfamily	247724	34	348	0	589.112	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19207 - 	CGI_10014760	superfamily	247724	34	54	6.77E-12	57.5364	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19208 - 	CGI_10014761	superfamily	248247	26	379	4.51E-107	334.187	cl17693	Integrin_beta superfamily	 - 	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#19208 - 	CGI_10014761	superfamily	149701	643	681	4.95E-09	53.3741	cl07373	Integrin_b_cyt superfamily	 - 	 - 	"Integrin beta cytoplasmic domain; Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion. Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit. Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity. This domain corresponds to the cytoplasmic domain of the beta subunit."
Q#19208 - 	CGI_10014761	superfamily	219669	545	609	0.00584176	35.8316	cl06832	Integrin_B_tail superfamily	C	 - 	Integrin beta tail domain; This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
Q#19210 - 	CGI_10014763	superfamily	219849	521	612	1.42E-16	77.9951	cl09597	RIH_assoc superfamily	 - 	 - 	"RyR and IP3R Homology associated; This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815."
Q#19211 - 	CGI_10014764	superfamily	216456	468	628	9.01E-07	49.6294	cl03182	RYDR_ITPR superfamily	 - 	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#19211 - 	CGI_10014764	superfamily	197746	322	368	0.000389882	40.0171	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#19213 - 	CGI_10014766	superfamily	241619	26	95	0.000453707	38.6049	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#19214 - 	CGI_10014767	superfamily	241787	92	170	1.33E-31	110.717	cl00326	Ribosomal_L23 superfamily	 - 	 - 	Ribosomal protein L23; Ribosomal protein L23.  
Q#19214 - 	CGI_10014767	superfamily	202819	46	85	2.47E-09	49.9922	cl04335	Ribosomal_L23eN superfamily	N	 - 	"Ribosomal protein L23, N-terminal domain; The N-terminal domain appears to be specific to the eukaryotic ribosomal proteins L25, L23, and L23a."
Q#19218 - 	CGI_10014771	superfamily	222429	11	91	4.02E-09	51.4724	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#19221 - 	CGI_10018282	superfamily	248391	25	259	5.67E-81	247.658	cl17837	DUF1295 superfamily	 - 	 - 	Protein of unknown function (DUF1295); This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long.
Q#19222 - 	CGI_10018283	superfamily	245814	135	190	5.31E-05	40.468	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19223 - 	CGI_10018284	superfamily	222150	148	170	5.05E-05	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#19223 - 	CGI_10018284	superfamily	222150	177	196	0.00104251	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#19223 - 	CGI_10018284	superfamily	222150	118	144	0.00274894	34.2897	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#19225 - 	CGI_10018286	superfamily	242406	131	276	2.59E-39	136.182	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#19235 - 	CGI_10018297	superfamily	241610	88	141	1.01E-19	82.683	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#19235 - 	CGI_10018297	superfamily	241610	182	230	3.98E-18	78.4458	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#19235 - 	CGI_10018297	superfamily	241610	354	407	9.09E-18	77.2902	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#19235 - 	CGI_10018297	superfamily	241646	290	339	4.62E-05	41.2007	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#19237 - 	CGI_10018299	superfamily	218118	54	134	8.53E-13	59.9353	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#19238 - 	CGI_10018300	superfamily	243107	945	989	1.28E-11	61.407	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#19238 - 	CGI_10018300	superfamily	243154	689	740	2.81E-06	46.0564	cl02715	Surp superfamily	 - 	 - 	Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
Q#19239 - 	CGI_10018301	superfamily	243098	80	128	1.59E-08	49.5187	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19240 - 	CGI_10018302	superfamily	202529	114	184	4.28E-09	50.6376	cl18228	MtN3_slv superfamily	 - 	 - 	"Sugar efflux transporter for intercellular exchange; This family includes proteins such as drosophila saliva, MtN3 involved in root nodule development and a protein involved in activation and expression of recombination activation genes (RAGs). Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This family contains a region of two transmembrane helices that is found in two copies in most members of the family. This family also contains specific sugar efflux transporters that are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. In many organisims it meditaes gluose transport; in Arabidopsis it is necessary for pollen viability; and two of the rice homologues are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter."
Q#19242 - 	CGI_10018304	superfamily	222302	204	290	1.87E-19	81.7141	cl16342	DUF4151 superfamily	 - 	 - 	Domain of unknown function (DUF4151); This domain is found on dynein heavy chain proteins. The exact function is not known but it is conserved from plants to Sch. pombe to human.
Q#19242 - 	CGI_10018304	superfamily	197732	46	73	0.000286785	38.0023	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#19243 - 	CGI_10018305	superfamily	241999	204	361	1.01E-05	44.7957	cl00641	Cas4_I-A_I-B_I-C_I-D_II-B superfamily	 - 	 - 	CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster
Q#19244 - 	CGI_10018306	superfamily	248289	584	636	0.000117059	40.4851	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#19244 - 	CGI_10018306	superfamily	248289	260	311	0.00164385	37.0183	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#19244 - 	CGI_10018306	superfamily	248289	318	368	0.00230877	36.6331	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#19244 - 	CGI_10018306	superfamily	243049	13	67	0.00344155	36.2895	cl02472	IGFBP superfamily	C	 - 	Insulin-like growth factor binding protein; Insulin-like growth factor binding protein.  
Q#19245 - 	CGI_10018307	superfamily	243212	176	304	2.15E-18	80.4657	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#19245 - 	CGI_10018307	superfamily	215866	6	149	4.08E-12	62.728	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#19246 - 	CGI_10018308	superfamily	215866	7	147	9.44E-18	77.3655	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#19246 - 	CGI_10018308	superfamily	243212	174	278	4.87E-13	63.9022	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#19247 - 	CGI_10018309	superfamily	247639	172	497	0	555.706	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#19247 - 	CGI_10018309	superfamily	247683	506	558	3.95E-24	96.1223	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#19248 - 	CGI_10018310	superfamily	201678	208	236	0.000185752	38.6352	cl03138	PPTA superfamily	 - 	 - 	"Protein prenyltransferase alpha subunit repeat; Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family."
Q#19255 - 	CGI_10018317	superfamily	245205	36	70	0.001345	35.2913	cl09930	RPA_2b-aaRSs_OBF_like superfamily	NC	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#19260 - 	CGI_10000425	superfamily	247866	3	153	1.05E-12	63.6256	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#19261 - 	CGI_10001632	superfamily	245201	108	429	0	648.445	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19261 - 	CGI_10001632	superfamily	241566	1	22	0.00445664	35.1227	cl00040	C1 superfamily	N	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#19262 - 	CGI_10001633	superfamily	243066	23	126	5.47E-17	77.6577	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19262 - 	CGI_10001633	superfamily	198867	136	234	3.03E-11	60.818	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#19263 - 	CGI_10003124	superfamily	217473	103	326	9.88E-25	104.369	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#19264 - 	CGI_10003125	superfamily	247750	10	84	1.31E-39	137.421	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#19265 - 	CGI_10007008	superfamily	205157	347	382	1.32E-06	45.6063	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#19265 - 	CGI_10007008	superfamily	241578	124	168	4.64E-05	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19267 - 	CGI_10007010	superfamily	245213	6	38	5.37E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19267 - 	CGI_10007010	superfamily	245213	132	172	0.00403164	35.305	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19268 - 	CGI_10007011	superfamily	245213	152	188	8.46E-07	47.6314	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19268 - 	CGI_10007011	superfamily	245213	39	74	1.42E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19268 - 	CGI_10007011	superfamily	245213	76	112	1.52E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19268 - 	CGI_10007011	superfamily	245213	114	150	4.27E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19268 - 	CGI_10007011	superfamily	245213	1055	1089	0.000403224	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19268 - 	CGI_10007011	superfamily	245213	801	832	0.00362789	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19268 - 	CGI_10007011	superfamily	241578	716	759	4.66E-09	56.6243	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19268 - 	CGI_10007011	superfamily	241578	962	1008	0.0033637	38.9052	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19270 - 	CGI_10007013	superfamily	241574	46	283	1.57E-102	318.376	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#19271 - 	CGI_10007014	superfamily	202711	2	145	2.06E-76	227.62	cl04190	Mob1_phocein superfamily	 - 	 - 	"Mob1/phocein family; Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin."
Q#19272 - 	CGI_10007015	superfamily	248097	17	46	3.79E-08	45.3338	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19274 - 	CGI_10003082	superfamily	241896	82	285	5.13E-96	284.008	cl00483	UDG_like superfamily	 - 	 - 	"Uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDG) catalyzes the removal of uracil from DNA, which initiates the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. At least five UDG families have been characterized so far; these families share similar overall folds and common active site motifs. They demonstrate different substrate specificities, but often the function of one enzyme can be complemented by the other. Family 1 enzymes are active against uracil in both ssDNA and dsDNA, and recognize uracil explicitly in an extrahelical conformation via a combination of protein and bound-water interactions. Family 2 enzymes are mismatch specific and explicitly recognize the widowed guanine on the complementary strand, rather than the extrahelical scissile pyrimidine. This allows a broader specificity so that some Family 2 enzymes can excise uracil as well as 3, N(4)-ethenocytosine from mismatches with guanine. A Family 3 UDG from human was first characterized to remove Uracil from ssDNA, hence the name hSMUG (single-strand-selective monofunctional uracil-DNA glycosylase). However, subsequent research has shown that hSMUG1 and its rat ortholog can remove uracil and its oxidized pyrimidine derivatives from both, ssDNA and dsDNA. Enzymes in Families 4 and 5 are both thermostable. Family 4 enzymes specifically recognize uracil in a manner similar to human UDG (Family 1), rather than guanine in the complementary strand DNA, as does E. coli MUG (Family 2). These results suggest that the mechanism by which Family 4 UDGs remove uracils from DNA is similar to that of Family 1 enzyme. Although Family 5 enzymes are close relatives of Family 4, they show different substrate specificities."
Q#19277 - 	CGI_10011615	superfamily	238012	1973	2009	1.52E-05	45.0378	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#19277 - 	CGI_10011615	superfamily	238012	1841	1875	6.44E-05	43.1118	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#19277 - 	CGI_10011615	superfamily	245213	1925	1957	0.000283114	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19277 - 	CGI_10011615	superfamily	202224	174	290	2.48E-49	173.636	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#19277 - 	CGI_10011615	superfamily	210240	13	54	1.75E-11	62.2802	cl15840	JmjN superfamily	 - 	 - 	jmjN domain; jmjN domain.  
Q#19277 - 	CGI_10011615	superfamily	248279	1609	1641	2.71E-10	60.4283	cl17725	zf-HC5HC2H superfamily	C	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#19277 - 	CGI_10011615	superfamily	247999	1570	1602	2.35E-06	47.2551	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#19277 - 	CGI_10011615	superfamily	238012	1887	1925	0.00499293	37.719	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#19281 - 	CGI_10011619	superfamily	241597	100	165	4.13E-13	63.4157	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#19283 - 	CGI_10011621	superfamily	248097	144	273	7.10E-15	68.4458	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19286 - 	CGI_10005435	superfamily	241563	61	97	1.65E-05	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19287 - 	CGI_10002625	superfamily	244843	98	622	5.11E-139	418.943	cl08040	Ggt superfamily	 - 	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#19288 - 	CGI_10002626	superfamily	244843	42	94	0.00141917	34.8993	cl08040	Ggt superfamily	N	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#19289 - 	CGI_10002627	superfamily	222617	256	394	2.48E-39	143.565	cl16738	YHYH superfamily	 - 	 - 	"YHYH protein; This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif."
Q#19289 - 	CGI_10002627	superfamily	222617	36	174	6.00E-39	142.409	cl16738	YHYH superfamily	 - 	 - 	"YHYH protein; This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif."
Q#19289 - 	CGI_10002627	superfamily	207546	689	749	5.11E-33	122.529	cl02165	CBFB_NFYA superfamily	 - 	 - 	CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B.  
Q#19290 - 	CGI_10002628	superfamily	241733	5	74	3.83E-40	128.403	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#19291 - 	CGI_10021774	superfamily	216653	155	276	3.10E-09	53.3699	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#19292 - 	CGI_10021775	superfamily	219000	185	345	3.10E-16	78.4571	cl05717	Drf_FH3 superfamily	 - 	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#19292 - 	CGI_10021775	superfamily	219001	70	177	1.57E-05	45.3775	cl05720	Drf_GBD superfamily	N	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#19293 - 	CGI_10021776	superfamily	247684	58	190	1.28E-08	54.976	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19294 - 	CGI_10021777	superfamily	247684	27	131	1.47E-06	44.9608	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19298 - 	CGI_10021781	superfamily	241563	45	82	1.41E-08	51.9043	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19298 - 	CGI_10021781	superfamily	128778	89	214	1.58E-21	91.1722	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#19298 - 	CGI_10021781	superfamily	216033	257	347	5.72E-20	85.8484	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#19298 - 	CGI_10021781	superfamily	110440	594	621	4.57E-07	47.4025	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19298 - 	CGI_10021781	superfamily	110440	547	574	2.30E-05	42.3949	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19298 - 	CGI_10021781	superfamily	110440	638	665	0.000308854	38.9281	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19298 - 	CGI_10021781	superfamily	110440	500	527	0.000978473	37.3873	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19300 - 	CGI_10021783	superfamily	219000	145	310	5.83E-22	95.4059	cl05717	Drf_FH3 superfamily	 - 	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#19300 - 	CGI_10021783	superfamily	219001	19	139	2.98E-10	59.6299	cl05720	Drf_GBD superfamily	N	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#19303 - 	CGI_10021786	superfamily	245226	170	359	1.46E-49	174.78	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#19305 - 	CGI_10021788	superfamily	248363	9	138	3.57E-59	181.657	cl17809	Sedlin_N superfamily	 - 	 - 	"Sedlin, N-terminal conserved region; Mutations in this protein are associated with the X-linked spondyloepiphyseal dysplasia tarda syndrome (OMIM:313400). This family represents an N-terminal conserved region."
Q#19306 - 	CGI_10021789	superfamily	245213	393	427	1.29E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19307 - 	CGI_10021790	superfamily	243074	9	55	7.12E-06	43.2641	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19308 - 	CGI_10021791	superfamily	243074	13	58	8.19E-05	40.1825	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19309 - 	CGI_10021792	superfamily	245814	55	146	0.000111938	40.4996	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19310 - 	CGI_10021793	superfamily	243119	128	173	0.00314156	33.5613	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#19312 - 	CGI_10021795	superfamily	247743	234	286	0.00128589	37.8959	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#19313 - 	CGI_10021796	superfamily	241600	1	165	1.23E-61	191.685	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19317 - 	CGI_10021800	superfamily	241578	219	373	5.17E-24	98.903	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19317 - 	CGI_10021800	superfamily	241578	411	549	7.47E-14	69.517	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19317 - 	CGI_10021800	superfamily	245213	136	172	1.56E-11	59.9578	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19317 - 	CGI_10021800	superfamily	245213	174	211	3.74E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19318 - 	CGI_10021801	superfamily	245213	14	50	4.20E-09	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19318 - 	CGI_10021801	superfamily	245213	52	89	0.000482888	33.7642	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19321 - 	CGI_10021804	superfamily	219000	149	337	2.72E-21	92.7095	cl05717	Drf_FH3 superfamily	 - 	 - 	Diaphanous FH3 Domain; This region is found in the Formin-like and and diaphanous proteins.
Q#19321 - 	CGI_10021804	superfamily	219001	7	145	2.12E-10	59.6299	cl05720	Drf_GBD superfamily	 - 	 - 	"Diaphanous GTPase-binding Domain; This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein."
Q#19325 - 	CGI_10011454	superfamily	245201	1	217	2.08E-94	279.421	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19326 - 	CGI_10011455	superfamily	241600	208	419	1.81E-85	262.176	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19326 - 	CGI_10011455	superfamily	241600	4	129	3.48E-38	138.142	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19327 - 	CGI_10011456	superfamily	245205	13	113	3.52E-06	45.7003	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#19327 - 	CGI_10011456	superfamily	241640	430	533	0.000175403	40.6337	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#19329 - 	CGI_10011458	superfamily	241563	52	92	7.50E-06	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19331 - 	CGI_10011460	superfamily	245596	16	217	5.05E-45	154.773	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#19333 - 	CGI_10011462	superfamily	241600	1	134	4.38E-40	135.061	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19334 - 	CGI_10011463	superfamily	241563	57	100	2.24E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19335 - 	CGI_10011464	superfamily	241563	63	102	3.05E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19336 - 	CGI_10011465	superfamily	243092	399	694	1.02E-65	222.595	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19336 - 	CGI_10011465	superfamily	243092	36	220	7.37E-40	149.793	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19336 - 	CGI_10011465	superfamily	217837	793	899	1.23E-19	86.1073	cl04367	Utp12 superfamily	 - 	 - 	Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.
Q#19337 - 	CGI_10013390	superfamily	219501	25	65	0.00286561	36.1542	cl06622	MNNL superfamily	C	 - 	N terminus of Notch ligand; This entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins.
Q#19338 - 	CGI_10013391	superfamily	243072	170	291	2.39E-32	119.796	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19338 - 	CGI_10013391	superfamily	243072	36	163	3.22E-29	111.321	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19338 - 	CGI_10013391	superfamily	243072	243	357	1.12E-27	107.084	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19338 - 	CGI_10013391	superfamily	246680	410	476	1.14E-05	43.5328	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#19339 - 	CGI_10013392	superfamily	207609	146	206	4.73E-07	45.9328	cl02481	NGF superfamily	N	 - 	Nerve growth factor family; Nerve growth factor family.  
Q#19340 - 	CGI_10013393	superfamily	198867	45	144	6.12E-27	104.163	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#19340 - 	CGI_10013393	superfamily	243146	231	282	1.95E-09	53.9913	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19340 - 	CGI_10013393	superfamily	243146	434	479	2.72E-08	50.3526	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19340 - 	CGI_10013393	superfamily	243146	335	378	5.54E-08	49.5822	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19340 - 	CGI_10013393	superfamily	243146	282	333	2.33E-06	44.9598	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19340 - 	CGI_10013393	superfamily	243146	192	240	1.07E-05	43.0467	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19340 - 	CGI_10013393	superfamily	243066	1	36	8.66E-05	40.6785	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19340 - 	CGI_10013393	superfamily	243146	405	444	0.000262372	39.0787	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#19344 - 	CGI_10013397	superfamily	219619	365	433	2.58E-12	62.6103	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#19344 - 	CGI_10013397	superfamily	243066	9	90	1.00E-08	52.5553	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19345 - 	CGI_10013398	superfamily	245304	115	404	2.50E-174	508.638	cl10459	Peptidases_S8_S53 superfamily	 - 	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#19345 - 	CGI_10013398	superfamily	241585	721	754	6.50E-05	41.7356	cl00066	FU superfamily	C	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#19345 - 	CGI_10013398	superfamily	241585	665	696	0.000231131	40.1948	cl00066	FU superfamily	N	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#19345 - 	CGI_10013398	superfamily	201820	489	575	2.32E-33	124.66	cl08326	P_proprotein superfamily	 - 	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#19346 - 	CGI_10013399	superfamily	243072	7	50	2.00E-09	53.5414	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19349 - 	CGI_10013402	superfamily	241733	2	66	2.59E-25	99.3152	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#19349 - 	CGI_10013402	superfamily	241779	343	494	2.54E-13	67.6415	cl00318	YjeF_N superfamily	 - 	 - 	"YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions."
Q#19349 - 	CGI_10013402	superfamily	220282	241	335	3.77E-09	54.4122	cl09757	FDF superfamily	 - 	 - 	"FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain."
Q#19350 - 	CGI_10013403	superfamily	241563	63	95	4.70E-06	44.2003	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19350 - 	CGI_10013403	superfamily	245027	97	228	0.000726515	38.5284	cl09176	FlgN superfamily	 - 	 - 	FlgN protein; This family includes the FlgN protein and export chaperone involved in flagellar synthesis.
Q#19354 - 	CGI_10018134	superfamily	247792	33	71	0.000422296	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19354 - 	CGI_10018134	superfamily	190233	176	233	0.00703345	33.5818	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#19355 - 	CGI_10018135	superfamily	246669	239	361	3.73E-51	172.056	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19355 - 	CGI_10018135	superfamily	246669	370	508	3.98E-39	139.393	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19356 - 	CGI_10018136	superfamily	247068	39	137	2.96E-24	98.1545	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19356 - 	CGI_10018136	superfamily	247068	249	348	1.07E-21	90.8357	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19356 - 	CGI_10018136	superfamily	247068	496	594	6.46E-14	68.4941	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19356 - 	CGI_10018136	superfamily	247068	603	687	1.93E-09	55.3974	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19357 - 	CGI_10018137	superfamily	243066	266	356	1.90E-13	66.5604	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19357 - 	CGI_10018137	superfamily	220077	462	508	7.11E-06	44.7331	cl07512	DUF1916 superfamily	N	 - 	Domain of unknown function (DUF1916); This domain is found in various eukaryotic HBS1-like proteins.
Q#19358 - 	CGI_10018138	superfamily	243161	14	101	3.97E-16	71.2713	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#19361 - 	CGI_10018141	superfamily	245201	269	437	2.86E-09	56.8613	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19362 - 	CGI_10018142	superfamily	247038	229	306	1.17E-07	50.3582	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#19362 - 	CGI_10018142	superfamily	208843	46	163	0.000984111	39.2112	cl08275	RHD-n superfamily	 - 	 - 	"N-terminal sub-domain of the Rel homology domain (RHD); Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal sub-domain, which may be distantly related to the DNA-binding domain found in P53. The C-terminal sub-domain has an immunoglobulin-like fold and serves as a dimerization module that also binds DNA (see cd00102). The RHD is found in NF-kappa B, nuclear factor of activated T-cells (NFAT), the tonicity-responsive enhancer binding protein (TonEBP), and the arthropod proteins Dorsal and Relish (Rel)."
Q#19363 - 	CGI_10018143	superfamily	219817	110	241	3.85E-15	74.5768	cl07129	Xpo1 superfamily	 - 	 - 	"Exportin 1-like protein; The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus."
Q#19363 - 	CGI_10018143	superfamily	243689	32	99	4.00E-09	54.9421	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#19365 - 	CGI_10018145	superfamily	247792	18	68	1.11E-06	46.2848	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19365 - 	CGI_10018145	superfamily	115400	562	584	0.00469044	35.6489	cl06002	SBBP superfamily	N	 - 	Beta-propeller repeat; This family is related to pfam00400 and is likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller.
Q#19366 - 	CGI_10018146	superfamily	247792	18	68	3.75E-07	47.8256	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19368 - 	CGI_10018148	superfamily	247792	18	68	4.49E-07	47.4404	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19374 - 	CGI_10018154	superfamily	247724	27	230	3.35E-35	126.881	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19377 - 	CGI_10018157	superfamily	187408	333	666	1.47E-127	399.743	cl14654	V_Alix_like superfamily	 - 	 - 	"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain."
Q#19377 - 	CGI_10018157	superfamily	187403	153	328	1.14E-73	250.808	cl14649	BRO1_Alix_like superfamily	N	 - 	"Protein-interacting Bro1-like domain of mammalian Alix and related domains; This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, HD-PTP, and Brox) and Snf7 (in the case of yeast Bro1, and Rim20). The single domain protein human Brox, and the isolated Bro1-like domains of Alix, HD-PTP and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V) domain, which in the case of Alix, has been shown to be a dimerization domain and to contain a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in this superfamily. Alix, HD-PTP and Bro1 also have a proline-rich region (PRR); the Alix PRR binds multiple partners. Rhophilin-1, and -2, in addition to this Bro1-like domain, have an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This protein has a C-terminal, catalytically inactive tyrosine phosphatase domain."
Q#19378 - 	CGI_10018158	superfamily	241574	272	501	1.54E-68	226.313	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#19381 - 	CGI_10018162	superfamily	243072	1246	1371	2.23E-35	132.893	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19381 - 	CGI_10018162	superfamily	243072	683	808	3.25E-32	124.033	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19381 - 	CGI_10018162	superfamily	243072	1147	1272	6.61E-32	122.877	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19381 - 	CGI_10018162	superfamily	243072	951	1074	1.19E-30	119.411	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19381 - 	CGI_10018162	superfamily	243072	782	907	1.76E-30	119.025	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19381 - 	CGI_10018162	superfamily	243072	1015	1140	3.67E-30	117.87	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19381 - 	CGI_10018162	superfamily	243072	1316	1437	4.92E-30	117.485	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19381 - 	CGI_10018162	superfamily	243072	919	950	0.000266905	40.6152	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19382 - 	CGI_10019630	superfamily	247725	8	146	2.11E-71	214.91	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19383 - 	CGI_10019631	superfamily	247799	157	221	1.44E-19	83.2947	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#19383 - 	CGI_10019631	superfamily	247799	79	140	5.43E-14	67.5015	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#19383 - 	CGI_10019631	superfamily	247799	472	535	4.17E-08	50.6363	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#19386 - 	CGI_10019634	superfamily	241559	67	174	1.28E-11	63.4839	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#19386 - 	CGI_10019634	superfamily	243094	1023	1302	1.27E-136	427.773	cl02569	RasGAP superfamily	 - 	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#19386 - 	CGI_10019634	superfamily	217754	1416	1551	2.64E-32	124.666	cl04284	RasGAP_C superfamily	 - 	 - 	RasGAP C-terminus; RasGAP C-terminus.  
Q#19386 - 	CGI_10019634	superfamily	210118	823	843	0.000377822	40.012	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#19386 - 	CGI_10019634	superfamily	210118	763	783	0.0023111	37.6903	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#19387 - 	CGI_10019635	superfamily	245814	130	204	2.35E-06	45.1727	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19388 - 	CGI_10019636	superfamily	243053	1141	1373	1.57E-67	229.061	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#19388 - 	CGI_10019636	superfamily	243096	157	340	4.94E-36	136.659	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#19388 - 	CGI_10019636	superfamily	243067	606	642	7.54E-05	42.7848	cl02520	REM superfamily	C	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#19388 - 	CGI_10019636	superfamily	243067	1034	1116	0.000167436	41.6292	cl02520	REM superfamily	N	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#19388 - 	CGI_10019636	superfamily	247725	10	53	0.00103012	39.6616	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19389 - 	CGI_10019637	superfamily	247725	20	91	4.91E-28	100.523	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19390 - 	CGI_10019638	superfamily	247042	76	240	2.72E-22	97.1103	cl15693	Sema superfamily	N	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#19394 - 	CGI_10019642	superfamily	220381	3	179	3.90E-32	118.717	cl10736	Use1 superfamily	 - 	 - 	Membrane fusion protein Use1; This entry is of a family of proteins all approximately 300 residues in length. The proteins have a single C-terminal trans-membrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport.
Q#19396 - 	CGI_10019644	superfamily	215724	50	355	5.15E-151	430.887	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#19397 - 	CGI_10019645	superfamily	217473	141	388	2.68E-05	45.0485	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#19398 - 	CGI_10019646	superfamily	217473	177	297	5.71E-12	65.0789	cl03978	Mab-21 superfamily	NC	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#19398 - 	CGI_10019646	superfamily	243034	481	502	0.00953095	34.3156	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#19399 - 	CGI_10019647	superfamily	247792	16	63	4.02E-07	47.4404	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19403 - 	CGI_10019652	superfamily	247941	224	348	5.08E-12	62.7384	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#19404 - 	CGI_10019653	superfamily	245304	196	429	1.11E-105	333.758	cl10459	Peptidases_S8_S53 superfamily	N	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#19404 - 	CGI_10019653	superfamily	241585	642	681	3.31E-05	42.8912	cl00066	FU superfamily	C	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#19404 - 	CGI_10019653	superfamily	201820	513	607	6.82E-37	135.061	cl08326	P_proprotein superfamily	 - 	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#19404 - 	CGI_10019653	superfamily	241585	788	829	2.59E-05	42.8822	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#19404 - 	CGI_10019653	superfamily	243212	2	68	3.18E-05	43.4866	cl02844	Arrestin_C superfamily	N	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#19404 - 	CGI_10019653	superfamily	241585	885	928	0.000161475	40.571	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#19404 - 	CGI_10019653	superfamily	241585	686	733	0.000906232	38.645	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#19405 - 	CGI_10019654	superfamily	241758	79	230	8.00E-49	164.651	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#19405 - 	CGI_10019654	superfamily	189709	267	352	1.09E-34	124.203	cl02960	ETF_alpha superfamily	 - 	 - 	"Electron transfer flavoprotein FAD-binding domain; This domain found at the C-terminus of electron transfer flavoprotein alpha chain and binds to FAD. The fold consists of a five-stranded parallel beta sheet as the core of the domain, flanked by alternating helices. A small part of this domain is donated by the beta chain."
Q#19409 - 	CGI_10019658	superfamily	220080	257	393	7.35E-67	216.646	cl07526	DUF1900 superfamily	 - 	 - 	"Domain of unknown function (DUF1900); This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It has no known function."
Q#19409 - 	CGI_10019658	superfamily	149883	5	67	1.99E-32	119.651	cl07525	DUF1899 superfamily	 - 	 - 	Domain of unknown function (DUF1899); This set of domains is found in various eukaryotic proteins. Function is unknown.
Q#19409 - 	CGI_10019658	superfamily	243092	77	301	3.10E-21	93.5536	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19411 - 	CGI_10007345	superfamily	218493	412	556	1.12E-48	166.378	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#19411 - 	CGI_10007345	superfamily	248054	13	69	0.00623642	35.1404	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#19412 - 	CGI_10007346	superfamily	247856	8	71	1.45E-05	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19413 - 	CGI_10007347	superfamily	149431	795	861	1.14E-28	113.177	cl07111	LLGL superfamily	C	 - 	LLGL2; This domain is found in lethal giant larvae homolog 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn. It has been identified in eukaryotes and tends to be found together with WD repeats (pfam00400).
Q#19413 - 	CGI_10007347	superfamily	243092	559	782	3.52E-11	64.6636	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19413 - 	CGI_10007347	superfamily	187408	294	498	0.00156796	41.1736	cl14654	V_Alix_like superfamily	C	 - 	"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain."
Q#19415 - 	CGI_10007349	superfamily	248458	100	419	9.91E-06	45.7677	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19423 - 	CGI_10004064	superfamily	245814	101	160	0.000430413	36.3293	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19424 - 	CGI_10004065	superfamily	245814	24	79	0.000205668	38.1568	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19425 - 	CGI_10007125	superfamily	247792	315	357	1.06E-05	42.4328	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19425 - 	CGI_10007125	superfamily	221597	97	242	9.61E-14	67.3805	cl13864	GIDE superfamily	 - 	 - 	"E3 Ubiquitin ligase; This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis."
Q#19426 - 	CGI_10007126	superfamily	247727	99	194	9.11E-07	45.8839	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19427 - 	CGI_10007127	superfamily	216301	45	243	1.38E-27	105.039	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#19428 - 	CGI_10007128	superfamily	243050	51	108	2.24E-13	66.6742	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#19428 - 	CGI_10007128	superfamily	247916	447	515	3.35E-06	45.8367	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#19429 - 	CGI_10007129	superfamily	243050	24	79	4.77E-14	68.215	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#19429 - 	CGI_10007129	superfamily	247916	381	449	1.55E-08	52.7703	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#19430 - 	CGI_10007130	superfamily	217879	47	94	7.43E-14	68.5418	cl04388	DNA_pol_delta_4 superfamily	N	 - 	"DNA polymerase delta, subunit 4; DNA polymerase delta, subunit 4.  "
Q#19430 - 	CGI_10007130	superfamily	238191	244	355	3.28E-09	57.7272	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#19431 - 	CGI_10007131	superfamily	243092	97	405	1.47E-103	311.191	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19431 - 	CGI_10007131	superfamily	199226	11	37	0.00273964	35.488	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#19432 - 	CGI_10007132	superfamily	247727	102	193	6.38E-05	41.2615	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19433 - 	CGI_10007133	superfamily	247710	83	130	2.34E-05	44.0251	cl17114	metX superfamily	NC	 - 	homoserine O-acetyltransferase; Provisional
Q#19433 - 	CGI_10007133	superfamily	217881	26	43	0.0084617	33.6791	cl04390	Abhydro_lipase superfamily	N	 - 	Partial alpha/beta-hydrolase lipase region; This family corresponds to a N-terminal part of an alpha/beta hydrolase domain.
Q#19434 - 	CGI_10007134	superfamily	247724	3	192	9.83E-118	336.056	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19435 - 	CGI_10007135	superfamily	243066	53	111	2.91E-09	49.6116	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19438 - 	CGI_10007138	superfamily	203593	49	123	5.04E-08	47.295	cl18243	Mod_r superfamily	C	 - 	"Modifier of rudimentary (Mod(r)) protein; This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic, and both of these regions are represented in this family. Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB). The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37). The mammalian homologue of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors."
Q#19440 - 	CGI_10007140	superfamily	215754	210	301	5.99E-21	85.3828	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#19440 - 	CGI_10007140	superfamily	215754	20	100	9.26E-19	79.2196	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#19440 - 	CGI_10007140	superfamily	215754	109	207	1.06E-13	65.3524	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#19441 - 	CGI_10007141	superfamily	241832	2	91	5.92E-30	103.505	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19442 - 	CGI_10007142	superfamily	243092	1119	1310	8.71E-06	48.1	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19443 - 	CGI_10007143	superfamily	241607	41	72	0.000120789	36.479	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#19444 - 	CGI_10007144	superfamily	247749	8	105	1.40E-42	143.013	cl17195	LDH_MDH_like superfamily	N	 - 	"NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others."
Q#19445 - 	CGI_10005354	superfamily	245864	72	540	5.79E-116	353.892	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#19446 - 	CGI_10005355	superfamily	245864	10	113	1.02E-39	138.565	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#19447 - 	CGI_10005356	superfamily	245864	33	458	5.58E-102	315.372	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#19453 - 	CGI_10004972	superfamily	241754	368	720	8.32E-175	506.339	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#19455 - 	CGI_10004974	superfamily	241754	21	326	6.58E-130	405.912	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#19456 - 	CGI_10004975	superfamily	191863	123	211	2.04E-28	105.841	cl06724	HCNGP superfamily	 - 	 - 	HCNGP-like protein; This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP. This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Q#19457 - 	CGI_10004976	superfamily	241568	94	128	0.000341618	37.0572	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#19458 - 	CGI_10006621	superfamily	247792	22	61	2.87E-07	48.596	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19460 - 	CGI_10006623	superfamily	247792	13	51	1.17E-08	52.8332	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19463 - 	CGI_10006658	superfamily	248028	28	266	2.69E-55	180.777	cl17474	Steroid_dh superfamily	 - 	 - 	"3-oxo-5-alpha-steroid 4-dehydrogenase; This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development."
Q#19464 - 	CGI_10006659	superfamily	243671	36	208	1.71E-07	52.7466	cl04219	UPF0104 superfamily	 - 	 - 	Uncharacterized protein family (UPF0104); This family of proteins are integral membrane proteins. These proteins are uncharacterized but contain a conserved PG motif. Some members of this family are annotated as dolichol-P-glucose synthetase and contain a pfam00535 domain.
Q#19467 - 	CGI_10006662	superfamily	241877	72	194	0.00714826	37.609	cl00459	MIT_CorA-like superfamily	NC	 - 	"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport."
Q#19468 - 	CGI_10022430	superfamily	109874	29	155	2.06E-09	53.4522	cl02980	Stathmin superfamily	 - 	 - 	Stathmin family; The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton. They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerisation of tubulin heterodimers.
Q#19468 - 	CGI_10022430	superfamily	109874	162	247	1.42E-07	48.4446	cl02980	Stathmin superfamily	N	 - 	Stathmin family; The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton. They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerisation of tubulin heterodimers.
Q#19469 - 	CGI_10022431	superfamily	248014	1	72	1.48E-21	83.0972	cl17460	Csf4_U superfamily	NC	 - 	CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Q#19470 - 	CGI_10022432	superfamily	248014	15	68	5.82E-19	83.7703	cl17460	Csf4_U superfamily	N	 - 	CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Q#19472 - 	CGI_10022434	superfamily	241783	18	241	6.13E-36	133.078	cl00322	Ribosomal_L1 superfamily	 - 	 - 	"Ribosomal protein L1.  The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA.  In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA.  Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity.  L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site."
Q#19473 - 	CGI_10022435	superfamily	244121	101	390	2.03E-149	427.482	cl05556	Apyrase superfamily	 - 	 - 	Apyrase; This family consists of several eukaryotic apyrase proteins (EC:3.6.1.5). The salivary apyrases of blood-feeding arthropods are nucleotide hydrolysing enzymes implicated in the inhibition of host platelet aggregation through the hydrolysis of extracellular adenosine diphosphate..
Q#19474 - 	CGI_10022436	superfamily	243077	108	161	6.51E-19	79.1265	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#19474 - 	CGI_10022436	superfamily	150099	260	360	1.87E-34	123.52	cl07818	DUF1977 superfamily	 - 	 - 	Domain of unknown function (DUF1977); Members of this family of functionally uncharacterized domains are predominantly found in dnaj-like proteins.
Q#19475 - 	CGI_10022437	superfamily	243092	71	319	1.43E-10	60.4264	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19476 - 	CGI_10022438	superfamily	247723	231	304	2.54E-36	128.532	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#19476 - 	CGI_10022438	superfamily	245716	159	185	5.67E-05	40.3053	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#19477 - 	CGI_10022439	superfamily	248097	168	283	4.11E-15	69.2162	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19477 - 	CGI_10022439	superfamily	221533	35	93	0.0078456	33.8244	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#19478 - 	CGI_10022440	superfamily	241596	10	70	8.65E-15	66.0835	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#19478 - 	CGI_10022440	superfamily	243123	93	134	6.93E-05	39.0786	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#19479 - 	CGI_10022441	superfamily	191220	401	439	0.000718778	38.3466	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#19479 - 	CGI_10022441	superfamily	191220	554	592	0.00073843	37.9614	cl04972	SapB_1 superfamily	 - 	 - 	"Saposin-like type B, region 1; Saposin-like type B, region 1.  "
Q#19480 - 	CGI_10022442	superfamily	243090	100	205	2.68E-70	212.324	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#19480 - 	CGI_10022442	superfamily	243090	1	100	1.75E-64	197.686	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#19487 - 	CGI_10022449	superfamily	243066	155	254	6.88E-14	68.0277	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19487 - 	CGI_10022449	superfamily	198867	265	365	2.21E-12	63.7167	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#19488 - 	CGI_10022450	superfamily	241578	366	485	9.99E-07	48.7162	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19488 - 	CGI_10022450	superfamily	115363	609	669	1.15E-15	73.5601	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#19488 - 	CGI_10022450	superfamily	115363	680	704	3.23E-05	43.1294	cl05972	MIB_HERC2 superfamily	C	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#19488 - 	CGI_10022450	superfamily	207713	967	1033	0.000776139	38.8602	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#19490 - 	CGI_10022452	superfamily	241733	10	88	2.38E-52	160.412	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#19491 - 	CGI_10022453	superfamily	219057	15	135	2.98E-61	187.086	cl05809	SAP18 superfamily	 - 	 - 	Sin3 associated polypeptide p18 (SAP18); This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex which is responsible for the repression of transcription via the modification of histone polypeptides. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death.
Q#19492 - 	CGI_10022454	superfamily	241571	92	205	2.93E-05	42.0143	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#19493 - 	CGI_10022455	superfamily	243072	10	131	5.23E-15	72.8014	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19493 - 	CGI_10022455	superfamily	243072	510	645	8.24E-14	69.3346	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19493 - 	CGI_10022455	superfamily	243072	367	491	9.50E-07	48.1486	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19493 - 	CGI_10022455	superfamily	243072	102	261	2.54E-06	46.6078	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19493 - 	CGI_10022455	superfamily	243072	583	763	0.000440302	39.6743	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19495 - 	CGI_10022457	superfamily	247736	330	426	5.68E-09	52.6632	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#19496 - 	CGI_10022459	superfamily	247675	68	342	2.13E-140	402.646	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#19497 - 	CGI_10022460	superfamily	241777	75	272	2.17E-12	65.3996	cl00316	Cation_efflux superfamily	 - 	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#19498 - 	CGI_10022461	superfamily	217414	322	692	1.68E-87	283.067	cl03927	Otopetrin superfamily	 - 	 - 	"Protein of unknown function, DUF270; Protein of unknown function, DUF270.  "
Q#19499 - 	CGI_10022462	superfamily	247683	499	560	2.71E-30	114.985	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#19499 - 	CGI_10022462	superfamily	241622	408	486	1.66E-13	67.5918	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19499 - 	CGI_10022462	superfamily	247744	686	868	3.99E-45	160.921	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#19499 - 	CGI_10022462	superfamily	243136	336	387	2.53E-05	42.8804	cl02672	L27 superfamily	 - 	 - 	L27 domain; The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.
Q#19500 - 	CGI_10022464	superfamily	241568	988	1034	0.00139248	38.2128	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#19500 - 	CGI_10022464	superfamily	243124	97	255	1.34E-43	157.204	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#19500 - 	CGI_10022464	superfamily	155088	469	537	1.52E-09	57.4599	cl02758	AMOP superfamily	C	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#19501 - 	CGI_10022465	superfamily	243124	94	186	3.14E-24	95.1864	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#19502 - 	CGI_10022466	superfamily	247038	271	342	0.00059945	38.9816	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#19502 - 	CGI_10022466	superfamily	241568	738	783	0.00218685	37.0572	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#19502 - 	CGI_10022466	superfamily	243124	99	256	2.64E-44	157.589	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#19502 - 	CGI_10022466	superfamily	243065	470	643	5.79E-09	55.1405	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#19502 - 	CGI_10022466	superfamily	155088	377	452	6.13E-07	48.7462	cl02758	AMOP superfamily	N	 - 	AMOP domain; This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Q#19502 - 	CGI_10022466	superfamily	241623	586	702	0.00776041	37.2932	cl00119	PI3Kc_like superfamily	N	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#19504 - 	CGI_10022468	superfamily	241592	34	122	9.17E-52	161.145	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#19506 - 	CGI_10022470	superfamily	247068	566	663	7.24E-23	95.4581	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19506 - 	CGI_10022470	superfamily	247068	460	539	1.66E-19	85.8281	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19506 - 	CGI_10022470	superfamily	247068	242	341	3.05E-17	79.2797	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19506 - 	CGI_10022470	superfamily	247068	131	233	3.39E-17	78.8945	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19506 - 	CGI_10022470	superfamily	247068	355	452	1.89E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19506 - 	CGI_10022470	superfamily	247068	683	770	1.24E-15	74.6573	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19506 - 	CGI_10022470	superfamily	247068	19	123	4.88E-06	46.1526	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19507 - 	CGI_10022471	superfamily	247068	569	665	5.59E-29	112.792	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19507 - 	CGI_10022471	superfamily	247068	465	560	8.92E-25	100.851	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19507 - 	CGI_10022471	superfamily	247068	251	351	1.97E-24	99.6953	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19507 - 	CGI_10022471	superfamily	247068	142	243	6.36E-16	75.0425	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19507 - 	CGI_10022471	superfamily	247068	679	769	9.72E-15	71.9609	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19507 - 	CGI_10022471	superfamily	247068	365	456	2.55E-12	64.6421	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19507 - 	CGI_10022471	superfamily	247068	30	132	1.55E-07	50.3898	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19508 - 	CGI_10022472	superfamily	114912	4	38	1.62E-05	39.7269	cl17946	zf-U1 superfamily	 - 	 - 	"U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family."
Q#19508 - 	CGI_10022472	superfamily	245716	55	76	0.00249195	33.6859	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#19509 - 	CGI_10022473	superfamily	245201	74	297	8.19E-133	392.549	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19511 - 	CGI_10004154	superfamily	241568	3	59	0.000312607	37.8276	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#19513 - 	CGI_10004156	superfamily	245201	15	343	0	649.74	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19515 - 	CGI_10004159	superfamily	220635	6	182	3.95E-55	189.668	cl12380	DUF2151 superfamily	N	 - 	"Cell cycle and development regulator; This is a set of proteins conserved from worms to humans. The proteins are a PAN GU kinase substrate, Mat89Bb, essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells."
Q#19516 - 	CGI_10004160	superfamily	247724	228	400	2.47E-06	46.2956	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19516 - 	CGI_10004160	superfamily	242902	32	122	9.77E-15	70.7386	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#19517 - 	CGI_10003507	superfamily	241645	1	72	2.41E-25	92.9067	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#19517 - 	CGI_10003507	superfamily	248233	73	125	2.10E-18	73.9447	cl17679	Ribosomal_S30 superfamily	 - 	 - 	Ribosomal protein S30; Ribosomal protein S30.  
Q#19518 - 	CGI_10003522	superfamily	243992	9	65	1.68E-06	40.635	cl05087	Complex1_LYR_1 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#19520 - 	CGI_10003524	superfamily	204376	201	270	2.01E-07	47.9081	cl10817	DUF2260 superfamily	C	 - 	"Uncharacterized conserved protein (DUF2260); This domain, found in various hypothetical bacterial proteins, has no known function."
Q#19521 - 	CGI_10020896	superfamily	207662	35	125	1.72E-37	133.34	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#19521 - 	CGI_10020896	superfamily	245599	395	496	2.86E-18	82.2706	cl11397	NR_LBD superfamily	N	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#19521 - 	CGI_10020896	superfamily	245599	248	310	8.04E-16	74.9518	cl11397	NR_LBD superfamily	C	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#19524 - 	CGI_10020899	superfamily	241578	127	291	1.82E-38	138.188	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19527 - 	CGI_10020902	superfamily	243100	79	135	6.75E-07	45.2476	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#19528 - 	CGI_10020903	superfamily	246669	411	545	3.87E-69	221.302	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19528 - 	CGI_10020903	superfamily	246669	274	402	5.60E-46	158.574	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19529 - 	CGI_10020904	superfamily	220393	2	253	1.46E-77	241.511	cl10751	Tmem26 superfamily	 - 	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#19530 - 	CGI_10020905	superfamily	241555	7	210	3.38E-77	239.766	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#19530 - 	CGI_10020905	superfamily	241555	203	371	6.43E-66	210.49	cl00020	GAT_1 superfamily	N	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#19531 - 	CGI_10020906	superfamily	241675	134	330	1.72E-51	172.871	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#19532 - 	CGI_10020907	superfamily	241675	137	333	7.80E-56	184.427	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#19533 - 	CGI_10020908	superfamily	206035	179	276	3.03E-21	85.6767	cl16440	Enkurin superfamily	 - 	 - 	"Calmodulin-binding; This is a family of apparent calmodulin-binding proteins found at high levels in the testis and vomeronasal organ and at lower levels in certain other tissues. Enkurin is a scaffold protein that binds PI3 kinase to sperm transient receptor potential (canonical) (TRPC) channels. The mammalian transient receptor potential (canonical) channels are the primary candidates for the Ca(2+) entry pathway activated by the hormones, growth factors, and neurotransmitters that exert their effect through activation of PLC. Calmodulin binds to the C-terminus of all TRPC channels, and dissociation of calmodulin from TRPC4 results in profound activation of the channel."
Q#19535 - 	CGI_10020910	superfamily	245835	231	474	6.18E-73	233.737	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#19535 - 	CGI_10020910	superfamily	243088	111	214	3.30E-55	182.043	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#19538 - 	CGI_10020913	superfamily	241733	151	208	1.03E-16	73.0618	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#19540 - 	CGI_10020915	superfamily	242414	143	284	1.10E-31	119.305	cl01285	Gar1 superfamily	 - 	 - 	"Gar1/Naf1 RNA binding region; Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex. In humans, Gar1 is also component of telomerase in vivo. Naf1 is an essentail protein that plays a role in ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis, and is homologous to Gar1."
Q#19541 - 	CGI_10020916	superfamily	243015	37	177	1.34E-09	53.6885	cl02381	Tim17 superfamily	 - 	 - 	"Tim17/Tim22/Tim23/Pmp24 family; The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane. This family includes Tim17, Tim22 and Tim23. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27 in."
Q#19542 - 	CGI_10020917	superfamily	246669	979	1117	8.77E-55	188.986	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19542 - 	CGI_10020917	superfamily	246669	101	317	2.18E-52	182.956	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19542 - 	CGI_10020917	superfamily	247912	1156	1472	7.59E-17	82.164	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#19542 - 	CGI_10020917	superfamily	220800	862	935	3.28E-12	65.4043	cl11172	Membr_traf_MHD superfamily	C	 - 	"Munc13 (mammalian uncoordinated) homology domain; Munc13 proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster, mouse, rat and human, some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical."
Q#19544 - 	CGI_10020919	superfamily	247792	100	143	5.21E-08	50.1368	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19544 - 	CGI_10020919	superfamily	241563	171	208	0.000266649	39.2427	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19545 - 	CGI_10020920	superfamily	218118	93	146	3.12E-11	55.6981	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#19546 - 	CGI_10020921	superfamily	241592	19	116	2.75E-48	160.964	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#19546 - 	CGI_10020921	superfamily	241554	183	368	1.86E-61	197.764	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19547 - 	CGI_10020922	superfamily	247723	60	131	5.50E-34	122.309	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#19547 - 	CGI_10020922	superfamily	163611	374	472	8.69E-27	103.525	cl10824	BLOC1_2 superfamily	 - 	 - 	"Biogenesis of lysosome-related organelles complex-1 subunit 2; Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system."
Q#19547 - 	CGI_10020922	superfamily	247723	144	208	4.41E-19	81.6435	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#19548 - 	CGI_10020923	superfamily	247792	78	124	5.94E-12	57.0704	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19550 - 	CGI_10020925	superfamily	241874	24	484	1.24E-174	504.361	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#19551 - 	CGI_10020926	superfamily	241874	8	490	0	521.695	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#19552 - 	CGI_10020927	superfamily	222070	85	170	0.00287271	36.1165	cl18634	DDE_3 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#19556 - 	CGI_10020931	superfamily	247097	359	393	0.000337232	38.5862	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#19558 - 	CGI_10020933	superfamily	246908	740	834	2.09E-18	82.7469	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#19560 - 	CGI_10020935	superfamily	241563	62	101	9.65E-06	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19560 - 	CGI_10020935	superfamily	241563	8	53	0.000407573	38.4723	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19560 - 	CGI_10020935	superfamily	110440	482	508	0.00558134	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19561 - 	CGI_10020936	superfamily	241563	62	101	2.49E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19561 - 	CGI_10020936	superfamily	110440	508	535	0.00828517	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19562 - 	CGI_10020937	superfamily	241563	40	80	6.25E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19563 - 	CGI_10020938	superfamily	241574	162	297	5.46E-57	184.349	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#19563 - 	CGI_10020938	superfamily	241626	9	116	8.02E-25	97.7378	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#19565 - 	CGI_10020940	superfamily	241563	81	122	6.54E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19567 - 	CGI_10020942	superfamily	241645	673	748	7.75E-34	124.875	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#19567 - 	CGI_10020942	superfamily	243154	40	93	1.08E-22	92.6505	cl02715	Surp superfamily	 - 	 - 	Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
Q#19567 - 	CGI_10020942	superfamily	243154	147	200	2.99E-19	83.0205	cl02715	Surp superfamily	 - 	 - 	Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
Q#19567 - 	CGI_10020942	superfamily	221473	205	297	7.07E-16	77.0971	cl18609	PRP21_like_P superfamily	C	 - 	"Pre-mRNA splicing factor PRP21 like protein; This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form."
Q#19567 - 	CGI_10020942	superfamily	221473	387	469	2.42E-11	62.8447	cl18609	PRP21_like_P superfamily	N	 - 	"Pre-mRNA splicing factor PRP21 like protein; This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form."
Q#19570 - 	CGI_10020945	superfamily	245847	70	160	3.62E-10	53.8953	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#19574 - 	CGI_10005086	superfamily	245009	33	159	5.71E-45	154.748	cl09109	NTF2_like superfamily	 - 	 - 	"Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example,  nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and  binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea and eukaryotes."
Q#19574 - 	CGI_10005086	superfamily	247723	360	440	1.51E-35	127.126	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#19575 - 	CGI_10005087	superfamily	247769	563	738	4.10E-11	61.5865	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#19575 - 	CGI_10005087	superfamily	248010	154	299	2.38E-21	92.0591	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#19575 - 	CGI_10005087	superfamily	248010	308	467	4.74E-21	91.2887	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#19576 - 	CGI_10005088	superfamily	238155	159	279	2.48E-28	105.92	cl08547	SPARC_EC superfamily	 - 	 - 	"SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate cell-matrix interactions; binds to such proteins as collagen and vitronectin and binds to endothelial cells thus inhibiting cellular proliferation. The EC domain interacts with a follistatin-like (FS) domain which appears to stabilize Ca2+ binding. The two EF-hands interact canonically but their conserved disulfide bonds confer a tight association between the EF-hand pair and an acid/amphiphilic N-terminal helix. Proposed active form involves a Ca2+ dependent symmetric homodimerization of EC-FS modules."
Q#19576 - 	CGI_10005088	superfamily	241607	71	156	4.07E-23	91.0006	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#19577 - 	CGI_10005089	superfamily	247724	62	116	6.74E-24	98.069	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19577 - 	CGI_10005089	superfamily	219841	116	204	9.12E-20	81.8475	cl07167	MMR_HSR1_C superfamily	 - 	 - 	"GTPase of unknown function C-terminal; This domain is found at the C-terminus of pfam01926 in archaeal and eukaryotic GTP-binding proteins. The C-terminal domain of the GTP-binding proteins is necessary for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotides."
Q#19578 - 	CGI_10008650	superfamily	241785	231	443	9.78E-42	148.776	cl00324	Ribosomal_L3 superfamily	 - 	 - 	Ribosomal protein L3; Ribosomal protein L3.  
Q#19578 - 	CGI_10008650	superfamily	243066	19	112	5.47E-20	84.9765	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19580 - 	CGI_10008652	superfamily	241554	121	222	3.42E-23	95.7903	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19580 - 	CGI_10008652	superfamily	241752	439	574	9.88E-16	75.8299	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#19580 - 	CGI_10008652	superfamily	241554	6	80	1.48E-07	50.4219	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19581 - 	CGI_10008653	superfamily	241554	33	162	1.18E-27	108.887	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19581 - 	CGI_10008653	superfamily	241554	197	317	3.43E-26	105.035	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19581 - 	CGI_10008653	superfamily	241752	424	669	5.66E-16	76.9855	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#19586 - 	CGI_10008658	superfamily	241554	36	152	2.51E-22	93.8643	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19586 - 	CGI_10008658	superfamily	241554	216	327	2.04E-20	88.4715	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19586 - 	CGI_10008658	superfamily	241752	415	658	2.24E-15	75.0595	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#19587 - 	CGI_10008659	superfamily	241554	235	353	1.11E-29	115.05	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19587 - 	CGI_10008659	superfamily	241554	40	169	4.09E-23	96.1755	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19587 - 	CGI_10008659	superfamily	241752	459	706	8.69E-16	76.2151	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#19590 - 	CGI_10008662	superfamily	192384	6	149	5.68E-47	151.611	cl10775	SYS1 superfamily	 - 	 - 	Integral membrane protein S linking to the trans Golgi network; Members of this family are integral membrane proteins involved in protein trafficking between the late Golgi and endosome. They may also serve as a receptor for ADP-ribosylation factor-related protein 1 (ARFRP1). Sys1p is a small integral membrane protein with four predicted transmembrane domains that localises to the Trans Golgi network TGN in yeast and human cells.
Q#19592 - 	CGI_10008664	superfamily	243188	61	194	4.22E-33	117.757	cl02792	Cyt_c_Oxidase_IV superfamily	 - 	 - 	"Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform."
Q#19593 - 	CGI_10008665	superfamily	246911	49	156	1.09E-26	107.909	cl15262	PUB superfamily	 - 	 - 	"PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.   The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes (except for fungi) and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97."
Q#19596 - 	CGI_10010047	superfamily	247986	557	668	2.72E-10	60.0794	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#19596 - 	CGI_10010047	superfamily	247986	369	425	1.91E-09	57.383	cl17432	PBPb superfamily	NC	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#19596 - 	CGI_10010047	superfamily	245225	1	314	5.24E-31	125.49	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#19597 - 	CGI_10010048	superfamily	241832	423	528	1.45E-35	129.984	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19597 - 	CGI_10010048	superfamily	241832	11	94	3.12E-24	98.6964	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19598 - 	CGI_10010049	superfamily	243072	261	386	3.16E-39	138.285	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19598 - 	CGI_10010049	superfamily	243072	162	287	1.19E-36	131.352	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19600 - 	CGI_10010051	superfamily	241874	316	435	3.76E-09	57.5168	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#19600 - 	CGI_10010051	superfamily	241874	69	196	2.47E-07	52.1814	cl00456	SLC5-6-like_sbd superfamily	NC	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#19601 - 	CGI_10010052	superfamily	217403	166	270	1.24E-16	73.611	cl18408	2OG-FeII_Oxy superfamily	 - 	 - 	"2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalyzing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB."
Q#19601 - 	CGI_10010052	superfamily	222608	1	113	5.28E-11	58.4198	cl18680	DIOX_N superfamily	 - 	 - 	non-haem dioxygenase in morphine synthesis N-terminal; This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.
Q#19602 - 	CGI_10010053	superfamily	245814	219	286	2.30E-07	48.6395	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19602 - 	CGI_10010053	superfamily	245814	295	373	1.24E-10	58.405	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19602 - 	CGI_10010053	superfamily	245814	119	194	2.84E-08	51.3521	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19602 - 	CGI_10010053	superfamily	245814	374	456	2.41E-07	48.6934	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19606 - 	CGI_10010057	superfamily	215754	4	97	5.83E-19	79.2196	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#19606 - 	CGI_10010057	superfamily	215754	97	187	1.07E-14	66.8932	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#19606 - 	CGI_10010057	superfamily	215754	191	250	5.99E-09	51.4852	cl02813	Mito_carr superfamily	C	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#19607 - 	CGI_10010058	superfamily	241578	4	181	1.78E-45	154.68	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#19608 - 	CGI_10010059	superfamily	207701	2	108	4.38E-30	109.306	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#19610 - 	CGI_10010061	superfamily	248097	129	259	1.21E-17	76.1498	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19610 - 	CGI_10010061	superfamily	248213	39	89	0.00446022	34.0877	cl17659	DivIC superfamily	N	 - 	Septum formation initiator; DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil.
Q#19611 - 	CGI_10016150	superfamily	241596	45	101	4.74E-07	45.6679	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#19612 - 	CGI_10016151	superfamily	241596	44	101	1.94E-08	49.5199	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#19613 - 	CGI_10016152	superfamily	241596	48	105	7.40E-08	47.9791	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#19614 - 	CGI_10016153	superfamily	245612	69	506	1.71E-63	215.238	cl11426	Amidase superfamily	 - 	 - 	Amidase; Amidase.  
Q#19615 - 	CGI_10016154	superfamily	216981	137	295	2.23E-06	47.1422	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#19615 - 	CGI_10016154	superfamily	209366	1006	1029	0.001751	37.5658	cl11604	zf-A20 superfamily	 - 	 - 	A20-like zinc finger; The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation.
Q#19620 - 	CGI_10016159	superfamily	217860	5	99	3.93E-26	95.8178	cl04379	APC8 superfamily	N	 - 	"Anaphase promoting complex subunit 8 / Cdc23; The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8)."
Q#19621 - 	CGI_10016160	superfamily	243072	67	176	2.94E-23	92.4466	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19621 - 	CGI_10016160	superfamily	243073	238	277	0.000142832	38.6053	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#19621 - 	CGI_10016160	superfamily	243072	32	56	0.00111696	35.9928	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19623 - 	CGI_10016162	superfamily	247684	68	440	0	772.318	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19624 - 	CGI_10016163	superfamily	217928	1	155	3.60E-60	189.087	cl04419	Erv26 superfamily	 - 	 - 	Transmembrane adaptor Erv26; Erv26 is an integral membrane protein that is packed into COPII vesicles and cycles between the ER and Golgi compartments. It directs pro-alkaline phosphatase into endoplasmic reticulum-derived COPII transport vesicles.
Q#19625 - 	CGI_10016164	superfamily	243066	18	121	5.18E-23	92.6805	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19625 - 	CGI_10016164	superfamily	198867	130	238	6.23E-15	70.448	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#19627 - 	CGI_10016167	superfamily	248458	322	494	3.97E-10	60.0201	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19627 - 	CGI_10016167	superfamily	248458	21	197	2.80E-08	54.2421	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19629 - 	CGI_10016169	superfamily	248458	21	197	1.93E-06	47.6937	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19629 - 	CGI_10016169	superfamily	248458	224	331	0.000291018	40.7601	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19630 - 	CGI_10016170	superfamily	219464	1	270	8.36E-114	351.182	cl06544	NAGidase superfamily	 - 	 - 	"beta-N-acetylglucosaminidase; This family has previously been described as a hyaluronidase. However, more recently it has been shown that this family has beta-N-acetylglucosaminidase activity."
Q#19631 - 	CGI_10016171	superfamily	245864	5	374	5.46E-23	98.8898	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#19632 - 	CGI_10016172	superfamily	217381	57	142	3.21E-43	146.943	cl15956	TB2_DP1_HVA22 superfamily	 - 	 - 	"TB2/DP1, HVA22 family; This family includes members from a wide variety of eukaryotes. It includes the TB2/DP1 (deleted in polyposis) protein, which in humans is deleted in severe forms of familial adenomatous polyposis, an autosomal dominant oncological inherited disease. The family also includes the plant protein of known similarity to TB2/DP1, the HVA22 abscisic acid-induced protein, which is thought to be a regulatory protein."
Q#19635 - 	CGI_10016175	superfamily	243072	132	241	5.90E-25	96.2986	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19635 - 	CGI_10016175	superfamily	243072	25	187	1.24E-22	90.1354	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19636 - 	CGI_10016176	superfamily	243072	62	166	5.28E-17	73.957	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19637 - 	CGI_10016177	superfamily	243072	104	225	3.22E-25	100.151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19637 - 	CGI_10016177	superfamily	243072	171	333	4.13E-21	88.5946	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19638 - 	CGI_10016178	superfamily	247856	394	440	3.69E-08	50.6241	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19638 - 	CGI_10016178	superfamily	246925	89	295	2.78E-18	84.7145	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#19639 - 	CGI_10016179	superfamily	241599	85	139	1.40E-14	68.424	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#19640 - 	CGI_10016180	superfamily	247999	650	702	1.80E-10	57.8856	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#19641 - 	CGI_10016181	superfamily	243100	280	332	2.99E-05	41.0601	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#19642 - 	CGI_10008943	superfamily	247723	16	95	3.84E-51	160.777	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#19642 - 	CGI_10008943	superfamily	247723	101	172	8.79E-46	146.928	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#19643 - 	CGI_10008944	superfamily	128937	4	69	1.49E-15	64.9764	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#19644 - 	CGI_10008945	superfamily	245815	24	155	6.81E-47	165.087	cl11961	ALDH-SF superfamily	N	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#19644 - 	CGI_10008945	superfamily	128937	254	314	4.41E-14	65.7468	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#19644 - 	CGI_10008945	superfamily	128937	179	244	3.76E-11	58.0428	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#19645 - 	CGI_10008946	superfamily	246722	369	512	1.30E-54	183.546	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#19645 - 	CGI_10008946	superfamily	241777	170	290	6.65E-31	122.036	cl00316	Cation_efflux superfamily	N	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#19646 - 	CGI_10008947	superfamily	246598	14	278	1.97E-106	314.59	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#19647 - 	CGI_10008948	superfamily	247727	45	150	2.54E-05	41.2615	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19649 - 	CGI_10008950	superfamily	207724	150	207	2.25E-11	59.5515	cl02772	BSD superfamily	 - 	 - 	BSD domain; This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function.
Q#19650 - 	CGI_10008951	superfamily	248012	9	128	5.14E-11	55.7924	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#19651 - 	CGI_10008952	superfamily	221744	27	205	4.22E-20	86.3358	cl18614	CABIT superfamily	C	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#19652 - 	CGI_10008953	superfamily	221744	25	207	8.21E-13	67.4611	cl18614	CABIT superfamily	C	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#19655 - 	CGI_10008956	superfamily	247057	304	365	6.90E-08	49.0716	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#19659 - 	CGI_10002672	superfamily	245847	19	155	1.12E-16	75.2857	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#19660 - 	CGI_10012721	superfamily	248097	81	207	2.00E-21	86.165	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19661 - 	CGI_10012722	superfamily	248012	9	119	7.11E-10	52.5801	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#19664 - 	CGI_10012725	superfamily	248012	10	106	0.000280864	38.4584	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#19665 - 	CGI_10012726	superfamily	241832	52	165	5.40E-70	210.614	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19666 - 	CGI_10012727	superfamily	247724	107	205	2.13E-42	143.754	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19668 - 	CGI_10012729	superfamily	243050	1295	1347	1.54E-24	99.2653	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#19672 - 	CGI_10012733	superfamily	245303	6	362	2.99E-31	122.156	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#19673 - 	CGI_10012734	superfamily	243058	146	266	3.09E-07	47.6943	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#19673 - 	CGI_10012734	superfamily	243058	101	180	7.38E-05	40.3756	cl02500	ARM superfamily	N	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#19674 - 	CGI_10012735	superfamily	243091	135	175	1.01E-08	51.724	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#19675 - 	CGI_10012736	superfamily	218358	38	157	1.21E-24	94.4023	cl04871	IPP-2 superfamily	 - 	 - 	"Protein phosphatase inhibitor 2 (IPP-2); Protein phosphotase inhibitor 2 (IPP-2) is a phosphoprotein conserved among all eukaryotes, and it appears in both the nucleus and cytoplasm of tissue culture cells."
Q#19676 - 	CGI_10012737	superfamily	216981	184	324	9.04E-11	61.0094	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#19677 - 	CGI_10012738	superfamily	222608	28	147	3.15E-25	98.0954	cl18680	DIOX_N superfamily	 - 	 - 	non-haem dioxygenase in morphine synthesis N-terminal; This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.
Q#19677 - 	CGI_10012738	superfamily	217403	198	298	6.30E-22	88.2486	cl18408	2OG-FeII_Oxy superfamily	 - 	 - 	"2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalyzing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB."
Q#19678 - 	CGI_10012739	superfamily	215647	19	206	8.89E-08	50.6849	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#19679 - 	CGI_10012740	superfamily	148314	1	139	5.61E-06	44.8754	cl05919	XRCC4 superfamily	C	 - 	"DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks."
Q#19680 - 	CGI_10001663	superfamily	242120	2	136	1.72E-63	196.21	cl00821	Ribosomal_S3Ae superfamily	N	 - 	Ribosomal S3Ae family; Ribosomal S3Ae family.  
Q#19685 - 	CGI_10024981	superfamily	243033	29	162	2.33E-27	101.241	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#19686 - 	CGI_10024982	superfamily	247755	1872	2075	3.19E-82	271.347	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#19686 - 	CGI_10024982	superfamily	243034	218	284	7.45E-13	67.7904	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#19686 - 	CGI_10024982	superfamily	247792	1830	1870	1.79E-12	65.1596	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19686 - 	CGI_10024982	superfamily	247789	2282	2421	4.59E-36	138.931	cl17235	ABC2_membrane superfamily	N	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#19687 - 	CGI_10024983	superfamily	243483	188	308	1.51E-30	117.898	cl03646	DUF159 superfamily	C	 - 	"Uncharacterized ACR, COG2135; Uncharacterized ACR, COG2135.  "
Q#19687 - 	CGI_10024983	superfamily	243483	396	516	3.63E-15	73.9854	cl03646	DUF159 superfamily	N	 - 	"Uncharacterized ACR, COG2135; Uncharacterized ACR, COG2135.  "
Q#19688 - 	CGI_10024984	superfamily	241602	129	198	1.32E-30	116.563	cl00087	HR1 superfamily	 - 	 - 	"Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases; The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and Rho-associated kinase (ROCK). Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 domains may occur in repeat arrangements (PKN contains three HR1 domains), separated by a short linker region."
Q#19688 - 	CGI_10024984	superfamily	241602	209	281	1.37E-28	110.843	cl00087	HR1 superfamily	 - 	 - 	"Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases; The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and Rho-associated kinase (ROCK). Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 domains may occur in repeat arrangements (PKN contains three HR1 domains), separated by a short linker region."
Q#19688 - 	CGI_10024984	superfamily	241602	38	102	2.57E-15	72.2986	cl00087	HR1 superfamily	 - 	 - 	"Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases; The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and Rho-associated kinase (ROCK). Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 domains may occur in repeat arrangements (PKN contains three HR1 domains), separated by a short linker region."
Q#19688 - 	CGI_10024984	superfamily	245201	678	953	9.17E-133	404.834	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19688 - 	CGI_10024984	superfamily	246669	388	475	2.24E-29	114.022	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#19689 - 	CGI_10024985	superfamily	247803	160	237	6.52E-38	137.363	cl17249	YlqF_related_GTPase superfamily	C	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#19689 - 	CGI_10024985	superfamily	247803	340	424	1.76E-35	130.43	cl17249	YlqF_related_GTPase superfamily	N	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#19693 - 	CGI_10024989	superfamily	241623	2098	2406	2.17E-165	515.449	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#19693 - 	CGI_10024989	superfamily	202180	3567	3595	6.37E-05	43.6064	cl03505	FATC superfamily	 - 	 - 	"FATC domain; The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability."
Q#19696 - 	CGI_10024992	superfamily	247745	55	339	0	536.795	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#19696 - 	CGI_10024992	superfamily	245003	385	462	7.22E-23	94.9562	cl08536	Alpha-mann_mid superfamily	 - 	 - 	"Alpha mannosidase, middle domain; Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase."
Q#19697 - 	CGI_10024993	superfamily	247745	37	284	5.11E-152	453.592	cl17191	GH38-57_N_LamB_YdjC_SF superfamily	 - 	 - 	"Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex.  GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22).  This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily."
Q#19697 - 	CGI_10024993	superfamily	245003	329	406	5.90E-23	94.9562	cl08536	Alpha-mann_mid superfamily	 - 	 - 	"Alpha mannosidase, middle domain; Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase."
Q#19698 - 	CGI_10024994	superfamily	247858	428	601	4.01E-40	144.068	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#19698 - 	CGI_10024994	superfamily	203913	23	154	2.22E-30	116.162	cl07084	P4Ha_N superfamily	 - 	 - 	"Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known."
Q#19699 - 	CGI_10024995	superfamily	243056	625	849	1.11E-45	164.402	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#19700 - 	CGI_10024996	superfamily	192111	732	831	0.000122467	41.5241	cl07316	BRE1 superfamily	 - 	 - 	BRE1 E3 ubiquitin ligase; BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions.
Q#19701 - 	CGI_10024997	superfamily	241572	412	498	3.20E-11	60.7152	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#19701 - 	CGI_10024997	superfamily	241572	314	402	7.37E-11	59.5596	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#19701 - 	CGI_10024997	superfamily	243074	38	78	9.58E-07	46.661	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19702 - 	CGI_10024998	superfamily	245230	2	432	0	958.283	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#19703 - 	CGI_10024999	superfamily	245230	2	432	0	956.742	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#19706 - 	CGI_10025002	superfamily	247954	19	295	1.27E-25	103.314	cl17400	PRK06823 superfamily	 - 	 - 	ornithine cyclodeaminase; Validated
Q#19707 - 	CGI_10025003	superfamily	219472	106	242	4.62E-12	63.8927	cl09593	Nucleopor_Nup85 superfamily	C	 - 	"Nup85 Nucleoporin; A family of nucleoporins conserved from yeast to human. THe nuclear pore complex is a large assembly composed of two essential complexes: the heptameric Nup84 complex and the heteromeric Nic96-containing complex. The Nup84 complex is composed of one copy each of Nup84, Nup85, Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure of a complex of Nup85 and Seh1 was solved. The N-terminus of Nup85 is inserted and forms a three-stranded blade that completes the Seh1 6-bladed beta-propeller in trans. Following its N-terminal insertion blade, Nup85 forms a compact cuboid structure composed of 20 helices, with two distinct modules, referred to as crown and trunk."
Q#19708 - 	CGI_10025004	superfamily	219472	2	336	1.33E-101	314.272	cl09593	Nucleopor_Nup85 superfamily	N	 - 	"Nup85 Nucleoporin; A family of nucleoporins conserved from yeast to human. THe nuclear pore complex is a large assembly composed of two essential complexes: the heptameric Nup84 complex and the heteromeric Nic96-containing complex. The Nup84 complex is composed of one copy each of Nup84, Nup85, Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure of a complex of Nup85 and Seh1 was solved. The N-terminus of Nup85 is inserted and forms a three-stranded blade that completes the Seh1 6-bladed beta-propeller in trans. Following its N-terminal insertion blade, Nup85 forms a compact cuboid structure composed of 20 helices, with two distinct modules, referred to as crown and trunk."
Q#19710 - 	CGI_10025006	superfamily	241629	26	157	5.18E-33	120.703	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#19710 - 	CGI_10025006	superfamily	247097	196	230	0.000215219	38.1293	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#19711 - 	CGI_10025007	superfamily	243035	718	812	0.00116778	38.755	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19711 - 	CGI_10025007	superfamily	243093	622	693	6.58E-06	45.599	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#19711 - 	CGI_10025007	superfamily	221533	7	68	0.00191805	37.6764	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#19712 - 	CGI_10025008	superfamily	248318	578	630	2.54E-23	94.0397	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#19712 - 	CGI_10025008	superfamily	243142	85	208	1.51E-38	138.528	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#19716 - 	CGI_10025012	superfamily	245312	103	304	2.68E-07	49.9552	cl10482	KefB superfamily	C	 - 	"Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]"
Q#19717 - 	CGI_10025013	superfamily	245312	46	447	1.95E-06	48.7751	cl10482	KefB superfamily	 - 	 - 	"Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]"
Q#19719 - 	CGI_10025015	superfamily	241645	1	76	5.12E-42	147.335	cl00155	UBQ superfamily	N	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#19719 - 	CGI_10025015	superfamily	207411	564	602	2.06E-13	65.4884	cl01438	zf-AN1 superfamily	 - 	 - 	"AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues."
Q#19720 - 	CGI_10025016	superfamily	241672	107	439	2.99E-133	389.281	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#19721 - 	CGI_10025017	superfamily	247736	950	1000	0.000436075	40.7221	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#19721 - 	CGI_10025017	superfamily	247999	265	312	7.62E-14	69.0564	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#19721 - 	CGI_10025017	superfamily	241591	103	159	6.00E-08	52.1946	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#19721 - 	CGI_10025017	superfamily	247999	208	265	1.51E-07	50.952	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#19721 - 	CGI_10025017	superfamily	201844	347	373	5.37E-07	48.831	cl03250	zf-C2HC superfamily	 - 	 - 	"Zinc finger, C2HC type; This is a DNA binding zinc finger domain."
Q#19726 - 	CGI_10025022	superfamily	247725	327	428	2.53E-43	150.474	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19726 - 	CGI_10025022	superfamily	241622	241	319	6.23E-16	73.3698	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19726 - 	CGI_10025022	superfamily	247725	456	548	1.57E-21	89.9973	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19727 - 	CGI_10025023	superfamily	222150	585	606	0.000236598	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#19727 - 	CGI_10025023	superfamily	222150	609	634	0.00311422	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#19727 - 	CGI_10025023	superfamily	222150	403	424	0.00647625	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#19728 - 	CGI_10025024	superfamily	202894	65	130	2.74E-20	80.7278	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#19729 - 	CGI_10025025	superfamily	241622	764	850	1.63E-20	89.163	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19729 - 	CGI_10025025	superfamily	241622	1199	1287	1.05E-19	86.8518	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19729 - 	CGI_10025025	superfamily	241622	896	980	8.70E-18	81.0738	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19729 - 	CGI_10025025	superfamily	241622	1295	1365	7.91E-07	49.1023	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19729 - 	CGI_10025025	superfamily	246925	31	235	1.56E-12	69.3065	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#19730 - 	CGI_10025026	superfamily	245716	1	24	1.29E-07	48.0093	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#19731 - 	CGI_10025027	superfamily	243066	18	118	9.68E-22	89.5989	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19731 - 	CGI_10025027	superfamily	198867	128	234	0.00028188	39.2469	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#19732 - 	CGI_10025028	superfamily	243098	83	122	1.80E-11	55.6819	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19733 - 	CGI_10025029	superfamily	247725	260	382	7.44E-60	192.905	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19733 - 	CGI_10025029	superfamily	243088	2	105	1.91E-58	189.078	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#19734 - 	CGI_10025030	superfamily	245815	24	480	0	738.608	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#19737 - 	CGI_10025033	superfamily	217062	66	218	4.09E-11	59.9755	cl12266	Branch superfamily	N	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#19738 - 	CGI_10025034	superfamily	247856	337	405	5.54E-13	65.6469	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19738 - 	CGI_10025034	superfamily	241566	497	545	8.35E-07	47.4868	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#19738 - 	CGI_10025034	superfamily	241566	429	481	9.54E-07	47.1016	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#19738 - 	CGI_10025034	superfamily	243037	750	937	2.35E-64	214.121	cl02440	DAGK_acc superfamily	 - 	 - 	Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
Q#19738 - 	CGI_10025034	superfamily	248019	605	726	6.00E-54	184.037	cl17465	DAGK_cat superfamily	 - 	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#19739 - 	CGI_10025035	superfamily	198738	366	450	1.37E-46	158.971	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#19740 - 	CGI_10025036	superfamily	247068	15	112	1.70E-08	51.9306	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#19741 - 	CGI_10025037	superfamily	247856	21	83	7.23E-11	54.0909	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19741 - 	CGI_10025037	superfamily	247856	95	157	1.11E-09	51.0093	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19742 - 	CGI_10025038	superfamily	219425	28	133	2.32E-09	51.0031	cl06494	Hydrolase_2 superfamily	 - 	 - 	"Cell Wall Hydrolase; These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance B. subtilis sleB is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex. A similar role is carried out by the partially redundant B. subtilis cwlJ. It is not clear whether these enzymes are amidases or peptidases."
Q#19744 - 	CGI_10021221	superfamily	202894	51	116	9.53E-17	71.8682	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#19746 - 	CGI_10021223	superfamily	247724	500	719	2.28E-131	397.247	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19746 - 	CGI_10021223	superfamily	243184	814	920	2.48E-41	148.139	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#19746 - 	CGI_10021223	superfamily	243185	725	808	1.03E-14	71.4024	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#19746 - 	CGI_10021223	superfamily	220077	1	132	5.30E-27	108.676	cl07512	DUF1916 superfamily	 - 	 - 	Domain of unknown function (DUF1916); This domain is found in various eukaryotic HBS1-like proteins.
Q#19747 - 	CGI_10021224	superfamily	241745	8	185	2.16E-74	224.322	cl00276	Maf_Ham1 superfamily	 - 	 - 	"Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides, such as hypoxanthine/xanthine NTP, but not standard nucleotides."
Q#19748 - 	CGI_10021225	superfamily	207654	159	224	6.58E-20	84.4166	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#19748 - 	CGI_10021225	superfamily	207654	368	433	6.58E-20	84.4166	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#19748 - 	CGI_10021225	superfamily	207654	90	152	4.57E-18	79.409	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#19748 - 	CGI_10021225	superfamily	207654	527	592	2.06E-15	71.705	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#19748 - 	CGI_10021225	superfamily	207654	242	308	2.46E-15	71.3198	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#19748 - 	CGI_10021225	superfamily	207654	451	517	2.46E-15	71.3198	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#19748 - 	CGI_10021225	superfamily	207654	309	361	6.72E-15	69.7435	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#19752 - 	CGI_10021229	superfamily	222575	76	174	2.04E-12	60.0956	cl16668	FAM110_C superfamily	 - 	 - 	Centrosome-associated C terminus; This is the C-terminus of a family of proteins that colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis.
Q#19752 - 	CGI_10021229	superfamily	206330	12	70	9.43E-09	49.5489	cl16669	FAM110_N superfamily	C	 - 	Centrosome-associated N terminus; This is the N-terminus of a family of proteins that colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis.
Q#19754 - 	CGI_10021231	superfamily	148646	61	366	1.15E-173	488.902	cl12343	DUF1394 superfamily	 - 	 - 	Protein of unknown function (DUF1394); This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown.
Q#19755 - 	CGI_10021232	superfamily	148646	1	122	8.79E-78	238.908	cl12343	DUF1394 superfamily	N	 - 	Protein of unknown function (DUF1394); This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown.
Q#19756 - 	CGI_10021233	superfamily	243077	2778	2823	0.00702518	37.51	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#19757 - 	CGI_10021234	superfamily	243072	250	369	1.60E-32	119.796	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19757 - 	CGI_10021234	superfamily	243072	143	270	1.69E-29	111.321	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19757 - 	CGI_10021234	superfamily	243072	44	169	4.44E-22	90.9058	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19758 - 	CGI_10021235	superfamily	218498	359	545	3.00E-59	201.775	cl18459	TRM13 superfamily	C	 - 	Methyltransferase TRM13; This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4. TRM13 shows no sequence similarity to other known methyltransferases.
Q#19758 - 	CGI_10021235	superfamily	218498	636	714	3.23E-17	81.2076	cl18459	TRM13 superfamily	N	 - 	Methyltransferase TRM13; This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4. TRM13 shows no sequence similarity to other known methyltransferases.
Q#19758 - 	CGI_10021235	superfamily	191243	270	296	0.00320612	36.2663	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#19759 - 	CGI_10021236	superfamily	241643	164	200	8.02E-11	57.0839	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#19759 - 	CGI_10021236	superfamily	241643	344	379	0.000123187	39.3647	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#19759 - 	CGI_10021236	superfamily	241645	1	74	9.46E-24	93.1628	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#19759 - 	CGI_10021236	superfamily	192241	254	312	1.53E-20	84.2046	cl18177	XPC-binding superfamily	 - 	 - 	"XPC-binding domain; Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair."
Q#19760 - 	CGI_10021237	superfamily	241881	376	716	5.35E-157	460.842	cl00464	URO-D_CIMS_like superfamily	 - 	 - 	"The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases. Despite their sequence similarities, members of this family have clearly different functions. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane, and methionine synthases transfer a methyl group from a folate cofactor to L-homocysteine in a reaction requiring zinc."
Q#19760 - 	CGI_10021237	superfamily	243092	124	343	1.56E-24	103.954	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19760 - 	CGI_10021237	superfamily	243074	49	92	3.27E-06	45.1901	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19761 - 	CGI_10021238	superfamily	247920	21	88	0.00207519	38.5689	cl17366	Herpes_HEPA superfamily	C	 - 	"Herpesvirus DNA helicase/primase complex associated protein; This family includes HSV UL8, EHV-1 54, VZV 52 AND HCMV 102."
Q#19763 - 	CGI_10021240	superfamily	191362	157	209	9.78E-23	87.7114	cl05351	zf-nanos superfamily	 - 	 - 	"Nanos RNA binding domain; This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development."
Q#19764 - 	CGI_10021241	superfamily	246921	284	338	2.52E-05	41.5921	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19764 - 	CGI_10021241	superfamily	246921	16	45	0.000425008	38.1253	cl15299	FG-GAP superfamily	NC	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19765 - 	CGI_10021242	superfamily	244880	52	218	4.61E-78	236.847	cl08263	TBP_TLF superfamily	 - 	 - 	"TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many equivalent positions, suggesting similar structure. However, TLFs contain distinct, conserved amino acids at several positions that distinguish them from TBP."
Q#19766 - 	CGI_10021243	superfamily	216574	72	154	5.70E-19	83.026	cl14794	FAD_binding_4 superfamily	N	 - 	"FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan."
Q#19767 - 	CGI_10021244	superfamily	247792	722	765	1.34E-08	52.448	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19767 - 	CGI_10021244	superfamily	243112	440	607	2.03E-67	221.356	cl02620	YDG_SRA superfamily	 - 	 - 	"YDG/SRA domain; The function of this domain is unknown, it contains a conserved motif YDG after which it has been named."
Q#19767 - 	CGI_10021244	superfamily	241645	1	77	5.08E-35	128.397	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#19767 - 	CGI_10021244	superfamily	152583	151	251	4.45E-24	97.878	cl13567	DUF3590 superfamily	 - 	 - 	"Protein of unknown function (DUF3590); This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with pfam00097, pfam02182, pfam00628, pfam00240. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed."
Q#19767 - 	CGI_10021244	superfamily	247999	350	387	0.000181055	40.273	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#19769 - 	CGI_10021246	superfamily	241584	127	218	3.14E-07	47.8763	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#19771 - 	CGI_10021248	superfamily	243857	27	696	0	1069.17	cl04712	Ceramidase_alk superfamily	 - 	 - 	Neutral/alkaline non-lysosomal ceramidase; This family represents a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes.
Q#19772 - 	CGI_10021249	superfamily	247824	213	273	1.16E-08	52.7921	cl17270	APH_ChoK_like superfamily	N	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#19778 - 	CGI_10021255	superfamily	242169	13	93	5.98E-13	59.8982	cl00886	Robl_LC7 superfamily	 - 	 - 	"Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role."
Q#19779 - 	CGI_10021256	superfamily	247640	27	148	2.94E-06	46.9373	cl16915	ZnPC_S1P1 superfamily	C	 - 	"Zinc dependent phospholipase C/S1-P1 nuclease; This model describes both the bacterial and archeal zinc-dependent phospholipase C, a domain found in the alpha toxin of Clostridium perfringens, as well as S1/P1 nucleases, which predominantly act on single-stranded DNA and RNA."
Q#19779 - 	CGI_10021256	superfamily	246921	508	549	0.00152154	37.7401	cl15299	FG-GAP superfamily	C	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19779 - 	CGI_10021256	superfamily	246921	708	739	0.00344614	36.5845	cl15299	FG-GAP superfamily	C	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19780 - 	CGI_10021257	superfamily	247640	9	127	3.95E-09	56.1821	cl16915	ZnPC_S1P1 superfamily	C	 - 	"Zinc dependent phospholipase C/S1-P1 nuclease; This model describes both the bacterial and archeal zinc-dependent phospholipase C, a domain found in the alpha toxin of Clostridium perfringens, as well as S1/P1 nucleases, which predominantly act on single-stranded DNA and RNA."
Q#19780 - 	CGI_10021257	superfamily	246921	678	730	1.78E-06	46.5997	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19780 - 	CGI_10021257	superfamily	246921	338	388	1.98E-06	46.5997	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19780 - 	CGI_10021257	superfamily	246921	415	472	3.60E-05	42.7477	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19780 - 	CGI_10021257	superfamily	246921	479	513	0.00620808	36.1993	cl15299	FG-GAP superfamily	C	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#19783 - 	CGI_10021260	superfamily	246709	222	362	6.46E-71	220.929	cl14782	RNase_H superfamily	 - 	 - 	"RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription."
Q#19783 - 	CGI_10021260	superfamily	150794	1	136	3.70E-45	153.279	cl10862	DUF2368 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2368); This family is conserved from nematodes to humans. The function is not known.
Q#19783 - 	CGI_10021260	superfamily	201924	156	182	3.48E-06	43.6725	cl03316	Cauli_VI superfamily	N	 - 	"Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner."
Q#19785 - 	CGI_10021262	superfamily	243035	449	566	2.29E-15	73.4229	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19785 - 	CGI_10021262	superfamily	241804	4	343	1.79E-179	516.029	cl00348	COG0182 superfamily	 - 	 - 	"Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]"
Q#19786 - 	CGI_10021263	superfamily	245201	4	284	0	569.089	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19787 - 	CGI_10021264	superfamily	247724	7	173	1.55E-117	334.236	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19788 - 	CGI_10021265	superfamily	243038	125	200	7.51E-14	66.9805	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#19788 - 	CGI_10021265	superfamily	218263	272	403	4.59E-37	132.242	cl04748	DUF547 superfamily	 - 	 - 	"Protein of unknown function, DUF547; Family of uncharacterized proteins from C. elegans and A. thaliana."
Q#19788 - 	CGI_10021265	superfamily	241832	7	86	2.58E-25	98.871	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#19790 - 	CGI_10021267	superfamily	247856	93	154	1.94E-13	65.6469	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19791 - 	CGI_10021268	superfamily	247739	49	246	3.93E-60	193.609	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#19792 - 	CGI_10021269	superfamily	247792	29	71	1.83E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19792 - 	CGI_10021269	superfamily	207713	97	147	1.30E-13	65.0537	cl02729	WWE superfamily	C	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#19793 - 	CGI_10021270	superfamily	220243	5	139	2.62E-52	173.625	cl09680	eIF3_N superfamily	 - 	 - 	eIF3 subunit 6 N terminal domain; This is the N terminal domain of subunit 6 translation initiation factor eIF3.
Q#19793 - 	CGI_10021270	superfamily	242889	291	392	2.33E-17	77.2581	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#19794 - 	CGI_10021271	superfamily	241585	72	115	0.00190617	34.802	cl00066	FU superfamily	 - 	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#19795 - 	CGI_10021272	superfamily	243072	175	268	3.00E-16	75.4978	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19799 - 	CGI_10021276	superfamily	247725	79	178	9.48E-36	132.405	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19799 - 	CGI_10021276	superfamily	243056	566	784	8.98E-59	201.381	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#19805 - 	CGI_10003153	superfamily	219188	8	44	4.16E-06	42.2723	cl18498	Lung_7-TM_R superfamily	N	 - 	Lung seven transmembrane receptor; This family represents a conserved region with eukaryotic lung seven transmembrane receptors and related proteins.
Q#19808 - 	CGI_10003912	superfamily	220388	98	457	3.99E-118	360.14	cl12372	FimP superfamily	 - 	 - 	"Fms-interacting protein; This entry carries part of the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C-terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes."
Q#19809 - 	CGI_10003913	superfamily	247856	56	100	3.61E-08	47.9277	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19809 - 	CGI_10003913	superfamily	247856	126	183	0.000873913	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19812 - 	CGI_10002782	superfamily	248458	38	118	9.27E-08	50.3901	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19813 - 	CGI_10005250	superfamily	214531	60	102	5.18E-07	46.4409	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#19813 - 	CGI_10005250	superfamily	215683	388	428	0.000384287	37.9199	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#19813 - 	CGI_10005250	superfamily	245213	170	206	0.00800473	34.1448	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19814 - 	CGI_10005251	superfamily	243056	1	107	1.74E-21	93.1925	cl02495	RabGAP-TBC superfamily	N	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#19815 - 	CGI_10009353	superfamily	247755	44	102	4.31E-08	51.8796	cl17201	ABC_ATPase superfamily	NC	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#19816 - 	CGI_10009354	superfamily	245814	498	570	7.09E-08	50.5655	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19816 - 	CGI_10009354	superfamily	241756	8	316	3.98E-51	180.212	cl00289	FIG superfamily	 - 	 - 	"FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule Inositol-1,4,5-triphosphate. Many of these enzymes are inhibited by Li+."
Q#19816 - 	CGI_10009354	superfamily	245814	396	475	3.16E-17	78.1952	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19817 - 	CGI_10009355	superfamily	245201	511	813	0	591.751	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19818 - 	CGI_10009356	superfamily	222090	333	507	2.25E-18	83.8614	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#19820 - 	CGI_10009358	superfamily	215647	200	445	9.19E-34	128.11	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#19820 - 	CGI_10009358	superfamily	243029	114	180	1.56E-13	66.2201	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#19823 - 	CGI_10006754	superfamily	241563	63	102	2.26E-05	42.2744	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19823 - 	CGI_10006754	superfamily	191851	101	213	4.14E-06	46.0839	cl06708	DUF1640 superfamily	 - 	 - 	Protein of unknown function (DUF1640); This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Q#19823 - 	CGI_10006754	superfamily	219497	11	37	0.0023524	36.1835	cl06619	C1_3 superfamily	 - 	 - 	C1-like domain; This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in pfam00130.
Q#19824 - 	CGI_10006755	superfamily	242902	25	174	1.60E-15	69.1978	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#19825 - 	CGI_10006756	superfamily	242902	25	87	1.24E-13	63.8051	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#19828 - 	CGI_10000503	superfamily	243035	77	188	8.59E-29	108.476	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19828 - 	CGI_10000503	superfamily	246918	311	362	2.45E-13	64.1451	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#19828 - 	CGI_10000503	superfamily	246918	197	249	1.40E-12	62.2191	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#19828 - 	CGI_10000503	superfamily	243035	26	59	7.70E-09	52.6835	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19830 - 	CGI_10005111	superfamily	241974	578	737	7.21E-18	80.7486	cl00604	STAS superfamily	 - 	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#19830 - 	CGI_10005111	superfamily	216188	242	523	9.47E-67	224.019	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#19830 - 	CGI_10005111	superfamily	205965	93	176	1.40E-35	130.225	cl18285	Sulfate_tra_GLY superfamily	 - 	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#19833 - 	CGI_10005114	superfamily	218493	434	581	2.77E-48	165.993	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#19833 - 	CGI_10005114	superfamily	248054	26	54	0.00456256	35.5256	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#19833 - 	CGI_10005114	superfamily	248054	228	294	0.00695902	36.8967	cl17500	NAD_binding_8 superfamily	NC	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#19834 - 	CGI_10005115	superfamily	245823	17	486	5.60E-179	517.99	cl11976	SNF superfamily	 - 	 - 	Sodium:neurotransmitter symporter family; Sodium:neurotransmitter symporter family.  
Q#19835 - 	CGI_10005116	superfamily	245213	234	270	1.85E-08	50.713	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19835 - 	CGI_10005116	superfamily	245213	348	383	9.68E-08	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19835 - 	CGI_10005116	superfamily	245213	272	307	2.99E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19835 - 	CGI_10005116	superfamily	245213	310	345	1.92E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19835 - 	CGI_10005116	superfamily	245213	424	459	2.18E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19835 - 	CGI_10005116	superfamily	245213	386	422	3.26E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19835 - 	CGI_10005116	superfamily	243124	87	228	2.49E-37	134.477	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#19839 - 	CGI_10000672	superfamily	241600	105	230	3.08E-37	130.86	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19840 - 	CGI_10000741	superfamily	241567	17	188	1.40E-19	83.0335	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#19843 - 	CGI_10019396	superfamily	217293	28	73	0.000592692	37.9975	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#19844 - 	CGI_10019397	superfamily	243074	4	42	7.39E-07	46.7309	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19844 - 	CGI_10019397	superfamily	243092	78	108	7.50E-05	40.7984	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19846 - 	CGI_10019399	superfamily	243074	8	52	6.75E-14	63.6797	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19846 - 	CGI_10019399	superfamily	243092	90	120	6.00E-08	47.732	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19847 - 	CGI_10019400	superfamily	243074	8	52	7.33E-14	61.3685	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#19847 - 	CGI_10019400	superfamily	243092	90	118	6.79E-06	39.2576	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19847 - 	CGI_10019400	superfamily	219215	44	76	0.00950437	31.924	cl06096	Elongin_A superfamily	NC	 - 	"RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin."
Q#19848 - 	CGI_10019401	superfamily	247792	51	88	0.00103488	37.4252	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19848 - 	CGI_10019401	superfamily	243039	398	576	8.56E-82	256.799	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#19848 - 	CGI_10019401	superfamily	190233	197	253	1.17E-12	63.6274	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#19848 - 	CGI_10019401	superfamily	190233	138	194	3.31E-06	45.1378	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#19849 - 	CGI_10019402	superfamily	227674	361	584	1.04E-21	98.2233	cl02227	Mpp10 superfamily	N	 - 	"U3 small nucleolar ribonucleoprotein component [Translation, ribosomal structure and biogenesis]"
Q#19849 - 	CGI_10019402	superfamily	227674	153	300	0.000612147	41.599	cl02227	Mpp10 superfamily	C	 - 	"U3 small nucleolar ribonucleoprotein component [Translation, ribosomal structure and biogenesis]"
Q#19850 - 	CGI_10019403	superfamily	215821	325	413	1.71E-29	110.793	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#19850 - 	CGI_10019403	superfamily	191166	417	490	2.16E-09	54.2094	cl04891	SRP40_C superfamily	 - 	 - 	"SRP40, C-terminal domain; This presumed domain is found at the C-terminus of the S. cerevisiae SRP40 protein and its homologues. SRP40/nopp40 is a chaperone involved in nucleocytoplasmic transport. SRP40 is also a suppressor of mutant AC40 subunit of RNA polymerase I and III."
Q#19851 - 	CGI_10019404	superfamily	148072	146	228	3.11E-32	115.222	cl09585	DUF1014 superfamily	N	 - 	Protein of unknown function (DUF1014); This family consists of several hypothetical eukaryotic proteins of unknown function.
Q#19852 - 	CGI_10019405	superfamily	242274	1	39	2.47E-05	40.0052	cl01053	SGNH_hydrolase superfamily	NC	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#19853 - 	CGI_10019406	superfamily	220692	60	348	2.39E-05	44.8877	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#19854 - 	CGI_10019407	superfamily	243035	141	190	2.67E-07	48.0698	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#19855 - 	CGI_10019408	superfamily	151671	291	394	9.81E-18	83.9355	cl12777	DUF3028 superfamily	C	 - 	Protein of unknown function (DUF3028); This eukaryotic family of proteins has no known function.
Q#19857 - 	CGI_10019410	superfamily	245596	1155	1396	4.86E-171	515.402	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#19857 - 	CGI_10019410	superfamily	219023	896	1073	2.29E-74	247.966	cl05763	UDP-g_GGTase superfamily	 - 	 - 	UDP-glucose:Glycoprotein Glucosyltransferase; The N-terminal region of this group of proteins is required for correct folding of the ER UDP-Glc: glucosyltransferase.
Q#19858 - 	CGI_10019411	superfamily	238191	19	526	2.19E-145	432.912	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#19858 - 	CGI_10019411	superfamily	149659	565	603	4.47E-05	41.4389	cl07334	AChE_tetra superfamily	 - 	 - 	Acetylcholinesterase tetramerisation domain; The acetylcholinesterase tetramerisation domain is found at the C terminus and forms a left handed superhelix.
Q#19859 - 	CGI_10019412	superfamily	222428	82	394	4.64E-154	466.673	cl18675	AAA_34 superfamily	 - 	 - 	P-loop containing NTP hydrolase pore-1; P-loop containing NTP hydrolase pore-1.  
Q#19859 - 	CGI_10019412	superfamily	222427	536	822	1.62E-117	368.051	cl18674	Helicase_C_4 superfamily	 - 	 - 	"Helicase_C-like; Strawberry notch proteins carry DExD/H-box groups and Helicase_C domains. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes."
Q#19860 - 	CGI_10019413	superfamily	247724	69	204	4.58E-36	126.537	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19861 - 	CGI_10019414	superfamily	247724	31	167	2.53E-29	107.662	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19863 - 	CGI_10019416	superfamily	247724	31	150	1.35E-20	84.9356	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19864 - 	CGI_10019417	superfamily	241599	188	246	2.11E-21	85.758	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#19865 - 	CGI_10019418	superfamily	241554	346	482	1.06E-28	111.198	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19866 - 	CGI_10019419	superfamily	241554	5	45	2.50E-10	53.8035	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#19868 - 	CGI_10001188	superfamily	245814	210	280	0.000116247	39.9154	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19869 - 	CGI_10002881	superfamily	241584	405	497	1.85E-11	62.5139	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#19869 - 	CGI_10002881	superfamily	245814	326	397	3.25E-07	49.4099	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19869 - 	CGI_10002881	superfamily	241584	733	831	8.80E-05	42.0983	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#19869 - 	CGI_10002881	superfamily	241584	614	727	0.000405417	40.1723	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#19869 - 	CGI_10002881	superfamily	241584	508	592	0.00787425	35.9351	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#19869 - 	CGI_10002881	superfamily	245814	233	293	2.05E-15	73.2099	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19869 - 	CGI_10002881	superfamily	245814	135	215	7.21E-15	71.6618	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19869 - 	CGI_10002881	superfamily	245814	45	106	1.45E-14	70.5135	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#19873 - 	CGI_10001303	superfamily	246918	157	200	4.43E-07	46.0407	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#19874 - 	CGI_10001304	superfamily	241619	37	101	0.000210296	35.6324	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#19877 - 	CGI_10000995	superfamily	218307	133	189	1.77E-14	69.5044	cl04818	NUDE_C superfamily	C	 - 	"NUDE protein, C-terminal conserved region; This family represents the C-terminal conserved region of the NUDE proteins. NUDE proteins are involved in nuclear migration."
Q#19879 - 	CGI_10002923	superfamily	243072	860	985	1.59E-35	132.893	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19879 - 	CGI_10002923	superfamily	243072	761	886	6.82E-35	130.967	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19879 - 	CGI_10002923	superfamily	243072	695	820	1.94E-32	124.033	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19879 - 	CGI_10002923	superfamily	243072	619	753	3.20E-28	111.707	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19879 - 	CGI_10002923	superfamily	243072	926	1049	4.03E-26	105.543	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#19879 - 	CGI_10002923	superfamily	247755	76	119	0.000275271	41.0763	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#19880 - 	CGI_10002924	superfamily	247856	12	74	3.40E-16	69.8841	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19880 - 	CGI_10002924	superfamily	247856	101	154	7.04E-16	68.7285	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#19882 - 	CGI_10002140	superfamily	248097	74	134	0.00658114	33.4297	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19883 - 	CGI_10002141	superfamily	248097	186	314	4.67E-17	75.3794	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19883 - 	CGI_10002141	superfamily	243066	8	79	3.23E-11	58.7829	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#19884 - 	CGI_10002154	superfamily	241550	1	217	3.42E-79	242.875	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#19890 - 	CGI_10001584	superfamily	241874	14	305	4.33E-130	392.64	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#19891 - 	CGI_10001585	superfamily	243058	439	544	0.000631544	38.8348	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#19895 - 	CGI_10006442	superfamily	241547	46	285	3.65E-94	294.947	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#19895 - 	CGI_10006442	superfamily	243092	312	601	5.46E-66	221.825	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#19897 - 	CGI_10006444	superfamily	240421	3	168	3.13E-09	53.1676	cl14774	PTZ00445 superfamily	 - 	 - 	p36-lilke protein; Provisional
Q#19898 - 	CGI_10006445	superfamily	241574	995	1243	1.27E-87	286.404	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#19898 - 	CGI_10006445	superfamily	241704	547	664	2.72E-24	102.066	cl00227	PEBP superfamily	 - 	 - 	"PhosphatidylEthanolamine-Binding Protein (PEBP) domain; PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer)."
Q#19898 - 	CGI_10006445	superfamily	247792	827	893	6.77E-06	45.5144	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#19898 - 	CGI_10006445	superfamily	243141	710	817	2.05E-26	107.017	cl02687	RWD superfamily	 - 	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#19898 - 	CGI_10006445	superfamily	241704	289	445	6.11E-07	49.6792	cl00227	PEBP superfamily	 - 	 - 	"PhosphatidylEthanolamine-Binding Protein (PEBP) domain; PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer)."
Q#19898 - 	CGI_10006445	superfamily	148004	19	78	9.42E-07	48.4749	cl05589	Ifi-6-16 superfamily	C	 - 	Interferon-induced 6-16 family; Interferon-induced 6-16 family.  
Q#19900 - 	CGI_10012306	superfamily	246664	13	203	3.12E-54	182.895	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#19901 - 	CGI_10012307	superfamily	246664	1	294	3.52E-129	380.767	cl14561	An_peroxidase_like superfamily	N	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#19902 - 	CGI_10012308	superfamily	246664	300	670	1.28E-148	440.473	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#19902 - 	CGI_10012308	superfamily	246664	153	237	7.89E-07	50.746	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#19904 - 	CGI_10012310	superfamily	245201	18	211	1.04E-49	173.577	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19904 - 	CGI_10012310	superfamily	240618	296	382	1.05E-08	53.4068	cl18927	UBL_TBK1_like superfamily	 - 	 - 	"Ubiquitin-Like Domain Of Human Tbk1 and similar proteins; This family contains ubiquitin-like domain (UBL) found in TANK-binding kinase 1 (TBK1) and similar proteins. TBK1 regulates factors such as IRF3 and IRF7, promoting antiviral activity in the interferon signaling pathways. In addition to the central UBL, these proteins have an N-terminal kinase domain and a C-terminal elongated helical domain. The ubiquitin-like domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the IFN pathway."
Q#19906 - 	CGI_10012312	superfamily	241563	68	109	1.06E-05	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19907 - 	CGI_10012313	superfamily	245201	18	211	7.32E-50	173.962	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19907 - 	CGI_10012313	superfamily	240618	296	382	7.94E-09	53.792	cl18927	UBL_TBK1_like superfamily	 - 	 - 	"Ubiquitin-Like Domain Of Human Tbk1 and similar proteins; This family contains ubiquitin-like domain (UBL) found in TANK-binding kinase 1 (TBK1) and similar proteins. TBK1 regulates factors such as IRF3 and IRF7, promoting antiviral activity in the interferon signaling pathways. In addition to the central UBL, these proteins have an N-terminal kinase domain and a C-terminal elongated helical domain. The ubiquitin-like domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the IFN pathway."
Q#19908 - 	CGI_10012314	superfamily	217064	1	86	2.07E-18	77.92	cl03617	CLN3 superfamily	N	 - 	CLN3 protein; This is a family of proteins from the CLN3 gene. A missense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease).
Q#19911 - 	CGI_10012317	superfamily	217064	51	230	4.24E-62	203.11	cl03617	CLN3 superfamily	C	 - 	CLN3 protein; This is a family of proteins from the CLN3 gene. A missense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease).
Q#19911 - 	CGI_10012317	superfamily	241683	234	256	3.15E-05	43.658	cl00204	PFK superfamily	N	 - 	"Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases. Some members evolved by gene duplication and thus have a large C-terminal/N-terminal extension comprising a second PFK domain. Generally, ATP-PFKs are allosteric homotetramers, and  PPi-PFKs are dimeric and nonallosteric except for plant PPi-PFKs which are allosteric heterotetramers."
Q#19912 - 	CGI_10012318	superfamily	247724	1	125	4.02E-42	146.141	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19914 - 	CGI_10012320	superfamily	248097	7	69	4.15E-05	37.2446	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19915 - 	CGI_10012321	superfamily	248097	14	133	5.89E-24	90.7874	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#19916 - 	CGI_10003329	superfamily	247724	9	179	5.59E-131	368.53	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19917 - 	CGI_10003330	superfamily	247727	53	166	1.57E-09	53.2027	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#19917 - 	CGI_10003330	superfamily	247844	32	70	0.00562815	35.7481	cl17290	Methyltransf_4 superfamily	C	 - 	Putative methyltransferase; This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.
Q#19919 - 	CGI_10003332	superfamily	219817	126	274	2.19E-37	138.52	cl07129	Xpo1 superfamily	 - 	 - 	"Exportin 1-like protein; The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus."
Q#19919 - 	CGI_10003332	superfamily	243689	49	119	0.00803334	35.6821	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#19920 - 	CGI_10003333	superfamily	241599	13	70	4.28E-19	78.4392	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#19921 - 	CGI_10003334	superfamily	241563	64	100	0.00011897	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19923 - 	CGI_10000659	superfamily	247684	11	48	0.00302228	32.6082	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19925 - 	CGI_10004643	superfamily	241584	60	101	0.000108548	37.0907	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#19926 - 	CGI_10004644	superfamily	221584	1	196	1.10E-57	185.197	cl13841	Dynactin superfamily	C	 - 	"Dynein associated protein; This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with pfam01302. There is a single completely conserved residue E that may be functionally important. Dynactin has been associated with Dynein, a kinesin protein which is involved in organelle transport, mitotic spindle assembly and chromosome segregation. Dynactin anchors Dynein to specific subcellular structures."
Q#19927 - 	CGI_10004645	superfamily	241752	70	190	7.61E-45	146.696	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#19928 - 	CGI_10002258	superfamily	241600	303	484	3.95E-64	209.404	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19928 - 	CGI_10002258	superfamily	241600	2	65	5.08E-13	67.3022	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19929 - 	CGI_10002259	superfamily	245226	18	116	3.59E-15	69.2516	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#19932 - 	CGI_10011763	superfamily	246664	333	701	6.46E-152	449.718	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#19932 - 	CGI_10011763	superfamily	246664	188	274	0.00509422	38.4196	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#19933 - 	CGI_10011764	superfamily	191507	62	116	0.000691197	34.3342	cl05726	Adipokin_hormo superfamily	 - 	 - 	"Adipokinetic hormone; This family consists of several insect adipokinetic hormone as well as the related crustacean red pigment concentrating hormone. Flight activity of insects comprises one of the most intense biochemical processes known in nature, and therefore provides an attractive model system to study the hormonal regulation of metabolism during physical exercise. In long-distance flying insects, such as the migratory locust, both carbohydrate and lipid reserves are utilised as fuels for sustained flight activity. The mobilization of these energy stores in Locusta migratoria is mediated by three structurally related adipokinetic hormones (AKHs), which are all capable of stimulating the release of both carbohydrates and lipids from the fat body."
Q#19934 - 	CGI_10011765	superfamily	245601	5	89	5.05E-30	110.875	cl11399	HP superfamily	C	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#19934 - 	CGI_10011765	superfamily	245601	159	230	5.29E-18	77.7476	cl11399	HP superfamily	N	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#19935 - 	CGI_10011766	superfamily	192445	45	174	7.61E-30	111.35	cl10818	Med4 superfamily	C	 - 	"Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter."
Q#19936 - 	CGI_10011767	superfamily	242885	41	202	5.63E-80	239.036	cl02106	IF4E superfamily	 - 	 - 	Eukaryotic initiation factor 4E; Eukaryotic initiation factor 4E.  
Q#19937 - 	CGI_10011768	superfamily	241563	60	102	0.000197505	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#19937 - 	CGI_10011768	superfamily	110440	481	508	0.0048006	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#19938 - 	CGI_10011769	superfamily	247684	59	542	0	701.754	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#19939 - 	CGI_10011770	superfamily	245206	103	390	0	542.228	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#19940 - 	CGI_10011771	superfamily	243098	839	886	2.71E-13	67.6231	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	2146	2196	1.60E-12	65.3119	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	1239	1286	1.29E-10	59.9191	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	1908	1955	1.29E-10	59.9191	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	209	254	2.23E-10	59.1487	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	615	660	7.78E-10	57.6079	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	428	472	1.27E-09	56.8375	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	1056	1102	1.90E-09	56.4523	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19940 - 	CGI_10011771	superfamily	243098	1725	1771	1.90E-09	56.4523	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#19941 - 	CGI_10011772	superfamily	216363	2	57	1.60E-08	46.3094	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#19948 - 	CGI_10011779	superfamily	222150	102	127	7.79E-05	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#19948 - 	CGI_10011779	superfamily	246975	89	110	0.00626374	33.0893	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#19949 - 	CGI_10006307	superfamily	244824	1	321	1.56E-71	230.709	cl07893	AmyAc_family superfamily	N	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#19950 - 	CGI_10006308	superfamily	244824	2	40	5.55E-05	38.5165	cl07893	AmyAc_family superfamily	N	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#19951 - 	CGI_10006309	superfamily	244859	62	301	1.26E-13	68.7273	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#19953 - 	CGI_10002542	superfamily	219542	51	129	7.27E-25	97.3123	cl18517	Cu-oxidase_3 superfamily	C	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#19953 - 	CGI_10002542	superfamily	215896	179	224	1.41E-05	43.0524	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#19955 - 	CGI_10003538	superfamily	247740	6	79	3.51E-24	92.5991	cl17186	TIM_phosphate_binding superfamily	C	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#19956 - 	CGI_10003539	superfamily	247740	1	166	1.66E-91	269.02	cl17186	TIM_phosphate_binding superfamily	N	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#19957 - 	CGI_10006974	superfamily	246748	12	355	9.42E-149	428.046	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#19958 - 	CGI_10006975	superfamily	216167	700	861	6.68E-47	166.993	cl02999	DNA_photolyase superfamily	 - 	 - 	DNA photolyase; This domain binds a light harvesting cofactor.
Q#19959 - 	CGI_10006976	superfamily	242920	52	141	1.20E-39	130.728	cl02174	TAF13 superfamily	 - 	 - 	"The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is  involved  in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID.   Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and are found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF13 interacts with TAF11 and makes a histone-like heterodimer similar to H3/H4-like proteins. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex."
Q#19960 - 	CGI_10006977	superfamily	243362	139	303	2.32E-48	161.054	cl03262	DnaJ_C superfamily	 - 	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#19960 - 	CGI_10006977	superfamily	243077	4	58	1.55E-23	91.4529	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#19961 - 	CGI_10006978	superfamily	241559	1747	1865	0.00360584	38.7996	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#19962 - 	CGI_10006979	superfamily	191166	264	337	3.31E-23	91.1886	cl04891	SRP40_C superfamily	 - 	 - 	"SRP40, C-terminal domain; This presumed domain is found at the C-terminus of the S. cerevisiae SRP40 protein and its homologues. SRP40/nopp40 is a chaperone involved in nucleocytoplasmic transport. SRP40 is also a suppressor of mutant AC40 subunit of RNA polymerase I and III."
Q#19963 - 	CGI_10006980	superfamily	152466	2246	2507	6.36E-99	321.768	cl13467	DUF3518 superfamily	 - 	 - 	Domain of unknown function (DUF3518); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 260 amino acids in length. This domain is found associated with pfam01388.
Q#19963 - 	CGI_10006980	superfamily	243120	893	985	1.36E-29	116.22	cl02633	ARID superfamily	 - 	 - 	"ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain."
Q#19964 - 	CGI_10006981	superfamily	248458	36	201	1.39E-14	73.8873	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#19964 - 	CGI_10006981	superfamily	113509	278	361	0.00143401	38.1801	cl17052	InvH superfamily	C	 - 	"InvH outer membrane lipoprotein; This family represents the Salmonella outer membrane lipoprotein InvH. The molecular function of this protein is unknown, but it is required for the localisation to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion."
Q#19965 - 	CGI_10006982	superfamily	247724	106	181	0.00483524	37.141	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#19967 - 	CGI_10014302	superfamily	247750	22	235	4.38E-94	284.37	cl17196	E1_enzyme_family superfamily	 - 	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#19967 - 	CGI_10014302	superfamily	241626	272	400	8.30E-36	128.581	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#19968 - 	CGI_10014303	superfamily	241592	1	143	2.61E-41	136.573	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#19969 - 	CGI_10014304	superfamily	243106	674	771	6.97E-34	127.133	cl02608	BAH superfamily	C	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#19970 - 	CGI_10014305	superfamily	245213	609	643	1.55E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#19972 - 	CGI_10014307	superfamily	245201	219	486	2.93E-53	181.986	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19973 - 	CGI_10014308	superfamily	245201	519	771	9.51E-41	150.4	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#19977 - 	CGI_10014312	superfamily	241622	863	945	5.61E-24	99.1782	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19977 - 	CGI_10014312	superfamily	241622	1730	1809	2.14E-18	83.385	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19977 - 	CGI_10014312	superfamily	241622	1113	1199	5.14E-17	79.1478	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19977 - 	CGI_10014312	superfamily	241622	1877	1951	3.49E-15	73.755	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19977 - 	CGI_10014312	superfamily	241622	1371	1440	4.96E-06	46.7911	cl00117	PDZ superfamily	C	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19977 - 	CGI_10014312	superfamily	247725	585	713	2.36E-35	133.583	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#19977 - 	CGI_10014312	superfamily	215882	499	610	5.16E-30	117.767	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#19977 - 	CGI_10014312	superfamily	220215	406	493	1.48E-14	71.8726	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#19978 - 	CGI_10014313	superfamily	241574	24	152	2.85E-47	155.822	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#19979 - 	CGI_10014314	superfamily	241838	140	342	3.98E-134	404.523	cl00395	FMT_core superfamily	 - 	 - 	"Formyltransferase, catalytic core domain; Formyltransferase, catalytic core domain. The proteins of this superfamily contain a formyltransferase domain that hydrolyzes the removal of a formyl group from its substrate as part of a multistep transfer mechanism, and this alignment model represents the catalytic core of the formyltransferase domain.  This family includes the following known members; Glycinamide Ribonucleotide Transformylase (GART), Formyl-FH4 Hydrolase, Methionyl-tRNA Formyltransferase, ArnA, and 10-Formyltetrahydrofolate Dehydrogenase (FDH).  Glycinamide Ribonucleotide Transformylase  (GART) catalyzes the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Methionyl-tRNA Formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA, which plays important role in translation initiation. ArnA is required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. 10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. Members of this family are multidomain proteins. The formyltransferase domain is located at the N-terminus of FDH, Methionyl-tRNA Formyltransferase and ArnA, and at the C-terminus of Formyl-FH4 Hydrolase.  Prokaryotic Glycinamide Ribonucleotide Transformylase (GART) is a single domain protein while eukaryotic GART is a trifunctional protein that catalyzes the second, third and fifth steps in de novo purine biosynthesis."
Q#19979 - 	CGI_10014314	superfamily	246712	345	444	1.07E-43	154.812	cl14785	FMT_C_like superfamily	 - 	 - 	"Carboxy-terminal domain of Formyltransferase and similar domains; This family represents the C-terminal domain of formyltransferase and similar proteins. This domain is found in a variety of enzymes with formyl transferase and alkyladenine DNA glycosylase activities. The proteins with formyltransferase function include methionyl-tRNA formyltransferase, ArnA, 10-formyltetrahydrofolate dehydrogenase and HypX proteins. Although most proteins with formyl transferase activity contain this C-terminal domain, prokaryotic glycinamide ribonucleotide transformylase (GART), a single domain protein, only contains the core catalytic domain. Thus, the C-terminal domain is not required for formyl transferase catalytic activity and may be involved in substrate binding. Some members of this family have shown nucleic acid binding capacity. The C-terminal domain of methionyl-tRNA formyltransferase is involved in tRNA binding. Alkyladenine DNA glycosylase is a distant member of this family with very low sequence similarity to other members. It catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site and shows ability to bind to DNA."
Q#19979 - 	CGI_10014314	superfamily	245815	708	986	0	570.206	cl11961	ALDH-SF superfamily	N	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#19979 - 	CGI_10014314	superfamily	245815	554	678	6.29E-72	247.408	cl11961	ALDH-SF superfamily	C	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#19979 - 	CGI_10014314	superfamily	245209	466	528	0.00198975	37.5342	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#19982 - 	CGI_10014317	superfamily	241600	154	350	9.35E-66	209.019	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19982 - 	CGI_10014317	superfamily	241600	32	147	1.19E-26	105.015	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19983 - 	CGI_10014318	superfamily	241600	156	364	5.54E-89	269.495	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19983 - 	CGI_10014318	superfamily	241600	1	128	2.52E-58	190.529	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#19984 - 	CGI_10014319	superfamily	243034	447	544	3.53E-17	78.5759	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#19984 - 	CGI_10014319	superfamily	243034	678	764	3.56E-15	72.7979	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#19984 - 	CGI_10014319	superfamily	243034	561	662	1.89E-13	67.7904	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#19984 - 	CGI_10014319	superfamily	149463	252	290	0.00318525	36.8089	cl07144	DUF1736 superfamily	C	 - 	Domain of unknown function (DUF1736); This domain of unknown function is found in various hypothetical metazoan proteins.
Q#19986 - 	CGI_10014321	superfamily	217584	33	152	4.23E-18	77.7827	cl04100	MOSC_N superfamily	 - 	 - 	"MOSC N-terminal beta barrel domain; This domain is found to the N-terminus of pfam03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold."
Q#19986 - 	CGI_10014321	superfamily	217583	197	289	3.63E-07	46.9724	cl04097	MOSC superfamily	 - 	 - 	"MOSC domain; The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters."
Q#19990 - 	CGI_10009817	superfamily	241589	64	198	1.04E-42	141.617	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#19995 - 	CGI_10009822	superfamily	248098	85	162	1.68E-13	65.0073	cl17544	U-box superfamily	 - 	 - 	U-box domain; This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
Q#19996 - 	CGI_10009823	superfamily	241622	215	307	3.17E-14	66.5092	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#19996 - 	CGI_10009823	superfamily	241640	39	174	6.35E-27	103.421	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#19997 - 	CGI_10009824	superfamily	246681	159	329	1.55E-63	203.29	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#20000 - 	CGI_10009827	superfamily	247769	472	670	8.69E-09	54.2677	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#20000 - 	CGI_10009827	superfamily	243045	156	258	2.79E-07	49.1687	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#20001 - 	CGI_10009828	superfamily	247724	48	168	8.83E-31	118.063	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20001 - 	CGI_10009828	superfamily	192499	427	511	6.82E-23	93.8394	cl10941	RNA_GG_bind superfamily	 - 	 - 	"PHAX RNA-binding domain; RNA_GG_bind is the highly conserved U3 snoRNA-binding domain of PHAX (phosphorylated adaptor for RNA export) whose function is to transport U3 snoRNA from the nucleus after transcription. It is characterized by having two pairs of adjacent glycines, as GGx12GG."
Q#20002 - 	CGI_10003930	superfamily	247068	489	580	4.03E-19	85.8281	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	698	787	7.24E-17	79.2797	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	588	685	1.04E-14	73.1165	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1836	1929	8.39E-14	70.4201	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1406	1502	7.91E-13	67.3385	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	2047	2141	8.40E-13	67.3385	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1074	1163	2.24E-12	66.1829	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	873	957	3.43E-11	62.7161	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1518	1605	4.21E-11	62.3309	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1942	2035	1.20E-09	58.0938	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	262	366	4.63E-08	53.4714	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1295	1393	5.77E-08	53.0862	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1177	1284	6.90E-08	52.701	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	970	1062	1.64E-07	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1623	1719	3.42E-06	47.6934	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	385	459	9.81E-05	43.071	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	1730	1811	0.00016208	42.3006	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20002 - 	CGI_10003930	superfamily	247068	107	167	0.000358493	41.145	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20003 - 	CGI_10003931	superfamily	247068	37	122	2.30E-13	62.7161	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20003 - 	CGI_10003931	superfamily	247068	135	207	0.00276375	34.5966	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20005 - 	CGI_10006389	superfamily	247692	111	653	0	542.372	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#20006 - 	CGI_10006390	superfamily	245814	139	217	6.04E-08	48.2543	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20006 - 	CGI_10006390	superfamily	245814	29	121	9.53E-07	44.8037	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20007 - 	CGI_10020528	superfamily	218493	5	152	2.77E-47	152.896	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#20008 - 	CGI_10020530	superfamily	218493	345	391	6.97E-12	62.3746	cl08434	GMC_oxred_C superfamily	C	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#20009 - 	CGI_10020531	superfamily	218493	1	50	4.52E-18	73.1602	cl08434	GMC_oxred_C superfamily	N	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#20010 - 	CGI_10020532	superfamily	218493	454	601	1.13E-45	158.674	cl08434	GMC_oxred_C superfamily	 - 	 - 	GMC oxidoreductase; This domain found associated with pfam00732.
Q#20010 - 	CGI_10020532	superfamily	130849	51	84	0.00525101	37.922	cl17981	lycopene_cycl superfamily	C	 - 	lycopene cyclase; This model represents a family of bacterial lycopene cyclases catalyzing the transformation of lycopene to carotene. These enzymes are found in a limited spectrum of alpha and gamma proteobacteria as well as Flavobacterium.
Q#20014 - 	CGI_10020536	superfamily	238076	22	144	8.32E-54	179.922	cl18938	PAX superfamily	 - 	 - 	Paired Box domain
Q#20016 - 	CGI_10020538	superfamily	243034	466	559	1.07E-06	47.76	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20017 - 	CGI_10020539	superfamily	247637	330	654	2.57E-177	510.446	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#20020 - 	CGI_10020542	superfamily	177822	23	278	1.16E-31	120.795	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#20021 - 	CGI_10020543	superfamily	243034	333	430	1.49E-11	61.242	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20021 - 	CGI_10020543	superfamily	243034	292	360	8.23E-05	40.8264	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20022 - 	CGI_10020544	superfamily	241622	1041	1125	2.66E-15	74.5254	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20022 - 	CGI_10020544	superfamily	241581	360	456	6.15E-09	56.2406	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#20022 - 	CGI_10020544	superfamily	241645	18	128	3.98E-42	153.21	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#20022 - 	CGI_10020544	superfamily	216736	804	909	7.53E-33	126.145	cl03379	DIL superfamily	 - 	 - 	DIL domain; The DIL domain has no known function.
Q#20022 - 	CGI_10020544	superfamily	241645	224	326	4.85E-28	111.962	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#20024 - 	CGI_10020546	superfamily	243072	1	86	2.80E-16	72.4162	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20025 - 	CGI_10020547	superfamily	245596	202	242	2.70E-24	98.0453	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#20027 - 	CGI_10020549	superfamily	198867	85	185	3.65E-33	121.497	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#20027 - 	CGI_10020549	superfamily	243066	2	80	4.20E-16	74.2644	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20027 - 	CGI_10020549	superfamily	243146	366	411	9.46E-13	63.4494	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20027 - 	CGI_10020549	superfamily	243146	332	377	3.69E-11	58.7239	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20027 - 	CGI_10020549	superfamily	243146	272	317	5.91E-11	58.4418	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20027 - 	CGI_10020549	superfamily	243146	426	471	2.52E-10	56.4127	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20027 - 	CGI_10020549	superfamily	243146	473	518	8.11E-10	54.8719	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20027 - 	CGI_10020549	superfamily	243146	237	282	9.56E-06	43.3159	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20028 - 	CGI_10020550	superfamily	198867	118	218	2.45E-34	125.349	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#20028 - 	CGI_10020550	superfamily	243066	7	109	7.13E-27	105.007	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20028 - 	CGI_10020550	superfamily	243146	411	457	4.73E-17	75.6727	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20028 - 	CGI_10020550	superfamily	243146	317	363	1.25E-13	66.0427	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20028 - 	CGI_10020550	superfamily	243146	352	396	4.32E-12	61.5234	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20028 - 	CGI_10020550	superfamily	243146	459	504	1.21E-10	57.5683	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20028 - 	CGI_10020550	superfamily	243146	493	538	9.38E-10	54.975	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20028 - 	CGI_10020550	superfamily	243146	270	315	1.16E-05	42.9307	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20029 - 	CGI_10020551	superfamily	245814	155	235	6.11E-05	40.1651	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20029 - 	CGI_10020551	superfamily	245814	36	135	6.81E-07	45.9593	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20032 - 	CGI_10020554	superfamily	217473	127	289	4.75E-25	105.14	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#20034 - 	CGI_10020556	superfamily	218088	3	133	3.12E-27	104.353	cl04518	RINT1_TIP1 superfamily	N	 - 	"RINT-1 / TIP-1 family; This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control, as well as the TIP-1 protein from yeast that seems to be involved in a complex with Sec20p that is required for golgi transport."
Q#20035 - 	CGI_10020557	superfamily	243540	64	256	8.59E-29	109.645	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#20037 - 	CGI_10020559	superfamily	245206	1	244	6.17E-96	283.593	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20038 - 	CGI_10020560	superfamily	243078	1	61	5.05E-14	67.3481	cl02544	VHS_ENTH_ANTH superfamily	N	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#20041 - 	CGI_10020563	superfamily	243034	105	216	1.02E-13	70.8719	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20041 - 	CGI_10020563	superfamily	216112	2537	2904	1.08E-58	209.075	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#20041 - 	CGI_10020563	superfamily	221913	1873	2089	9.08E-46	167.332	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#20041 - 	CGI_10020563	superfamily	221913	3638	3831	1.95E-31	125.731	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#20041 - 	CGI_10020563	superfamily	222005	3392	3461	2.62E-05	45.4208	cl18632	AAA_19 superfamily	 - 	 - 	Part of AAA domain; Part of AAA domain.  
Q#20041 - 	CGI_10020563	superfamily	222258	1674	1738	7.00E-05	45.2516	cl18656	AAA_30 superfamily	C	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#20041 - 	CGI_10020563	superfamily	248275	1184	1208	0.000194166	42.182	cl17721	zf-C2H2_jaz superfamily	 - 	 - 	"Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation."
Q#20044 - 	CGI_10020567	superfamily	248097	14	117	1.20E-17	73.4534	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20045 - 	CGI_10008096	superfamily	215724	1	138	1.26E-51	170.492	cl14706	wnt superfamily	C	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#20048 - 	CGI_10008099	superfamily	247743	256	399	5.23E-20	87.9719	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#20048 - 	CGI_10008099	superfamily	247743	545	657	7.32E-07	48.2963	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#20048 - 	CGI_10008099	superfamily	216993	7	86	2.84E-10	57.9553	cl15641	CDC48_N superfamily	 - 	 - 	"Cell division protein 48 (CDC48), N-terminal domain; This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain."
Q#20050 - 	CGI_10008101	superfamily	241791	1	131	3.23E-78	231.456	cl00331	Ribosomal_S13 superfamily	 - 	 - 	Ribosomal protein S13/S18; This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
Q#20052 - 	CGI_10008103	superfamily	243091	4357	4476	3.11E-40	149.022	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#20052 - 	CGI_10008103	superfamily	248279	1655	1734	6.85E-26	106.297	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#20052 - 	CGI_10008103	superfamily	243127	4193	4273	1.02E-18	85.424	cl02651	FYRC superfamily	 - 	 - 	F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.
Q#20052 - 	CGI_10008103	superfamily	247999	994	1038	4.22E-10	59.1478	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#20052 - 	CGI_10008103	superfamily	243126	1780	1830	4.41E-10	59.1416	cl02650	FYRN superfamily	 - 	 - 	F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.
Q#20052 - 	CGI_10008103	superfamily	243084	1475	1548	1.72E-09	58.9855	cl02556	Bromodomain superfamily	N	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#20052 - 	CGI_10008103	superfamily	202085	711	738	0.000182964	42.7326	cl03401	zf-CXXC superfamily	C	 - 	"CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR."
Q#20054 - 	CGI_10008105	superfamily	241559	57	162	3.23E-10	58.0911	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#20054 - 	CGI_10008105	superfamily	198670	644	723	7.79E-28	108.083	cl02426	DIX superfamily	 - 	 - 	DIX domain; The DIX domain is present in Dishevelled and axin. This domain is involved in homo- and hetero-oligomerisation. It is involved in the homo- oligomerisation of mouse axin. The axin DIX domain also interacts with the dishevelled DIX domain. The DIX domain has also been called the DAX domain.
Q#20054 - 	CGI_10008105	superfamily	221533	402	471	9.52E-05	41.1432	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#20055 - 	CGI_10008106	superfamily	247755	1308	1528	9.05E-129	400.716	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20055 - 	CGI_10008106	superfamily	247755	643	844	1.37E-101	324.037	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20055 - 	CGI_10008106	superfamily	216049	330	599	1.07E-33	132.795	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#20055 - 	CGI_10008106	superfamily	216049	1003	1261	5.45E-33	130.869	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#20056 - 	CGI_10008107	superfamily	241599	100	158	9.17E-21	83.0616	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#20057 - 	CGI_10009636	superfamily	241584	176	244	0.000504073	37.4035	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20057 - 	CGI_10009636	superfamily	246925	54	135	0.00050561	39.6462	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#20058 - 	CGI_10009637	superfamily	218849	8	213	1.02E-72	237.136	cl05508	Nop52 superfamily	 - 	 - 	"Nucleolar protein,Nop52; Nop52 believed to be involved in the generation of 28S rRNA."
Q#20059 - 	CGI_10009638	superfamily	219903	1430	1603	8.80E-33	128.541	cl09456	Cut8 superfamily	 - 	 - 	"Cut8; In Schizosaccharomyces pombe, Cut8 is a nuclear envelope protein that physically interacts with and tethers 26S proteasome in the nucleus resulting in the nuclear accumulation of proteasome. Cut8 is a proteasome substrate and amino terminal residues 1-72 are polyubiquitinated and function as a degron tag. Ubiquitination of the amino terminal is essential to the function of Cut8. Lysine residues in the amino terminal 72 amino acids of Cut8 are required for physical interaction with proteasome. In fission yeast the function of Cut8 has been demonstrated to be regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating enzymes Ubr1. Cut8 homologs have been identified in Drosophila melanogaster, Anopheles gambiae and Dictyostelium discoideum."
Q#20059 - 	CGI_10009638	superfamily	243091	450	553	8.35E-05	43.0919	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#20059 - 	CGI_10009638	superfamily	197676	915	937	0.00944111	36.2897	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#20061 - 	CGI_10009640	superfamily	243267	35	399	4.04E-131	383.888	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#20062 - 	CGI_10009641	superfamily	241550	458	733	3.92E-108	344.23	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#20062 - 	CGI_10009641	superfamily	241550	132	287	5.48E-84	278.361	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#20062 - 	CGI_10009641	superfamily	245839	733	870	3.27E-60	202.787	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#20062 - 	CGI_10009641	superfamily	222257	309	406	1.34E-11	64.0343	cl16317	tRNA-synt_1_2 superfamily	C	 - 	"Leucyl-tRNA synthetase, Domain 2; This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4."
Q#20063 - 	CGI_10009642	superfamily	241832	210	322	7.15E-59	189.136	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20063 - 	CGI_10009642	superfamily	241832	6	101	4.82E-54	176.427	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20063 - 	CGI_10009642	superfamily	241832	109	196	8.13E-21	85.8442	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20064 - 	CGI_10009643	superfamily	221761	4	153	1.10E-14	69.8183	cl15080	SAGA-Tad1 superfamily	N	 - 	"Transcriptional regulator of RNA polII, SAGA, subunit; The yeast SAGA complex is a multifunctional coactivator that regulates transcription by RNA polymerase II. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA. The complex can also be conceived of as consisting of two histone-fold-containing core subunits, and this family is one of these. As a family it is likely to carry binding regions for interactions with a number of the other components of the complex."
Q#20065 - 	CGI_10009644	superfamily	111019	5	270	1.95E-117	340.529	cl17927	SURF4 superfamily	 - 	 - 	SURF4 family; SURF4 family.  
Q#20066 - 	CGI_10009645	superfamily	247744	270	462	5.19E-56	186.674	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#20066 - 	CGI_10009645	superfamily	247744	59	249	9.35E-35	128.509	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#20066 - 	CGI_10009645	superfamily	213107	17	54	0.00510957	34.9384	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#20067 - 	CGI_10009646	superfamily	241622	384	455	3.64E-15	72.5994	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20067 - 	CGI_10009646	superfamily	246669	223	340	9.70E-33	124.103	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#20067 - 	CGI_10009646	superfamily	243096	546	727	3.36E-09	56.0698	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#20069 - 	CGI_10009648	superfamily	220662	110	311	2.50E-73	236.968	cl10947	DUF2217 superfamily	N	 - 	Uncharacterized conserved protein (DUF2217); This is a family of conserved proteins of from 500 - 600 residues found from worms to humans. Its function is not known.
Q#20069 - 	CGI_10009648	superfamily	220662	33	149	5.29E-09	55.9245	cl10947	DUF2217 superfamily	NC	 - 	Uncharacterized conserved protein (DUF2217); This is a family of conserved proteins of from 500 - 600 residues found from worms to humans. Its function is not known.
Q#20070 - 	CGI_10009649	superfamily	241568	644	686	4.89E-05	42.0648	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#20070 - 	CGI_10009649	superfamily	214531	70	121	2.96E-06	45.2853	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20070 - 	CGI_10009649	superfamily	214531	491	531	3.52E-06	45.2853	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20070 - 	CGI_10009649	superfamily	205157	602	627	0.00126246	37.5171	cl18264	EGF_3 superfamily	C	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#20071 - 	CGI_10009650	superfamily	241607	126	153	0.000865852	36.479	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#20071 - 	CGI_10009650	superfamily	241607	293	311	0.004274	34.5671	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#20072 - 	CGI_10009651	superfamily	241774	1	128	2.98E-83	244.677	cl00313	Ribosomal_S7 superfamily	N	 - 	Ribosomal protein S7p/S5e; This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.
Q#20073 - 	CGI_10003285	superfamily	245815	37	558	0	913.125	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#20075 - 	CGI_10017821	superfamily	248097	6	126	2.13E-11	56.5046	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20077 - 	CGI_10017823	superfamily	243175	130	243	4.84E-51	165.859	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#20077 - 	CGI_10017823	superfamily	241832	18	75	4.28E-12	60.4636	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20084 - 	CGI_10017830	superfamily	216056	35	163	4.39E-38	140.137	cl08279	Peptidase_M16 superfamily	 - 	 - 	Insulinase (Peptidase family M16); Insulinase (Peptidase family M16).  
Q#20084 - 	CGI_10017830	superfamily	218490	190	368	9.31E-23	97.1619	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#20084 - 	CGI_10017830	superfamily	218490	626	809	2.72E-10	59.7975	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#20086 - 	CGI_10002556	superfamily	215647	106	265	6.36E-13	66.0928	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#20088 - 	CGI_10002558	superfamily	247755	252	487	4.54E-154	441.593	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20088 - 	CGI_10002558	superfamily	216049	17	205	6.42E-39	143.195	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#20090 - 	CGI_10005936	superfamily	142268	1	32	0.00954306	30.2948	cl09807	Lin0512_fam superfamily	C	 - 	"Conserved hypothetical protein (Lin0512_fam); This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a well conserved motif GxGxDxHG near the N-terminus."
Q#20091 - 	CGI_10005937	superfamily	247792	582	626	5.71E-06	44.3588	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20091 - 	CGI_10005937	superfamily	141623	91	211	8.79E-42	147.457	cl02685	Neuralized superfamily	 - 	 - 	Neuralized; This family contains a conserved region approximately 60 residues long within eukaryotic neuralized and neuralized-like proteins. Neuralized belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the Drosophila nervous system. Some family members contain multiple copies of this region.
Q#20091 - 	CGI_10005937	superfamily	141623	316	439	2.83E-23	95.8405	cl02685	Neuralized superfamily	 - 	 - 	Neuralized; This family contains a conserved region approximately 60 residues long within eukaryotic neuralized and neuralized-like proteins. Neuralized belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the Drosophila nervous system. Some family members contain multiple copies of this region.
Q#20094 - 	CGI_10005940	superfamily	247986	43	83	0.000638447	40.8194	cl17432	PBPb superfamily	NC	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#20094 - 	CGI_10005940	superfamily	197504	194	326	1.04E-07	51.1361	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#20095 - 	CGI_10004403	superfamily	214531	24	63	1.32E-07	43.7445	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20096 - 	CGI_10004404	superfamily	241568	124	178	2.24E-05	43.6056	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#20096 - 	CGI_10004404	superfamily	241568	930	963	0.000604454	39.3684	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#20096 - 	CGI_10004404	superfamily	214531	761	801	1.07E-08	52.9893	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20096 - 	CGI_10004404	superfamily	214531	353	394	6.52E-06	44.9001	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20096 - 	CGI_10004404	superfamily	214531	308	351	4.82E-05	42.2037	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20096 - 	CGI_10004404	superfamily	215683	735	775	0.000411875	39.4607	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#20098 - 	CGI_10004406	superfamily	246669	58	175	3.26E-21	84.6375	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#20099 - 	CGI_10004407	superfamily	221377	248	344	5.81E-07	47.4635	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#20102 - 	CGI_10027874	superfamily	241571	24	124	1.57E-08	50.8739	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#20102 - 	CGI_10027874	superfamily	241571	128	226	0.00628194	34.6955	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#20103 - 	CGI_10027875	superfamily	241734	69	288	1.54E-75	245.856	cl00261	PLPDE_III superfamily	C	 - 	"Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity."
Q#20103 - 	CGI_10027875	superfamily	241734	373	522	7.07E-53	185.379	cl00261	PLPDE_III superfamily	N	 - 	"Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity."
Q#20104 - 	CGI_10027876	superfamily	247916	141	199	2.30E-07	48.9183	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20105 - 	CGI_10027877	superfamily	247916	184	247	2.52E-08	51.9999	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20105 - 	CGI_10027877	superfamily	193253	601	713	0.00686469	38.0941	cl15084	MT superfamily	NC	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#20106 - 	CGI_10027878	superfamily	247916	141	194	2.95E-08	51.6147	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20107 - 	CGI_10027879	superfamily	247916	38	145	3.63E-07	50.0918	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20107 - 	CGI_10027879	superfamily	247916	789	842	8.03E-06	45.4515	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20107 - 	CGI_10027879	superfamily	192292	516	577	0.00705568	36.4822	cl09671	Wbp11 superfamily	 - 	 - 	WW domain binding protein 11; The WW domain is a small protein module with a triple-stranded beta-sheet fold. This is a family of WW domain binding proteins.
Q#20109 - 	CGI_10027881	superfamily	241640	20	260	1.62E-84	254.894	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#20110 - 	CGI_10027882	superfamily	241777	407	721	3.71E-68	227.966	cl00316	Cation_efflux superfamily	 - 	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#20111 - 	CGI_10027883	superfamily	243689	28	95	9.40E-13	65.343	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#20112 - 	CGI_10027884	superfamily	243074	125	170	1.78E-06	45.1901	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#20113 - 	CGI_10027885	superfamily	243146	69	121	1.84E-08	50.1393	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20113 - 	CGI_10027885	superfamily	243146	253	295	4.68E-07	46.1154	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20113 - 	CGI_10027885	superfamily	243146	26	78	3.57E-05	40.7355	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20113 - 	CGI_10027885	superfamily	243146	200	238	0.000205878	38.4114	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20117 - 	CGI_10027889	superfamily	215754	128	225	2.34E-25	96.1684	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#20117 - 	CGI_10027889	superfamily	215754	28	123	5.28E-23	90.0052	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#20119 - 	CGI_10027891	superfamily	215754	211	308	2.89E-25	97.324	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#20119 - 	CGI_10027891	superfamily	215754	111	206	8.64E-24	93.0868	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#20119 - 	CGI_10027891	superfamily	215754	11	104	4.97E-21	85.3828	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#20121 - 	CGI_10027893	superfamily	241874	25	551	0	852.353	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#20122 - 	CGI_10027894	superfamily	247724	2	108	6.16E-39	129.704	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20123 - 	CGI_10027895	superfamily	218708	58	286	4.19E-33	122.458	cl05328	DUF829 superfamily	 - 	 - 	Eukaryotic protein of unknown function (DUF829); This family consists of several uncharacterized eukaryotic proteins.
Q#20125 - 	CGI_10027897	superfamily	241862	58	267	5.59E-09	55.4702	cl00437	COG0428 superfamily	C	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#20126 - 	CGI_10027898	superfamily	245206	6	250	1.03E-61	196.753	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20129 - 	CGI_10027901	superfamily	245206	6	251	1.75E-72	224.487	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20130 - 	CGI_10027902	superfamily	245206	6	251	1.46E-71	221.791	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20133 - 	CGI_10027905	superfamily	243110	135	356	1.62E-21	93.6481	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#20135 - 	CGI_10027907	superfamily	245226	20	213	7.07E-48	164.765	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#20136 - 	CGI_10027908	superfamily	241874	9	547	8.33E-168	492.381	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#20137 - 	CGI_10027909	superfamily	241992	1	304	1.61E-102	309.966	cl00628	Piwi-like superfamily	C	 - 	"Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism."
Q#20138 - 	CGI_10027910	superfamily	241765	1395	1480	5.92E-37	137.392	cl00301	PAZ superfamily	N	 - 	"PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain."
Q#20139 - 	CGI_10027911	superfamily	242122	88	205	1.89E-08	51.0937	cl00824	HEPN superfamily	 - 	 - 	HEPN domain; HEPN domain.  
Q#20139 - 	CGI_10027911	superfamily	243077	3	34	0.000920298	36.4437	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#20141 - 	CGI_10027913	superfamily	243053	755	991	1.95E-63	216.735	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#20141 - 	CGI_10027913	superfamily	247725	430	539	1.09E-42	152.872	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#20141 - 	CGI_10027913	superfamily	243067	599	722	1.01E-29	116.358	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#20141 - 	CGI_10027913	superfamily	243096	197	381	1.89E-17	81.9604	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#20141 - 	CGI_10027913	superfamily	241592	99	169	7.30E-09	55.2534	cl00074	H2A superfamily	C	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#20143 - 	CGI_10027915	superfamily	206354	147	230	2.78E-27	103.978	cl16692	Aida_C2 superfamily	C	 - 	"Cytoskeletal adhesion; This is the C-terminal domain of the axin-interacting protein family, and is a distinct version of the C2 domain. This domain is critical for interactions with cytoskeletal in the context of cellular adhesion points."
Q#20143 - 	CGI_10027915	superfamily	204091	15	113	2.45E-24	94.5577	cl07485	Aida-C2 superfamily	 - 	 - 	"C2 domain of Aida; This is the C2 domain in the axin interaction dorsal-associated (Aida) proteins. In all proteins the Aida-C2 domain is found in the C-terminal portion of the protein. these proteins also contain diverse domains related to cytoskeletal functions, e.g. EF hands, coiled coils, IQ calmodulin-binding motifs, ankyrin repeats and myosin head motor domain. Aida blocks Axin-mediated JNK (c-Jun N-terminal kinases) activation by disrupting Axin homodimerisation, thereby having an anti-dorsalisation action in zebrafish. Axin is a scaffold protein that controls multiple, important pathways, including the canonical Wnt pathway and the JNK signalling pathway and besides its ventralising activity mediated though facilitating beta-catenin degradation, possesses a dorsalising activity that is mediated by Axin-induced JNK activation."
Q#20144 - 	CGI_10027917	superfamily	241832	6	155	2.22E-76	227.06	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20145 - 	CGI_10027918	superfamily	241581	11	100	7.81E-19	82.4342	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#20145 - 	CGI_10027918	superfamily	247792	391	433	1.16E-10	57.8408	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20147 - 	CGI_10027920	superfamily	243035	33	156	9.76E-26	96.1497	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20148 - 	CGI_10027921	superfamily	243035	33	156	1.73E-26	98.0757	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20149 - 	CGI_10027922	superfamily	243035	36	158	7.20E-28	101.928	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20150 - 	CGI_10027923	superfamily	245864	30	477	1.39E-62	212.524	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#20151 - 	CGI_10027924	superfamily	241749	54	194	8.35E-29	105.931	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#20152 - 	CGI_10027925	superfamily	241749	49	154	1.76E-10	55.0845	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#20153 - 	CGI_10027926	superfamily	241749	37	185	4.26E-18	77.8113	cl00280	globin_like superfamily	 - 	 - 	superfamily containing globins and truncated hemoglobins
Q#20155 - 	CGI_10027928	superfamily	217293	4	209	1.48E-73	230.983	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#20155 - 	CGI_10027928	superfamily	202474	202	374	4.17E-07	49.1893	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#20156 - 	CGI_10027929	superfamily	247044	129	152	5.63E-07	44.1361	cl15697	ADF_gelsolin superfamily	C	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#20158 - 	CGI_10027931	superfamily	245814	51	134	3.93E-16	72.9232	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20159 - 	CGI_10027932	superfamily	243075	3	33	5.97E-05	40.7643	cl02536	SAND superfamily	N	 - 	"SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain."
Q#20160 - 	CGI_10027933	superfamily	218871	172	289	4.43E-21	92.3948	cl15997	Sec6 superfamily	C	 - 	"Exocyst complex component Sec6; Sec6 is a component of the multiprotein exocyst complex. Sec6 interacts with Sec8, Sec10 and Exo70.These exocyst proteins localise to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis- independent manner."
Q#20161 - 	CGI_10027934	superfamily	218871	1	150	1.02E-35	129.374	cl15997	Sec6 superfamily	NC	 - 	"Exocyst complex component Sec6; Sec6 is a component of the multiprotein exocyst complex. Sec6 interacts with Sec8, Sec10 and Exo70.These exocyst proteins localise to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis- independent manner."
Q#20162 - 	CGI_10027935	superfamily	243035	1	67	2.27E-16	68.0301	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20166 - 	CGI_10027939	superfamily	247637	1039	1359	8.91E-50	182.045	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#20167 - 	CGI_10027940	superfamily	243072	327	452	2.02E-32	123.263	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20167 - 	CGI_10027940	superfamily	243072	32	157	2.00E-30	117.485	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20167 - 	CGI_10027940	superfamily	243072	494	618	3.96E-30	116.714	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20167 - 	CGI_10027940	superfamily	243072	131	259	1.74E-24	100.536	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20167 - 	CGI_10027940	superfamily	243072	592	726	1.18E-23	97.8394	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20167 - 	CGI_10027940	superfamily	243072	469	497	0.00164269	37.1484	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20170 - 	CGI_10027943	superfamily	193235	220	269	6.92E-26	97.2351	cl15075	HTH_Tnp_IS1 superfamily	 - 	 - 	InsA C-terminal domain; This short domain is found at the C-terminus of the InsA protein. This domain contains a helix-turn-helix domain.
Q#20170 - 	CGI_10027943	superfamily	190760	182	217	2.87E-14	64.8683	cl09312	Zn_Tnp_IS1 superfamily	 - 	 - 	InsA N-terminal domain; This appears to be a short zinc binding domain found in IS1 InsA family protein. It is found at the N-terminus of the protein and may be a DNA-binding domain.
Q#20173 - 	CGI_10027948	superfamily	110440	381	408	0.000254445	38.5429	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20173 - 	CGI_10027948	superfamily	243092	144	232	0.00992645	36.1588	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20174 - 	CGI_10027949	superfamily	247755	182	211	1.63E-10	58.2852	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20175 - 	CGI_10027950	superfamily	247755	1375	1593	7.31E-101	323.688	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20175 - 	CGI_10027950	superfamily	247755	504	723	7.61E-100	320.991	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20175 - 	CGI_10027950	superfamily	247789	1062	1209	0.00275187	39.9346	cl17235	ABC2_membrane superfamily	 - 	 - 	ABC-2 type transporter; ABC-2 type transporter.  
Q#20176 - 	CGI_10027951	superfamily	247724	45	181	6.92E-90	262.838	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20177 - 	CGI_10027952	superfamily	247755	582	802	1.56E-119	362.967	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20177 - 	CGI_10027952	superfamily	216049	373	531	6.46E-17	80.793	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#20177 - 	CGI_10027952	superfamily	110440	315	339	4.60E-05	41.6245	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20179 - 	CGI_10027954	superfamily	248469	90	187	5.03E-11	57.3799	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#20179 - 	CGI_10027954	superfamily	247756	12	116	0.000532612	38.1099	cl17202	HAD superfamily	C	 - 	haloacid dehalogenase-like hydrolase; haloacid dehalogenase-like hydrolase.  
Q#20180 - 	CGI_10027955	superfamily	243072	36	148	2.96E-36	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20182 - 	CGI_10027957	superfamily	247724	1	283	0	582.248	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20183 - 	CGI_10027958	superfamily	241572	13	102	1.55E-18	77.2788	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20183 - 	CGI_10027958	superfamily	241572	112	195	1.16E-16	72.2712	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20184 - 	CGI_10027959	superfamily	241572	209	298	5.03E-20	84.2124	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20184 - 	CGI_10027959	superfamily	241572	308	383	1.51E-17	77.2788	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20185 - 	CGI_10027960	superfamily	245213	4	34	0.000586984	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20185 - 	CGI_10027960	superfamily	245213	45	73	0.000910963	36.0754	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20187 - 	CGI_10027962	superfamily	243035	135	250	2.29E-18	78.8157	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20187 - 	CGI_10027962	superfamily	241619	34	98	0.000109558	39.4877	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#20191 - 	CGI_10018592	superfamily	241599	153	210	1.20E-20	82.6764	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#20193 - 	CGI_10018594	superfamily	247724	9	80	7.61E-31	109.184	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20194 - 	CGI_10018595	superfamily	241718	2	218	3.78E-115	340.417	cl00241	IF6 superfamily	 - 	 - 	"Ribosome anti-association factor IF6 binds the large ribosomal subunit and prevents the two subunits from associating during translation initiation. IF6 comprises a family of translation factors that includes both eukaryotic (eIF6) and archeal (aIF6) members.  All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved C-terminal extension which is not required for ribosomal binding, and may have an alternative function."
Q#20197 - 	CGI_10018599	superfamily	245213	1497	1526	0.00016304	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1621	1650	0.00016304	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1373	1406	0.000210379	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1580	1614	0.00126151	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1456	1491	0.00224176	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	996	1029	0.00362898	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1704	1738	0.00931724	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	241578	1244	1283	2.85E-06	48.9204	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20197 - 	CGI_10018599	superfamily	241578	1160	1204	6.43E-06	47.7648	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20197 - 	CGI_10018599	superfamily	243124	345	404	1.47E-05	45.4957	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#20197 - 	CGI_10018599	superfamily	241578	828	868	3.17E-05	45.8388	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20197 - 	CGI_10018599	superfamily	241578	1410	1452	0.000125151	43.9128	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20197 - 	CGI_10018599	superfamily	241578	1070	1111	0.00120858	41.2164	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20197 - 	CGI_10018599	superfamily	245213	1330	1368	0.00149227	38.382	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1207	1236	0.00287097	37.6116	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1660	1692	0.007114	36.456	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	245213	1536	1568	0.007114	36.456	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20197 - 	CGI_10018599	superfamily	241578	910	950	0.00945096	38.1348	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20198 - 	CGI_10018600	superfamily	247905	190	296	5.12E-12	62.2552	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#20198 - 	CGI_10018600	superfamily	247805	43	130	7.27E-05	41.4759	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#20200 - 	CGI_10018602	superfamily	241596	52	111	2.06E-14	65.6983	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#20201 - 	CGI_10018603	superfamily	241599	156	214	2.21E-21	84.9876	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#20201 - 	CGI_10018603	superfamily	247725	112	168	0.00557175	35.5242	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#20204 - 	CGI_10019337	superfamily	245847	286	363	0.00101741	37.9214	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20205 - 	CGI_10019338	superfamily	241563	40	76	3.73E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20205 - 	CGI_10019338	superfamily	110440	460	487	0.000910138	37.3873	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20206 - 	CGI_10019339	superfamily	245847	161	306	2.14E-18	79.5229	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20206 - 	CGI_10019339	superfamily	241568	128	149	0.0064174	33.9756	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#20207 - 	CGI_10019340	superfamily	247097	78	112	0.001111	35.4329	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#20207 - 	CGI_10019340	superfamily	245226	20	62	0.0012325	37.2801	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#20208 - 	CGI_10019341	superfamily	245226	12	60	0.000136356	39.2061	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#20212 - 	CGI_10019345	superfamily	245213	197	232	5.33E-09	52.639	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20212 - 	CGI_10019345	superfamily	245847	238	304	3.87E-14	69.8929	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20213 - 	CGI_10019346	superfamily	245847	113	250	1.25E-16	73.7449	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20218 - 	CGI_10019351	superfamily	245847	1	142	1.65E-19	79.9081	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20219 - 	CGI_10019352	superfamily	245213	74	109	5.42E-11	57.6466	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20219 - 	CGI_10019352	superfamily	245213	112	147	5.88E-11	57.6466	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20219 - 	CGI_10019352	superfamily	245847	288	429	4.91E-19	82.9897	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20219 - 	CGI_10019352	superfamily	245847	153	219	8.36E-11	59.4925	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20220 - 	CGI_10019353	superfamily	242406	1	119	7.93E-35	119.233	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#20222 - 	CGI_10019357	superfamily	248097	4	114	3.18E-19	77.6906	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20223 - 	CGI_10019358	superfamily	241563	348	383	2.66E-05	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20223 - 	CGI_10019358	superfamily	110440	813	840	0.00289866	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20226 - 	CGI_10019361	superfamily	241564	157	222	2.21E-21	86.9359	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#20226 - 	CGI_10019361	superfamily	241564	2	68	1.65E-13	65.3647	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#20226 - 	CGI_10019361	superfamily	247792	368	406	0.00152227	36.2696	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20229 - 	CGI_10002198	superfamily	246723	12	829	0	960.562	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#20230 - 	CGI_10002199	superfamily	241678	5	400	3.43E-174	495.236	cl00198	Phosphoglycerate_kinase superfamily	 - 	 - 	"Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level phosphorylation events in the glycolytic pathway. Substrate-level phosphorylation is defined as production of  ATP by a process, which is catalyzed by water-soluble enzymes in the cytosol; not involving membranes and ion gradients."
Q#20231 - 	CGI_10002201	superfamily	248262	1	237	1.43E-72	227.112	cl17708	HMBS superfamily	 - 	 - 	"Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12.  HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB).  HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II.  HMBS is found in all organisms except viruses."
Q#20232 - 	CGI_10002204	superfamily	241550	549	741	3.23E-80	267.962	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#20232 - 	CGI_10002204	superfamily	247896	2	264	4.18E-69	242.22	cl17342	Pyruvate_Kinase superfamily	N	 - 	"Pyruvate kinase (PK):  Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors.  Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state.  PK exists as several different isozymes, depending on organism and tissue type.  In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung.  PK forms a homotetramer, with each subunit containing three domains.  The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer."
Q#20232 - 	CGI_10002204	superfamily	222257	753	914	1.11E-57	198.854	cl16317	tRNA-synt_1_2 superfamily	 - 	 - 	"Leucyl-tRNA synthetase, Domain 2; This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4."
Q#20232 - 	CGI_10002204	superfamily	241550	1035	1194	8.90E-49	178.21	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#20232 - 	CGI_10002204	superfamily	241870	288	434	1.53E-22	97.1692	cl00451	MoCF_BD superfamily	 - 	 - 	"MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin."
Q#20232 - 	CGI_10002204	superfamily	245839	1194	1325	2.74E-12	65.7041	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#20232 - 	CGI_10002204	superfamily	241550	935	962	9.90E-06	47.9971	cl00015	nt_trans superfamily	NC	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#20233 - 	CGI_10002205	superfamily	247755	386	619	1.22E-97	301.072	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20233 - 	CGI_10002205	superfamily	216049	93	297	4.81E-10	59.607	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#20234 - 	CGI_10002209	superfamily	241808	2	138	1.25E-22	88.6854	cl00352	PTH superfamily	N	 - 	"Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts."
Q#20235 - 	CGI_10002213	superfamily	247794	3	193	5.52E-81	245.825	cl17240	FDH_GDH_like superfamily	N	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#20236 - 	CGI_10004926	superfamily	247724	35	202	4.73E-96	279.998	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20237 - 	CGI_10004927	superfamily	241547	38	226	2.61E-59	189.788	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#20239 - 	CGI_10004929	superfamily	241573	877	1200	7.94E-106	340.078	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#20239 - 	CGI_10004929	superfamily	246669	1368	1493	1.01E-29	116.609	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#20239 - 	CGI_10004929	superfamily	241653	1211	1352	8.76E-27	108.925	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#20240 - 	CGI_10004930	superfamily	244539	463	547	1.47E-16	78.8858	cl06868	FNR_like superfamily	C	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#20240 - 	CGI_10004930	superfamily	244539	593	721	1.10E-15	76.1894	cl06868	FNR_like superfamily	N	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#20240 - 	CGI_10004930	superfamily	247856	127	196	5.09E-09	53.7057	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#20240 - 	CGI_10004930	superfamily	247856	92	153	2.24E-06	46.0017	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#20240 - 	CGI_10004930	superfamily	242267	287	425	5.52E-15	72.3228	cl01043	Ferric_reduct superfamily	 - 	 - 	"Ferric reductase like transmembrane component; This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease."
Q#20246 - 	CGI_10006870	superfamily	247683	544	590	1.88E-29	112.207	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#20246 - 	CGI_10006870	superfamily	243056	162	375	7.46E-54	185.588	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#20246 - 	CGI_10006870	superfamily	243142	617	771	3.83E-34	127.743	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#20247 - 	CGI_10006871	superfamily	241546	371	488	4.84E-36	133.449	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#20247 - 	CGI_10006871	superfamily	243072	698	822	2.26E-31	120.181	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20248 - 	CGI_10006872	superfamily	245827	119	534	1.03E-141	446.281	cl11986	TOP1Ac superfamily	 - 	 - 	"DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand."
Q#20248 - 	CGI_10006872	superfamily	242046	1	110	2.25E-37	140.061	cl00718	TOPRIM superfamily	N	 - 	"Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function."
Q#20248 - 	CGI_10006872	superfamily	149077	1560	1634	2.31E-27	110.022	cl06719	TMC superfamily	 - 	 - 	"TMC domain; These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters."
Q#20248 - 	CGI_10006872	superfamily	219199	866	908	7.90E-18	80.502	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#20248 - 	CGI_10006872	superfamily	219199	940	983	5.15E-17	78.1908	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#20248 - 	CGI_10006872	superfamily	219199	740	782	7.77E-16	74.724	cl06070	zf-GRF superfamily	 - 	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#20248 - 	CGI_10006872	superfamily	219199	800	831	1.86E-11	62.0124	cl06070	zf-GRF superfamily	N	 - 	GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.
Q#20248 - 	CGI_10006872	superfamily	110400	572	610	0.000144453	41.8683	cl15497	zf-C4_Topoisom superfamily	 - 	 - 	Topoisomerase DNA binding C4 zinc finger; Topoisomerase DNA binding C4 zinc finger.  
Q#20249 - 	CGI_10006873	superfamily	143631	1	107	5.22E-32	110.892	cl12007	Cby_like superfamily	 - 	 - 	"Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins; Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif."
Q#20252 - 	CGI_10003521	superfamily	241559	33	137	1.37E-26	108.167	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#20252 - 	CGI_10003521	superfamily	241559	159	203	2.11E-07	51.9279	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#20252 - 	CGI_10003521	superfamily	216033	1714	1800	1.48E-23	98.9452	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2398	2483	9.94E-23	96.634	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	735	826	6.55E-22	94.3228	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2215	2302	1.57E-21	93.1672	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1317	1404	2.72E-21	92.3968	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1223	1309	8.30E-21	90.856	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1033	1119	1.43E-20	90.4708	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2612	2695	1.56E-20	90.0856	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1614	1707	3.28E-20	89.3152	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1806	1897	6.41E-20	88.5448	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	640	725	6.88E-20	88.5448	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1514	1598	3.95E-19	86.2336	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1128	1214	5.47E-19	85.8484	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	542	635	9.60E-19	85.078	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	841	931	1.72E-17	81.226	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	429	535	2.65E-16	77.7592	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2799	2884	3.62E-16	77.374	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	337	421	4.47E-16	77.374	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2924	3011	4.83E-16	76.9888	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1904	1993	5.51E-16	76.9888	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1999	2085	1.59E-15	75.8332	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2703	2791	1.71E-15	75.448	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	1415	1498	2.24E-12	66.5884	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	939	1026	8.12E-12	64.6624	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2144	2210	3.76E-11	62.7364	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2541	2600	3.45E-10	60.04	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	216033	2310	2389	1.10E-08	55.4176	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#20252 - 	CGI_10003521	superfamily	241559	232	315	6.53E-08	53.4372	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#20253 - 	CGI_10011808	superfamily	247725	394	503	1.86E-57	190.295	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#20253 - 	CGI_10011808	superfamily	215882	538	592	5.36E-13	66.1502	cl09511	FERM_M superfamily	N	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#20253 - 	CGI_10011808	superfamily	215882	302	337	5.87E-09	54.209	cl09511	FERM_M superfamily	C	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#20254 - 	CGI_10011809	superfamily	243034	346	447	5.51E-12	62.3976	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20254 - 	CGI_10011809	superfamily	243034	282	377	1.03E-11	61.6272	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20254 - 	CGI_10011809	superfamily	243034	215	304	2.08E-06	45.834	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20254 - 	CGI_10011809	superfamily	243034	416	485	0.00116876	37.3596	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20255 - 	CGI_10011810	superfamily	243092	248	548	3.13E-33	127.836	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20255 - 	CGI_10011810	superfamily	128914	85	134	2.65E-06	45.2546	cl15352	CTLH superfamily	 - 	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#20257 - 	CGI_10011812	superfamily	247739	118	321	4.73E-97	299.874	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#20258 - 	CGI_10011813	superfamily	248458	34	367	7.14E-25	103.548	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20259 - 	CGI_10011814	superfamily	202715	26	117	3.53E-21	82.2408	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#20260 - 	CGI_10011815	superfamily	241563	58	99	2.51E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20261 - 	CGI_10011816	superfamily	243519	12	174	7.74E-89	281.418	cl03757	phosphohexomutase superfamily	C	 - 	"The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model."
Q#20261 - 	CGI_10011816	superfamily	202715	310	407	1.79E-22	90.7152	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#20263 - 	CGI_10011818	superfamily	243519	12	593	0	992.496	cl03757	phosphohexomutase superfamily	 - 	 - 	"The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model."
Q#20264 - 	CGI_10011819	superfamily	245201	91	367	9.44E-63	206.602	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20265 - 	CGI_10011820	superfamily	243154	13	60	7.82E-18	75.3165	cl02715	Surp superfamily	 - 	 - 	Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
Q#20265 - 	CGI_10011820	superfamily	243078	210	273	6.51E-12	59.5358	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#20267 - 	CGI_10011822	superfamily	243992	5	72	3.81E-09	48.7242	cl05087	Complex1_LYR_1 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#20268 - 	CGI_10011823	superfamily	241624	60	354	8.43E-45	159.414	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#20269 - 	CGI_10011824	superfamily	247986	205	298	2.28E-08	53.531	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#20269 - 	CGI_10011824	superfamily	197504	417	578	4.28E-27	106.99	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#20270 - 	CGI_10011825	superfamily	247986	206	307	1.94E-05	44.6714	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#20271 - 	CGI_10011826	superfamily	116798	43	166	4.63E-13	64.6202	cl17955	Lipocalin_2 superfamily	 - 	 - 	"Lipocalin-like domain; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel."
Q#20271 - 	CGI_10011826	superfamily	245225	198	314	7.79E-13	66.9188	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#20274 - 	CGI_10019084	superfamily	145792	18	38	0.000938664	33.3883	cl10597	Antistasin superfamily	 - 	 - 	Antistasin family; Members of this family are inhibitors of trypsin family proteases. This domain is highly disulphide bonded. The domain is also found in some large extracellular proteins in multiple copies.
Q#20275 - 	CGI_10019085	superfamily	222150	301	326	9.37E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#20275 - 	CGI_10019085	superfamily	206083	61	87	0.00035152	39.5136	cl16471	zf-C2H2_6 superfamily	 - 	 - 	C2H2-type zinc finger; C2H2-type zinc finger.  
Q#20275 - 	CGI_10019085	superfamily	222150	631	655	0.00617349	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#20276 - 	CGI_10019086	superfamily	248020	20	371	5.79E-62	207.702	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#20277 - 	CGI_10019087	superfamily	245201	35	131	8.76E-16	70.258	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20280 - 	CGI_10019090	superfamily	110440	481	508	0.00129764	37.0021	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20280 - 	CGI_10019090	superfamily	110440	523	550	0.00933853	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20281 - 	CGI_10019092	superfamily	242902	23	119	2.45E-14	68.0422	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#20283 - 	CGI_10019094	superfamily	247675	198	456	4.36E-103	314.277	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#20283 - 	CGI_10019094	superfamily	247675	10	110	1.68E-44	159.783	cl17011	Arginase_HDAC superfamily	N	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#20284 - 	CGI_10019095	superfamily	217473	146	322	8.63E-27	110.532	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#20286 - 	CGI_10019097	superfamily	217473	221	368	9.14E-21	92.8133	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#20287 - 	CGI_10019098	superfamily	241563	136	182	8.61E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20289 - 	CGI_10019100	superfamily	114751	156	257	8.87E-56	176.843	cl05538	SynMuv_product superfamily	 - 	 - 	Ras-induced vulval development antagonist; This family is from synthetic multi-vulval genes which encode chromatin-associated proteins involved in transcriptional repression. This protein has a role in antagonising Ras-induced vulval development.
Q#20290 - 	CGI_10019101	superfamily	247792	16	66	1.87E-06	46.2848	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20291 - 	CGI_10019102	superfamily	219619	389	438	2.17E-05	42.58	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#20296 - 	CGI_10019107	superfamily	243092	608	864	1.90E-16	79.6864	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20296 - 	CGI_10019107	superfamily	208095	74	130	4.93E-07	48.3587	cl04084	dDENN superfamily	 - 	 - 	dDENN domain; This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
Q#20300 - 	CGI_10015041	superfamily	248097	60	141	1.21E-05	42.6374	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20301 - 	CGI_10015042	superfamily	248097	21	137	9.30E-14	63.4382	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20302 - 	CGI_10015043	superfamily	248097	23	139	2.33E-15	68.0606	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20303 - 	CGI_10015044	superfamily	248097	80	196	2.41E-13	63.053	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20304 - 	CGI_10015045	superfamily	245210	4	391	0	537.448	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#20305 - 	CGI_10015046	superfamily	242039	73	143	2.52E-31	109.228	cl00706	Ribosomal_L44 superfamily	 - 	 - 	Ribosomal protein L44; Ribosomal protein L44.  
Q#20308 - 	CGI_10015049	superfamily	217062	5	209	5.28E-27	105.044	cl12266	Branch superfamily	N	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#20309 - 	CGI_10015050	superfamily	243051	17	42	5.90E-06	40.8242	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#20311 - 	CGI_10005243	superfamily	245612	39	462	7.84E-87	275.329	cl11426	Amidase superfamily	 - 	 - 	Amidase; Amidase.  
Q#20313 - 	CGI_10005245	superfamily	241570	6	56	7.95E-09	51.5578	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#20313 - 	CGI_10005245	superfamily	241570	135	180	1.41E-06	45.0094	cl00047	CAP_ED superfamily	N	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#20313 - 	CGI_10005245	superfamily	241570	200	257	0.00266803	35.3794	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#20316 - 	CGI_10005248	superfamily	243079	704	754	2.27E-10	57.724	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	309	351	2.58E-10	57.3199	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	155	197	2.58E-10	57.3199	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	611	661	3.24E-10	57.3388	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	222	272	3.86E-10	56.9536	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	376	426	4.14E-10	56.9536	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	452	502	4.61E-10	56.9536	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	68	118	6.60E-10	56.5684	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	781	831	6.60E-10	56.5684	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	538	580	1.15E-09	55.7792	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	867	912	3.71E-07	48.4792	cl02546	Granulin superfamily	 - 	 - 	Granulin; Granulin.  
Q#20316 - 	CGI_10005248	superfamily	243079	18	43	0.00220789	37.2896	cl02546	Granulin superfamily	N	 - 	Granulin; Granulin.  
Q#20317 - 	CGI_10005499	superfamily	243072	155	271	5.62E-26	105.158	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	860	981	1.34E-25	104.003	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	793	913	3.47E-25	102.847	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	928	1047	5.49E-25	102.462	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	60	176	2.38E-24	100.536	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	347	463	2.62E-24	100.536	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	505	623	2.81E-24	100.151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	668	783	1.14E-22	95.5282	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	252	399	1.58E-20	89.365	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20317 - 	CGI_10005499	superfamily	243072	1	112	9.17E-15	72.8014	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20318 - 	CGI_10005500	superfamily	241574	217	264	3.90E-13	66.8405	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#20318 - 	CGI_10005500	superfamily	241574	281	367	2.81E-09	55.6697	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#20319 - 	CGI_10000762	superfamily	241832	14	68	9.19E-26	96.3692	cl00388	Thioredoxin_like superfamily	NC	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20321 - 	CGI_10017162	superfamily	219619	40	118	1.13E-11	58.3731	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#20323 - 	CGI_10017164	superfamily	198867	127	223	4.09E-33	122.652	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#20323 - 	CGI_10017164	superfamily	243066	15	118	1.19E-26	104.622	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20323 - 	CGI_10017164	superfamily	243146	481	534	1.16E-08	51.8934	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20323 - 	CGI_10017164	superfamily	243146	447	492	7.84E-06	43.7011	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20323 - 	CGI_10017164	superfamily	243146	386	432	8.63E-06	43.8042	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20324 - 	CGI_10017165	superfamily	227412	114	268	1.67E-07	49.7746	cl18811	YIP1 superfamily	N	 - 	"Rab GTPase interacting factor, Golgi membrane protein [Intracellular trafficking and secretion]"
Q#20325 - 	CGI_10017166	superfamily	246722	1	207	2.27E-121	362.199	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#20325 - 	CGI_10017166	superfamily	246724	214	247	1.40E-14	69.9117	cl14815	H3TH_StructSpec-5'-nucleases superfamily	C	 - 	"H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases."
Q#20326 - 	CGI_10017167	superfamily	247739	2	205	2.43E-34	124.658	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#20327 - 	CGI_10017168	superfamily	247744	358	559	1.02E-27	111.175	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#20327 - 	CGI_10017168	superfamily	147395	660	701	1.69E-15	71.8468	cl04973	Dpy-30 superfamily	 - 	 - 	Dpy-30 motif; This motif is found in a wide variety of domain contexts. It is found in the Dpy-30 proteins hence the motifs name. It is about 40 residues long and is probably fomed of two alpha-helices. It may be a dimerisation motif analogous to pfam02197 (Bateman A pers obs).
Q#20327 - 	CGI_10017168	superfamily	245206	73	287	3.69E-05	44.5889	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20328 - 	CGI_10017169	superfamily	247044	17	98	9.26E-38	125.427	cl15697	ADF_gelsolin superfamily	N	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#20329 - 	CGI_10017170	superfamily	241574	547	728	5.48E-63	216.298	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#20329 - 	CGI_10017170	superfamily	241574	1311	1448	2.08E-49	177.393	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#20329 - 	CGI_10017170	superfamily	241574	791	874	2.76E-11	64.1441	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#20329 - 	CGI_10017170	superfamily	238012	224	269	0.00293748	37.719	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20329 - 	CGI_10017170	superfamily	241574	1537	1584	0.00325106	39.4914	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#20330 - 	CGI_10017171	superfamily	243859	175	258	4.49E-17	74.2886	cl04722	PLAC8 superfamily	 - 	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#20331 - 	CGI_10017172	superfamily	247724	137	341	1.23E-43	151.403	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20332 - 	CGI_10017173	superfamily	241874	45	604	0	571.43	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#20333 - 	CGI_10017174	superfamily	246597	83	311	3.36E-81	254.148	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#20335 - 	CGI_10017176	superfamily	149105	144	253	3.94E-44	153.745	cl12353	TMPIT superfamily	N	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#20335 - 	CGI_10017176	superfamily	149105	14	133	3.79E-24	98.6612	cl12353	TMPIT superfamily	C	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#20336 - 	CGI_10001150	superfamily	220672	3	190	3.38E-37	131.6	cl10957	Frag1 superfamily	 - 	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#20337 - 	CGI_10001151	superfamily	241571	257	365	8.91E-15	69.7486	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#20337 - 	CGI_10001151	superfamily	243072	28	124	4.61E-13	65.0974	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20337 - 	CGI_10001151	superfamily	243073	205	243	1.83E-07	47.4649	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#20338 - 	CGI_10004033	superfamily	243066	132	215	6.15E-15	67.1929	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20339 - 	CGI_10004034	superfamily	247057	9	53	2.32E-05	42.2265	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#20339 - 	CGI_10004034	superfamily	241594	341	374	0.00805592	36.774	cl00077	HECTc superfamily	C	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#20340 - 	CGI_10004035	superfamily	243092	1424	1492	6.03E-06	48.4852	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20340 - 	CGI_10004035	superfamily	243092	958	1206	6.53E-06	48.4852	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20341 - 	CGI_10004036	superfamily	247916	219	277	3.47E-05	42.3699	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20342 - 	CGI_10004037	superfamily	241609	112	165	1.75E-18	76.2627	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#20342 - 	CGI_10004037	superfamily	241568	61	102	0.000232964	36.672	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#20343 - 	CGI_10004038	superfamily	247916	181	247	0.000140915	40.8291	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20343 - 	CGI_10004038	superfamily	247916	142	202	0.0030793	36.995	cl17362	Transglut_core superfamily	C	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#20344 - 	CGI_10006887	superfamily	245201	123	240	1.46E-07	50.2276	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20345 - 	CGI_10006888	superfamily	243092	176	410	9.46E-42	151.334	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20345 - 	CGI_10006888	superfamily	243074	68	112	3.94E-11	58.6721	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#20346 - 	CGI_10006889	superfamily	220964	5626	5695	3.61E-05	46.0549	cl12630	DUF2869 superfamily	C	 - 	Protein of unknown function (DUF2869); This bacterial family of proteins has no known function.
Q#20346 - 	CGI_10006889	superfamily	219525	528	563	0.00297599	39.3246	cl06646	GCC2_GCC3 superfamily	N	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#20349 - 	CGI_10006892	superfamily	245814	21	102	4.91E-11	59.8264	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20349 - 	CGI_10006892	superfamily	245814	115	147	5.69E-05	41.661	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20351 - 	CGI_10006894	superfamily	241750	13	342	9.41E-158	455.596	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#20352 - 	CGI_10017058	superfamily	248097	194	308	1.66E-15	73.0682	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20352 - 	CGI_10017058	superfamily	248097	387	516	1.22E-14	70.7941	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20353 - 	CGI_10017059	superfamily	245248	10	444	1.73E-59	203.228	cl10080	RPE65 superfamily	 - 	 - 	"Retinal pigment epithelial membrane protein; This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria."
Q#20355 - 	CGI_10017061	superfamily	241563	38	73	0.00408687	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20356 - 	CGI_10017062	superfamily	204985	1156	1252	1.60E-37	140.385	cl14987	Chorein_N superfamily	 - 	 - 	"N-terminal region of Chorein, a TM vesicle-mediated sorter; Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport."
Q#20356 - 	CGI_10017062	superfamily	241750	986	1156	5.51E-12	67.5986	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#20357 - 	CGI_10017063	superfamily	241563	17	49	0.000263826	38.9996	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20360 - 	CGI_10017066	superfamily	218226	43	119	2.71E-05	39.1883	cl04703	ATP-synt_G superfamily	 - 	 - 	"Mitochondrial ATP synthase g subunit; The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport. It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L). The function of subunit g is currently unknown. The conserved region covers all but the very N-terminus of the member sequences. No prokaryotic members have been identified thus far."
Q#20361 - 	CGI_10017067	superfamily	242323	127	237	7.62E-19	79.4747	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#20363 - 	CGI_10017069	superfamily	219542	45	149	6.08E-41	144.692	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#20363 - 	CGI_10017069	superfamily	215896	158	327	1.88E-21	91.5876	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#20363 - 	CGI_10017069	superfamily	219541	438	582	2.57E-19	85.2127	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#20364 - 	CGI_10017070	superfamily	247724	186	339	2.77E-67	215.012	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20364 - 	CGI_10017070	superfamily	247724	14	186	1.39E-66	213.086	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20365 - 	CGI_10017071	superfamily	246908	182	269	4.47E-30	112.621	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#20365 - 	CGI_10017071	superfamily	243034	11	99	2.30E-08	51.612	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20366 - 	CGI_10017072	superfamily	217380	59	372	1.88E-58	198.703	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#20367 - 	CGI_10017073	superfamily	217380	108	415	1.08E-53	187.532	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#20368 - 	CGI_10017074	superfamily	222090	284	490	7.18E-16	76.1574	cl18636	Methyltransf_22 superfamily	 - 	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#20369 - 	CGI_10017075	superfamily	243072	80	165	9.83E-07	48.1486	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20369 - 	CGI_10017075	superfamily	149414	165	227	2.70E-20	86.5566	cl07091	TRP_2 superfamily	 - 	 - 	Transient receptor ion channel II; This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023).
Q#20372 - 	CGI_10017078	superfamily	215724	40	347	1.70E-157	447.066	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#20373 - 	CGI_10017079	superfamily	215724	6	313	1.58E-140	402.383	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#20374 - 	CGI_10017080	superfamily	215724	40	396	1.62E-158	451.688	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#20375 - 	CGI_10009916	superfamily	241584	522	607	2.60E-10	59.0471	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20375 - 	CGI_10009916	superfamily	241584	428	520	8.87E-10	57.5063	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20375 - 	CGI_10009916	superfamily	241584	619	708	3.23E-09	55.9655	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20375 - 	CGI_10009916	superfamily	241584	811	902	4.80E-09	55.1951	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20375 - 	CGI_10009916	superfamily	245814	147	208	2.04E-06	47.0987	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20375 - 	CGI_10009916	superfamily	241584	719	802	2.58E-06	47.1059	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20375 - 	CGI_10009916	superfamily	245814	39	125	5.27E-13	67.118	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20375 - 	CGI_10009916	superfamily	245814	251	327	4.31E-11	61.3672	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20375 - 	CGI_10009916	superfamily	245814	349	411	2.61E-10	58.7656	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20378 - 	CGI_10009919	superfamily	241629	53	107	1.54E-20	80.8225	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#20382 - 	CGI_10003458	superfamily	247042	166	283	1.47E-10	62.2565	cl15693	Sema superfamily	N	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#20385 - 	CGI_10000562	superfamily	248372	7	114	8.49E-14	63.3724	cl17818	Nuc_deoxyrib_tr superfamily	 - 	 - 	Nucleoside 2-deoxyribosyltransferase; Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyzes the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides.
Q#20388 - 	CGI_10001360	superfamily	216502	5	128	9.74E-32	113.456	cl03209	Peptidase_M41 superfamily	N	 - 	Peptidase family M41; Peptidase family M41.  
Q#20389 - 	CGI_10001361	superfamily	245213	363	399	5.76E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20389 - 	CGI_10001361	superfamily	241571	218	306	9.62E-07	47.77	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#20391 - 	CGI_10001513	superfamily	241567	6	74	0.00485106	34.9066	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#20394 - 	CGI_10010272	superfamily	241563	724	760	4.37E-05	42.6595	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20394 - 	CGI_10010272	superfamily	243092	965	1075	0.00228072	40.0108	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20394 - 	CGI_10010272	superfamily	110440	387	413	0.00714069	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20394 - 	CGI_10010272	superfamily	149105	12	129	0.00761059	38.5701	cl12353	TMPIT superfamily	C	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#20395 - 	CGI_10010273	superfamily	246936	23	139	5.83E-42	140.055	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#20396 - 	CGI_10010274	superfamily	128778	5	78	0.00113691	37.6295	cl17972	BBC superfamily	N	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#20397 - 	CGI_10010275	superfamily	246936	267	387	1.09E-44	152.381	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#20397 - 	CGI_10010275	superfamily	246936	111	239	7.17E-36	128.127	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#20401 - 	CGI_10010279	superfamily	247986	440	546	5.46E-13	68.939	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#20401 - 	CGI_10010279	superfamily	197504	653	790	2.12E-14	71.9369	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#20402 - 	CGI_10010280	superfamily	241571	74	176	1.16E-10	57.037	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#20403 - 	CGI_10010281	superfamily	241583	171	262	5.70E-21	87.2414	cl00064	ZnMc superfamily	NC	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#20404 - 	CGI_10010282	superfamily	241571	576	642	1.96E-09	55.8814	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#20404 - 	CGI_10010282	superfamily	241583	432	532	3.12E-28	111.894	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#20406 - 	CGI_10010284	superfamily	247908	121	314	4.20E-109	319.071	cl17354	NIF superfamily	 - 	 - 	NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.
Q#20406 - 	CGI_10010284	superfamily	241645	9	81	5.48E-17	74.104	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#20409 - 	CGI_10015654	superfamily	243035	81	196	2.11E-14	66.8745	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20409 - 	CGI_10015654	superfamily	243035	198	266	4.92E-12	60.3875	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20410 - 	CGI_10015655	superfamily	243035	7	113	3.42E-20	79.9713	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20413 - 	CGI_10015658	superfamily	219542	1	61	4.02E-20	82.6747	cl18517	Cu-oxidase_3 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#20417 - 	CGI_10010645	superfamily	243077	240	261	0.00154839	36.7396	cl02542	DnaJ superfamily	N	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#20418 - 	CGI_10010646	superfamily	247684	7	382	0	774.593	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#20419 - 	CGI_10010647	superfamily	247684	7	382	0	774.208	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#20420 - 	CGI_10010648	superfamily	220831	1	96	8.63E-41	132.82	cl11248	UPF0546 superfamily	 - 	 - 	Uncharacterized protein family UPF0546; This family of proteins has no known function. Many members are annotated as potential transmembrane proteins.
Q#20421 - 	CGI_10010649	superfamily	241622	1431	1522	3.45E-22	94.1706	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	2229	2311	9.84E-21	89.9334	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	139	223	5.02E-18	82.2294	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	1966	2046	1.35E-17	81.0738	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	1725	1807	1.59E-17	80.6886	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	1870	1951	1.24E-16	77.9922	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	416	502	2.81E-15	74.1402	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	632	709	1.12E-13	69.5178	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	791	872	3.60E-13	67.977	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	1599	1682	7.16E-13	67.2066	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	289	344	1.37E-12	66.4362	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	241622	2121	2177	4.52E-11	61.8138	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20421 - 	CGI_10010649	superfamily	117611	12	64	1.14E-07	51.485	cl07602	L27_2 superfamily	 - 	 - 	"L27_2; The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer."
Q#20421 - 	CGI_10010649	superfamily	241622	1265	1322	9.76E-05	43.1364	cl00117	PDZ superfamily	C	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20422 - 	CGI_10010650	superfamily	244859	54	309	5.25E-12	64.1049	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#20425 - 	CGI_10010653	superfamily	241645	114	126	0.000787508	34.3808	cl00155	UBQ superfamily	N	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#20427 - 	CGI_10010655	superfamily	245201	39	281	2.62E-73	235.209	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20428 - 	CGI_10010656	superfamily	247725	34	141	1.45E-47	161.223	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#20428 - 	CGI_10010656	superfamily	241620	207	249	7.31E-10	55.1373	cl00113	CRIB superfamily	 - 	 - 	"PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules."
Q#20429 - 	CGI_10010657	superfamily	243091	338	447	1.30E-26	108.191	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#20430 - 	CGI_10005156	superfamily	247755	1152	1372	1.40E-115	362.967	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20430 - 	CGI_10005156	superfamily	247755	466	683	1.79E-87	283.591	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20430 - 	CGI_10005156	superfamily	216049	818	1101	3.78E-30	122.395	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#20430 - 	CGI_10005156	superfamily	216049	155	423	7.87E-17	81.5634	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#20431 - 	CGI_10005157	superfamily	201778	6	65	1.29E-08	51.0554	cl18219	GFO_IDH_MocA superfamily	N	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#20431 - 	CGI_10005157	superfamily	217272	82	189	6.30E-06	43.292	cl18400	GFO_IDH_MocA_C superfamily	 - 	 - 	"Oxidoreductase family, C-terminal alpha/beta domain; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#20433 - 	CGI_10001872	superfamily	241867	58	302	3.88E-78	240.516	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#20436 - 	CGI_10001875	superfamily	245608	1	204	2.81E-80	240.678	cl11421	FAA_hydrolase superfamily	 - 	 - 	"Fumarylacetoacetate (FAA) hydrolase family; This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase, encoded by mhpD in E. coli, is involved in the phenylpropionic acid pathway of E. coli and catalyzes the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli is involved in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida is a 4-Oxalocrotonate decarboxylase."
Q#20437 - 	CGI_10001449	superfamily	203841	2	118	5.59E-23	88.5488	cl17716	NAD_binding_6 superfamily	N	 - 	Ferric reductase NAD binding domain; Ferric reductase NAD binding domain.  
Q#20438 - 	CGI_10001450	superfamily	241733	5	82	1.51E-30	106.855	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#20439 - 	CGI_10001451	superfamily	244539	16	97	8.14E-18	80.4266	cl06868	FNR_like superfamily	N	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#20440 - 	CGI_10001452	superfamily	241733	1	36	1.83E-11	55.2386	cl00259	Sm_like superfamily	N	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#20444 - 	CGI_10018261	superfamily	215872	51	129	1.21E-10	53.7366	cl08261	Ribosomal_L6 superfamily	 - 	 - 	Ribosomal protein L6; Ribosomal protein L6.  
Q#20444 - 	CGI_10018261	superfamily	215872	9	39	0.00618865	32.5506	cl08261	Ribosomal_L6 superfamily	N	 - 	Ribosomal protein L6; Ribosomal protein L6.  
Q#20445 - 	CGI_10018262	superfamily	227412	88	283	1.84E-26	103.703	cl18811	YIP1 superfamily	N	 - 	"Rab GTPase interacting factor, Golgi membrane protein [Intracellular trafficking and secretion]"
Q#20446 - 	CGI_10018263	superfamily	245814	248	316	7.55E-08	50.1803	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20446 - 	CGI_10018263	superfamily	214507	174	230	3.49E-08	50.8916	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#20447 - 	CGI_10018264	superfamily	247727	149	259	2.92E-06	44.3431	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#20448 - 	CGI_10018265	superfamily	247068	110	194	8.04E-14	63.8717	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20450 - 	CGI_10018267	superfamily	241563	61	97	4.27E-05	43.0447	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20452 - 	CGI_10018269	superfamily	248458	51	164	2.41E-14	71.5761	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20453 - 	CGI_10018270	superfamily	248281	3	64	4.11E-06	41.8723	cl17727	GT1 superfamily	C	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#20455 - 	CGI_10018272	superfamily	201217	69	121	4.72E-09	54.0688	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#20455 - 	CGI_10018272	superfamily	201217	278	329	2.66E-07	48.676	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#20455 - 	CGI_10018272	superfamily	205718	165	194	2.89E-06	45.559	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#20455 - 	CGI_10018272	superfamily	205718	51	80	8.68E-06	44.0182	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#20455 - 	CGI_10018272	superfamily	201217	232	275	2.27E-05	43.2832	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#20455 - 	CGI_10018272	superfamily	201217	137	177	0.00146722	37.8904	cl08266	RCC1 superfamily	N	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#20455 - 	CGI_10018272	superfamily	205718	215	240	0.00436112	36.3142	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#20456 - 	CGI_10018273	superfamily	245599	182	433	3.39E-167	472.325	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#20456 - 	CGI_10018273	superfamily	207662	83	155	4.67E-53	173.877	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#20459 - 	CGI_10018276	superfamily	247912	26	339	5.35E-35	133.01	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#20459 - 	CGI_10018276	superfamily	221337	397	480	4.49E-07	47.6967	cl13401	DUF3471 superfamily	 - 	 - 	"Domain of unknown function (DUF3471); This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144."
Q#20460 - 	CGI_10018277	superfamily	247912	44	358	2.94E-38	142.64	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#20460 - 	CGI_10018277	superfamily	221337	420	454	6.79E-06	44.2299	cl13401	DUF3471 superfamily	C	 - 	"Domain of unknown function (DUF3471); This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144."
Q#20461 - 	CGI_10018278	superfamily	247912	32	232	3.67E-30	115.291	cl17358	Beta-lactamase superfamily	C	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#20465 - 	CGI_10008617	superfamily	248013	33	49	0.00027423	36.7824	cl17459	CHROMO superfamily	NC	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#20466 - 	CGI_10008618	superfamily	207794	4	67	6.43E-21	85.4212	cl02948	GH20_hexosaminidase superfamily	N	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#20468 - 	CGI_10008620	superfamily	216363	96	197	3.65E-20	82.133	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#20470 - 	CGI_10008622	superfamily	216363	146	247	5.75E-21	85.2145	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#20474 - 	CGI_10002035	superfamily	217900	55	120	3.43E-23	91.4895	cl04403	APG9 superfamily	C	 - 	"Autophagy protein Apg9; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways."
Q#20476 - 	CGI_10002009	superfamily	198738	214	305	1.11E-28	106.583	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#20477 - 	CGI_10001849	superfamily	217685	216	362	2.04E-27	107.42	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#20477 - 	CGI_10001849	superfamily	216290	80	201	5.65E-22	91.5809	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#20480 - 	CGI_10016063	superfamily	247805	24	98	1.69E-10	53.8023	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#20483 - 	CGI_10016066	superfamily	241619	617	681	0.000587186	39.1025	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#20486 - 	CGI_10016069	superfamily	245596	243	539	3.72E-149	437.021	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#20486 - 	CGI_10016069	superfamily	247085	555	633	9.49E-07	47.5002	cl15820	RICIN superfamily	C	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#20487 - 	CGI_10016070	superfamily	241575	107	155	2.12E-12	61.5195	cl00054	DSRM superfamily	C	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#20487 - 	CGI_10016070	superfamily	241575	9	51	1.83E-06	44.5707	cl00054	DSRM superfamily	C	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#20487 - 	CGI_10016070	superfamily	241575	251	317	0.000819931	36.8667	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#20488 - 	CGI_10016071	superfamily	242025	57	119	5.41E-13	65.3455	cl00682	Alba superfamily	 - 	 - 	Alba; Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.
Q#20488 - 	CGI_10016071	superfamily	216574	284	419	1.09E-10	59.914	cl14794	FAD_binding_4 superfamily	 - 	 - 	"FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan."
Q#20489 - 	CGI_10016072	superfamily	245201	17	297	1.34E-47	161.897	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20492 - 	CGI_10002637	superfamily	216939	104	171	0.00061031	37.2573	cl03492	PC4 superfamily	 - 	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#20493 - 	CGI_10002638	superfamily	243091	202	245	0.000868406	38.2421	cl02566	SET superfamily	C	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#20494 - 	CGI_10002508	superfamily	245864	33	337	1.31E-53	185.945	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#20494 - 	CGI_10002508	superfamily	245864	343	395	4.35E-07	50.3546	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#20495 - 	CGI_10002509	superfamily	245864	12	261	8.08E-84	260.674	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#20496 - 	CGI_10002510	superfamily	245864	33	188	2.23E-20	86.9486	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#20498 - 	CGI_10028131	superfamily	241584	358	421	0.000329445	39.0167	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20500 - 	CGI_10028133	superfamily	241754	628	944	1.31E-140	425.447	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#20501 - 	CGI_10028134	superfamily	219111	172	284	2.33E-16	72.899	cl05914	DUF1151 superfamily	 - 	 - 	Protein of unknown function (DUF1151); This family consists of several hypothetical eukaryotic proteins of unknown function.
Q#20502 - 	CGI_10028135	superfamily	247683	18	61	5.35E-07	42.3438	cl17036	SH3 superfamily	N	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#20503 - 	CGI_10028136	superfamily	241597	99	162	1.54E-11	56.8674	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#20503 - 	CGI_10028136	superfamily	241597	20	86	7.52E-10	52.245	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#20504 - 	CGI_10028137	superfamily	241563	63	102	2.83E-05	41.8892	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20505 - 	CGI_10028138	superfamily	241563	13	55	5.00E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20506 - 	CGI_10028139	superfamily	216421	240	397	2.27E-05	44.7209	cl03153	Lamp superfamily	N	 - 	Lysosome-associated membrane glycoprotein (Lamp); Lysosome-associated membrane glycoprotein (Lamp).  
Q#20507 - 	CGI_10028140	superfamily	241773	26	139	3.99E-76	241.79	cl00312	Ribosomal_S12_like superfamily	 - 	 - 	"Ribosomal protein S12-like family; composed of  prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code."
Q#20507 - 	CGI_10028140	superfamily	243066	168	275	1.90E-20	87.6729	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20507 - 	CGI_10028140	superfamily	198867	284	383	1.22E-14	70.8332	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#20507 - 	CGI_10028140	superfamily	243146	630	698	3.42E-09	53.7163	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20507 - 	CGI_10028140	superfamily	243146	568	619	0.000380378	38.9686	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20507 - 	CGI_10028140	superfamily	243146	420	454	0.00118139	37.5379	cl02701	Kelch_3 superfamily	C	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20508 - 	CGI_10028141	superfamily	243072	379	539	2.19E-20	88.2094	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20508 - 	CGI_10028141	superfamily	243072	603	702	1.61E-19	85.8982	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20508 - 	CGI_10028141	superfamily	243072	96	221	2.90E-14	70.4902	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20508 - 	CGI_10028141	superfamily	243072	22	131	3.14E-07	49.3042	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20510 - 	CGI_10028143	superfamily	248264	338	497	1.09E-56	187.83	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#20510 - 	CGI_10028143	superfamily	222263	259	346	1.84E-07	48.8533	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#20510 - 	CGI_10028143	superfamily	243161	3	60	2.57E-05	42.3814	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#20511 - 	CGI_10028144	superfamily	241583	225	364	5.11E-31	118.245	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#20511 - 	CGI_10028144	superfamily	216572	33	139	1.55E-05	42.6471	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#20512 - 	CGI_10028145	superfamily	243072	178	335	3.12E-15	73.957	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20512 - 	CGI_10028145	superfamily	243072	440	571	3.34E-11	62.0158	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20512 - 	CGI_10028145	superfamily	243072	116	231	1.45E-07	50.845	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20512 - 	CGI_10028145	superfamily	243072	316	370	0.000118167	41.6003	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20512 - 	CGI_10028145	superfamily	241583	794	934	2.77E-30	120.942	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#20513 - 	CGI_10028146	superfamily	245303	2	115	5.53E-57	180.967	cl10447	GH18_chitinase-like superfamily	N	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#20514 - 	CGI_10028147	superfamily	245815	204	597	0	537.787	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#20514 - 	CGI_10028147	superfamily	241871	8	181	7.23E-86	272.383	cl00452	AAK superfamily	C	 - 	"Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that phosphorylate a variety of amino acid substrates. These kinases catalyze the formation of phosphoric anhydrides, generally with a carboxylate, and use ATP as the source of the phosphoryl group; are involved in amino acid biosynthesis. Some of these kinases control the process via allosteric feed-back inhibition."
Q#20515 - 	CGI_10028148	superfamily	246723	17	461	0	742.073	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#20517 - 	CGI_10028150	superfamily	241578	4	131	4.23E-11	61.813	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20518 - 	CGI_10028151	superfamily	248097	93	217	9.14E-22	87.3206	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20518 - 	CGI_10028151	superfamily	128778	4	50	0.0044113	34.9331	cl17972	BBC superfamily	C	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#20521 - 	CGI_10028154	superfamily	247744	59	249	1.94E-35	128.894	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#20521 - 	CGI_10028154	superfamily	247744	270	323	1.95E-15	72.6546	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#20521 - 	CGI_10028154	superfamily	213107	17	54	0.00213244	35.7088	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#20522 - 	CGI_10028155	superfamily	241622	76	147	4.05E-15	71.4438	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#20522 - 	CGI_10028155	superfamily	243096	238	419	6.43E-10	57.6106	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#20522 - 	CGI_10028155	superfamily	246669	6	32	0.000249656	40.1296	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#20526 - 	CGI_10028161	superfamily	241592	9	133	6.96E-26	97.3433	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#20528 - 	CGI_10028163	superfamily	207794	174	392	7.64E-102	308.372	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#20528 - 	CGI_10028163	superfamily	111707	53	172	5.42E-16	73.6032	cl03741	Glyco_hydro_20b superfamily	 - 	 - 	"Glycosyl hydrolase family 20, domain 2; This domain has a zincin-like fold."
Q#20532 - 	CGI_10028167	superfamily	247684	2	367	2.98E-179	514.552	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#20534 - 	CGI_10028169	superfamily	147626	55	110	0.000228059	38.7755	cl05227	DUF1519 superfamily	N	 - 	Protein of unknown function (DUF1519); This family consists of several putative homing endonuclease proteins of around 245 residues in length which appear to be found exclusively in Naegleria species. The function of this family is unclear.
Q#20536 - 	CGI_10028171	superfamily	243050	141	196	1.95E-37	131.318	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#20536 - 	CGI_10028171	superfamily	241599	214	272	8.19E-20	82.6764	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#20536 - 	CGI_10028171	superfamily	243050	44	99	1.47E-28	106.401	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#20538 - 	CGI_10028173	superfamily	247684	26	399	0	586.199	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#20539 - 	CGI_10028174	superfamily	241995	1	249	2.28E-76	236.344	cl00635	Ntn_Asparaginase_2_like superfamily	N	 - 	"Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and  L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue."
Q#20540 - 	CGI_10028175	superfamily	247725	46	185	1.07E-78	248.122	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#20540 - 	CGI_10028175	superfamily	219103	204	322	6.95E-56	186.038	cl05893	Myotub-related superfamily	 - 	 - 	"Myotubularin-related; This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease."
Q#20540 - 	CGI_10028175	superfamily	206020	382	436	1.18E-35	128.009	cl18286	Y_phosphatase_m superfamily	 - 	 - 	"Myotubularin Y_phosphatase-like; This short region is highly conserved and seems to be common to many myotubularin proteins with protein tyrosine pyrophosphate activity. As the family has a number of highly conserved residues such as histidine, cysteine, glutamine and aspartate, it is possible that this represents a catalytic core of the active enzymatic part of the proteins."
Q#20543 - 	CGI_10028178	superfamily	245814	733	802	1.28E-10	59.8103	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20543 - 	CGI_10028178	superfamily	245213	65	101	1.00E-09	56.1058	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20543 - 	CGI_10028178	superfamily	245213	33	63	1.74E-05	43.7794	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20543 - 	CGI_10028178	superfamily	245201	836	1160	4.74E-126	395.758	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20543 - 	CGI_10028178	superfamily	245814	345	444	5.42E-05	43.1397	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20544 - 	CGI_10028179	superfamily	114091	1	79	1.11E-20	80.1902	cl05088	UMP1 superfamily	N	 - 	Proteasome maturation factor UMP1; UMP1 is a short-lived chaperone present in the precursor form of the 20S proteasome and absent in the mature complex. UMP1 is required for the correct assembly and enzymatic activation of the proteasome. UMP1 seems to be degraded by the proteasome upon its formation
Q#20545 - 	CGI_10028180	superfamily	241640	43	121	8.14E-29	107.379	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#20545 - 	CGI_10028180	superfamily	241640	121	169	1.64E-13	64.605	cl00149	Tryp_SPc superfamily	N	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#20547 - 	CGI_10028182	superfamily	245033	1	115	7.99E-21	82.2899	cl09208	Tim44 superfamily	N	 - 	Tim44-like domain; Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region. This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast. This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane.
Q#20548 - 	CGI_10028183	superfamily	241754	16	699	0	1026.37	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#20548 - 	CGI_10028183	superfamily	218855	880	1079	4.27E-30	119.329	cl10652	Myosin_TH1 superfamily	 - 	 - 	Myosin tail; Myosin tail.  
Q#20549 - 	CGI_10028184	superfamily	241584	340	423	5.68E-15	70.2179	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20549 - 	CGI_10028184	superfamily	246664	157	263	7.52E-44	158.507	cl14561	An_peroxidase_like superfamily	N	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#20549 - 	CGI_10028184	superfamily	246664	64	153	1.41E-15	77.3501	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#20549 - 	CGI_10028184	superfamily	243091	27	63	0.00019722	39.6251	cl02566	SET superfamily	C	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#20549 - 	CGI_10028184	superfamily	241584	280	328	0.00843439	34.3943	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20552 - 	CGI_10028187	superfamily	248097	153	285	3.88E-19	80.7722	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20553 - 	CGI_10028188	superfamily	234278	96	308	6.86E-19	86.8937	cl15938	non_repeat_PQQ superfamily	C	 - 	"dehydrogenase, PQQ-dependent, s-GDH family; PQQ, or pyrroloquinoline-quinone, serves as a cofactor for a number of sugar and alcohol dehydrogenases in a limited number of bacterial species. Most characterized PQQ-dependent enzymes have multiple repeats of a sequence region described by pfam01011 (PQQ enzyme repeat), but this protein family in unusual in lacking that repeat. Below the noise cutoff are related proteins mostly from species that lack PQQ biosynthesis."
Q#20554 - 	CGI_10028189	superfamily	247986	14	103	3.18E-09	55.457	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#20554 - 	CGI_10028189	superfamily	197504	232	362	2.58E-12	63.8477	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#20555 - 	CGI_10028190	superfamily	241613	69	102	1.13E-07	44.1198	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#20555 - 	CGI_10028190	superfamily	241613	28	64	0.00574187	31.023	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#20556 - 	CGI_10028191	superfamily	221574	331	411	4.36E-25	102.471	cl13819	DUF3677 superfamily	 - 	 - 	"Protein of unknown function (DUF3677); This domain family is found in eukaryotes, and is approximately 80 amino acids in length."
Q#20558 - 	CGI_10028193	superfamily	217408	674	1155	1.34E-51	192.755	cl15645	Nucleoporin_C superfamily	 - 	 - 	"Non-repetitive/WGA-negative nucleoporin C-terminal; This is the C-termainl half of a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and proteins. Two nucleoporin classes are known: one is characterized by the FG repeat pfam03093; the other is represented by this family, and lacks any repeats. RNA undergoing nuclear export first encounters the basket of the nuclear pore and many nucleoporins are accessible on the basket side of the pore."
Q#20558 - 	CGI_10028193	superfamily	217408	1154	1370	1.45E-35	143.065	cl15645	Nucleoporin_C superfamily	N	 - 	"Non-repetitive/WGA-negative nucleoporin C-terminal; This is the C-termainl half of a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and proteins. Two nucleoporin classes are known: one is characterized by the FG repeat pfam03093; the other is represented by this family, and lacks any repeats. RNA undergoing nuclear export first encounters the basket of the nuclear pore and many nucleoporins are accessible on the basket side of the pore."
Q#20559 - 	CGI_10028194	superfamily	247727	195	279	4.43E-11	58.9806	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#20560 - 	CGI_10028195	superfamily	247057	36	110	5.31E-27	97.3738	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#20561 - 	CGI_10028196	superfamily	241625	20	143	3.37E-15	67.3504	cl00123	PROF superfamily	 - 	 - 	"Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway."
Q#20562 - 	CGI_10028197	superfamily	241733	8	83	4.32E-51	171.99	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#20562 - 	CGI_10028197	superfamily	245852	194	501	9.81E-14	70.4562	cl12050	TraB superfamily	 - 	 - 	"TraB family; pAD1 is a hemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans, suggesting that members of the TraB family have some more general function. This family also includes the bacterial GumN protein. The family has a conserved GXXH motif close to the N-terminus, a conserved glutamate and a conserved arginine that may be catalytic. The family also includes a second conserved GXXH motif near the C-terminus."
Q#20563 - 	CGI_10028198	superfamily	243310	30	270	7.30E-74	229.818	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#20564 - 	CGI_10028199	superfamily	247856	76	135	6.90E-09	50.6241	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#20564 - 	CGI_10028199	superfamily	247856	146	212	0.000150855	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#20565 - 	CGI_10028200	superfamily	217380	125	410	8.90E-78	256.098	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#20565 - 	CGI_10028200	superfamily	248034	593	653	0.00101916	41.763	cl17480	Herpes_ICP4_N superfamily	NC	 - 	"Herpesvirus ICP4-like protein N-terminal region; The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation."
Q#20567 - 	CGI_10028202	superfamily	241972	21	116	5.80E-31	108.05	cl00600	Ribosomal_L7Ae superfamily	 - 	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#20568 - 	CGI_10028203	superfamily	245226	279	331	1.01E-07	49.9917	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#20569 - 	CGI_10028205	superfamily	247794	54	96	0.000459396	39.9077	cl17240	FDH_GDH_like superfamily	NC	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#20571 - 	CGI_10028207	superfamily	217390	156	286	0.000165357	39.8505	cl18407	TPT superfamily	 - 	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#20572 - 	CGI_10028208	superfamily	247744	95	294	2.77E-89	275.587	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#20572 - 	CGI_10028208	superfamily	241770	394	518	4.96E-06	45.0792	cl00309	PRTases_typeI superfamily	 - 	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#20573 - 	CGI_10028209	superfamily	243092	17	314	3.71E-18	83.5384	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20578 - 	CGI_10028218	superfamily	242274	1	169	6.20E-08	49.333	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#20579 - 	CGI_10028219	superfamily	243035	29	143	3.04E-25	96.9201	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20579 - 	CGI_10028219	superfamily	243035	172	240	7.33E-14	64.9485	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20581 - 	CGI_10028221	superfamily	242889	260	360	3.81E-18	79.1841	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#20582 - 	CGI_10028222	superfamily	241640	136	388	1.89E-82	262.598	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#20582 - 	CGI_10028222	superfamily	241640	437	674	5.22E-65	215.988	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#20583 - 	CGI_10028223	superfamily	241640	44	275	3.73E-74	228.7	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#20585 - 	CGI_10028225	superfamily	243072	269	344	0.00624243	35.8223	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20586 - 	CGI_10028226	superfamily	247792	281	324	8.03E-10	55.5296	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20587 - 	CGI_10028227	superfamily	198842	7	49	0.00714014	31.5037	cl04338	TAP_C superfamily	 - 	 - 	"TAP C-terminal domain; The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for nuclear export of mRNA. Tap has a modular structure, and its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling. The structure of the C-terminal domain is composed of four helices. The structure is related to the UBA domain."
Q#20589 - 	CGI_10028229	superfamily	207654	236	300	1.47E-22	89.039	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#20590 - 	CGI_10003002	superfamily	243035	71	183	3.49E-10	56.8593	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20590 - 	CGI_10003002	superfamily	243035	194	309	2.16E-06	45.6886	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20591 - 	CGI_10003003	superfamily	243035	4	117	2.88E-13	63.7929	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20592 - 	CGI_10003004	superfamily	243035	35	160	4.90E-17	72.6525	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20593 - 	CGI_10003371	superfamily	245303	11	366	7.91E-125	366.758	cl10447	GH18_chitinase-like superfamily	 - 	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#20594 - 	CGI_10003372	superfamily	217331	39	418	2.97E-58	198.844	cl03851	Perilipin superfamily	 - 	 - 	Perilipin family; The perilipin family includes lipid droplet-associated protein (perilipin) and adipose differentiation-related protein (adipophilin).
Q#20595 - 	CGI_10003373	superfamily	245201	1040	1326	5.32E-170	513.814	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20595 - 	CGI_10003373	superfamily	241584	584	623	8.95E-06	45.5651	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20595 - 	CGI_10003373	superfamily	241584	881	975	8.23E-05	42.8687	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20595 - 	CGI_10003373	superfamily	241585	209	249	0.000223919	40.9652	cl00066	FU superfamily	C	 - 	Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Q#20595 - 	CGI_10003373	superfamily	216254	20	131	7.14E-30	116.579	cl08303	Recep_L_domain superfamily	 - 	 - 	Receptor L domain; The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
Q#20595 - 	CGI_10003373	superfamily	216254	328	442	3.14E-26	106.178	cl08303	Recep_L_domain superfamily	 - 	 - 	Receptor L domain; The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
Q#20597 - 	CGI_10002392	superfamily	201956	7	91	3.31E-25	93.8134	cl08333	ACOX superfamily	N	 - 	Acyl-CoA oxidase; This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA.
Q#20600 - 	CGI_10017444	superfamily	241584	304	380	0.000266713	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20600 - 	CGI_10017444	superfamily	241584	109	172	0.000928497	38.2463	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20600 - 	CGI_10017444	superfamily	243124	568	635	3.73E-05	42.7993	cl02648	NIDO superfamily	C	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#20602 - 	CGI_10017446	superfamily	241596	21	80	3.59E-08	49.5199	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#20602 - 	CGI_10017446	superfamily	243123	102	137	5.55E-06	42.9306	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#20604 - 	CGI_10017448	superfamily	241596	15	47	0.00125148	36.0379	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#20604 - 	CGI_10017448	superfamily	243123	61	100	7.81E-14	64.1165	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#20605 - 	CGI_10017449	superfamily	241596	25	45	0.000378898	37.1935	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#20605 - 	CGI_10017449	superfamily	243123	61	98	4.97E-11	55.6421	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#20606 - 	CGI_10017450	superfamily	217926	361	444	1.75E-37	134.225	cl04418	YTH superfamily	C	 - 	"YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily."
Q#20607 - 	CGI_10017451	superfamily	216554	130	270	8.41E-27	103.713	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#20608 - 	CGI_10017452	superfamily	222150	1224	1249	0.003509	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#20610 - 	CGI_10017454	superfamily	216056	53	200	3.29E-69	219.489	cl08279	Peptidase_M16 superfamily	 - 	 - 	Insulinase (Peptidase family M16); Insulinase (Peptidase family M16).  
Q#20610 - 	CGI_10017454	superfamily	218490	205	393	3.07E-34	126.822	cl08432	Peptidase_M16_C superfamily	 - 	 - 	"Peptidase M16 inactive domain; Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp."
Q#20611 - 	CGI_10017455	superfamily	245208	71	513	0	568.253	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#20613 - 	CGI_10017457	superfamily	110998	33	469	1.46E-64	218.276	cl03422	Glyco_hydro_30 superfamily	 - 	 - 	O-Glycosyl hydrolase family 30; O-Glycosyl hydrolase family 30.  
Q#20614 - 	CGI_10017458	superfamily	243072	978	1110	8.28E-26	105.158	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20614 - 	CGI_10017458	superfamily	243072	857	1002	6.35E-09	55.4674	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20614 - 	CGI_10017458	superfamily	247743	185	285	0.00624028	36.8089	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#20617 - 	CGI_10017461	superfamily	201540	25	111	3.20E-05	40.2245	cl16960	Troponin superfamily	C	 - 	"Troponin; Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin."
Q#20618 - 	CGI_10017462	superfamily	243035	39	158	5.93E-27	99.2313	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20619 - 	CGI_10017463	superfamily	243035	157	276	3.78E-27	102.698	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20619 - 	CGI_10017463	superfamily	243035	91	138	1.46E-06	45.3034	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20620 - 	CGI_10017464	superfamily	243035	77	193	5.32E-27	100.387	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20620 - 	CGI_10017464	superfamily	243035	19	60	7.11E-05	39.5254	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20621 - 	CGI_10017465	superfamily	241644	236	375	1.06E-49	166.224	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#20621 - 	CGI_10017465	superfamily	243074	138	185	2.34E-07	47.1161	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#20625 - 	CGI_10017469	superfamily	247637	21	369	4.10E-136	395.801	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#20626 - 	CGI_10017470	superfamily	218652	8	410	2.56E-115	350.825	cl12311	CLPTM1 superfamily	 - 	 - 	"Cleft lip and palate transmembrane protein 1 (CLPTM1); This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family. This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis."
Q#20627 - 	CGI_10017471	superfamily	247792	197	238	2.83E-09	51.6776	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20628 - 	CGI_10017472	superfamily	241645	8	82	5.21E-05	41.9	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#20629 - 	CGI_10017473	superfamily	241578	1	125	9.79E-16	75.0206	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20629 - 	CGI_10017473	superfamily	243119	194	243	1.39E-05	43.1913	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#20629 - 	CGI_10017473	superfamily	241611	433	589	0.000141287	41.22	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#20630 - 	CGI_10017474	superfamily	245206	535	814	7.68E-60	202.853	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20632 - 	CGI_10017476	superfamily	148285	102	207	1.45E-40	142.489	cl05876	DIRP superfamily	 - 	 - 	"DIRP; DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of fruit fly and mustard weed. Studies of lin-9 and aly of fruit fly proteins containing DIRP suggest that this domain might be involved in development. Aly, lin-9, act in parallel to, or downstream of, activation of MAPK by the RTK-Ras signalling pathway."
Q#20633 - 	CGI_10017477	superfamily	241626	174	291	1.07E-53	174.33	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#20634 - 	CGI_10017478	superfamily	245819	254	430	2.76E-69	222.069	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#20634 - 	CGI_10017478	superfamily	245201	3	180	2.03E-20	90.2884	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20634 - 	CGI_10017478	superfamily	219526	199	240	2.13E-07	50.3103	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#20637 - 	CGI_10002357	superfamily	243091	818	936	9.67E-14	69.058	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#20638 - 	CGI_10002837	superfamily	247724	50	252	7.12E-60	195.061	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20638 - 	CGI_10002837	superfamily	221533	295	350	0.00359185	35.3652	cl13726	TMF_DNA_bd superfamily	C	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#20639 - 	CGI_10002838	superfamily	243035	80	128	2.26E-10	53.901	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20639 - 	CGI_10002838	superfamily	243035	46	98	2.16E-05	39.623	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20640 - 	CGI_10002839	superfamily	243035	130	248	7.86E-29	106.935	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20644 - 	CGI_10006510	superfamily	241559	8	151	2.57E-23	93.314	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#20645 - 	CGI_10006511	superfamily	241739	73	403	9.89E-95	291.043	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#20645 - 	CGI_10006511	superfamily	241738	417	508	1.16E-13	67.1796	cl00266	HGTP_anticodon superfamily	 - 	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#20645 - 	CGI_10006511	superfamily	241805	11	35	8.58E-05	40.5307	cl00349	S15_NS1_EPRS_RNA-bind superfamily	C	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#20646 - 	CGI_10006512	superfamily	241743	37	86	3.85E-05	41.7898	cl00274	ML superfamily	NC	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#20647 - 	CGI_10006513	superfamily	243124	95	254	2.45E-34	124.462	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#20648 - 	CGI_10006515	superfamily	245814	22	97	5.95E-07	43.2467	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20649 - 	CGI_10011080	superfamily	245011	61	153	2.14E-41	135.327	cl09113	cpn10 superfamily	 - 	 - 	"Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface."
Q#20650 - 	CGI_10011081	superfamily	243176	25	533	0	787.034	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#20653 - 	CGI_10011084	superfamily	245847	307	448	4.09E-08	52.1738	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20653 - 	CGI_10011084	superfamily	221377	95	183	4.94E-05	42.8411	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#20655 - 	CGI_10011086	superfamily	202484	20	84	2.41E-18	73.032	cl03798	zf-Tim10_DDP superfamily	 - 	 - 	Tim10/DDP family zinc finger; Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein TIMM8A. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localised to the mitochondrial intermembrane space.
Q#20656 - 	CGI_10011087	superfamily	243742	15	304	6.46E-107	346.497	cl04407	Dopey_N superfamily	 - 	 - 	"Dopey, N-terminal; DopA is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Aspergillus nidulans. DopA homologues are found in mammals. S. cerevisiae DOP1 is essential for viability and, affects cellular morphogenesis."
Q#20656 - 	CGI_10011087	superfamily	243742	1932	2092	0.00010712	46.4604	cl04407	Dopey_N superfamily	N	 - 	"Dopey, N-terminal; DopA is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Aspergillus nidulans. DopA homologues are found in mammals. S. cerevisiae DOP1 is essential for viability and, affects cellular morphogenesis."
Q#20657 - 	CGI_10011088	superfamily	218050	300	445	3.19E-49	167.254	cl18439	ATE_C superfamily	 - 	 - 	"Arginine-tRNA-protein transferase, C terminus; This family represents the C terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyzes the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway of protein degradation by conjugating a destabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N terminal cysteine is sometimes modified."
Q#20657 - 	CGI_10011088	superfamily	202988	17	93	1.17E-24	97.6027	cl04490	ATE_N superfamily	 - 	 - 	"Arginine-tRNA-protein transferase, N terminus; This family represents the N terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyzes the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway of protein degradation by conjugating a de-stabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N terminal cysteine is sometimes modified. In S cerevisiae, Cys20, 23, 94 and/or 95 are thought to be important for activity. Of these, only Cys 94 appears to be completely conserved in this family."
Q#20658 - 	CGI_10011089	superfamily	245606	56	224	4.31E-76	235.45	cl11410	TPP_enzyme_PYR superfamily	 - 	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#20658 - 	CGI_10011089	superfamily	217227	266	380	1.76E-37	133.105	cl08363	Transketolase_C superfamily	 - 	 - 	"Transketolase, C-terminal domain; The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site."
Q#20659 - 	CGI_10011090	superfamily	245864	19	428	1.70E-110	335.788	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#20660 - 	CGI_10011091	superfamily	245201	343	603	8.15E-82	260.547	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20661 - 	CGI_10007693	superfamily	243029	10	73	2.90E-09	49.6565	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#20661 - 	CGI_10007693	superfamily	215647	84	130	0.00739585	33.7361	cl18338	7tm_2 superfamily	NC	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#20662 - 	CGI_10007694	superfamily	241738	108	228	1.43E-19	81.3106	cl00266	HGTP_anticodon superfamily	 - 	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#20666 - 	CGI_10007698	superfamily	192535	34	151	0.000448797	40.2718	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#20667 - 	CGI_10007699	superfamily	202367	24	208	4.47E-74	227.808	cl18226	3HCDH_N superfamily	 - 	 - 	"3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda crystallin."
Q#20667 - 	CGI_10007699	superfamily	216084	210	307	1.04E-45	151.976	cl08285	3HCDH superfamily	 - 	 - 	"3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; This family also includes lambda crystallin. Some proteins include two copies of this domain."
Q#20669 - 	CGI_10007701	superfamily	247724	41	146	6.55E-39	145.945	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20669 - 	CGI_10007701	superfamily	244558	165	251	9.41E-38	137.687	cl06950	AARP2CN superfamily	 - 	 - 	AARP2CN (NUC121) domain; This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU.
Q#20670 - 	CGI_10007702	superfamily	242225	3	137	1.60E-75	232.779	cl00969	Ribosomal_S19e superfamily	 - 	 - 	Ribosomal protein S19e; Ribosomal protein S19e.  
Q#20671 - 	CGI_10010204	superfamily	247805	133	282	1.49E-18	80.074	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#20671 - 	CGI_10010204	superfamily	204187	21	67	0.000270713	38.2484	cl08537	MerR-DNA-bind superfamily	N	 - 	"MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold."
Q#20672 - 	CGI_10010205	superfamily	241644	51	174	1.30E-28	108.058	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#20673 - 	CGI_10010206	superfamily	243039	450	598	3.34E-69	222.868	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#20673 - 	CGI_10010206	superfamily	247792	54	92	2.02E-09	53.9888	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20673 - 	CGI_10010206	superfamily	190233	138	192	3.30E-07	47.8342	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#20673 - 	CGI_10010206	superfamily	190233	196	251	5.23E-07	47.449	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#20682 - 	CGI_10010215	superfamily	247068	498	571	9.36E-05	41.1811	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#20684 - 	CGI_10004559	superfamily	144608	2	39	2.15E-05	39.0353	cl18013	Mg_chelatase superfamily	C	 - 	"Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa."
Q#20686 - 	CGI_10005317	superfamily	245874	207	270	0.00214401	35.865	cl12111	TNFR superfamily	C	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#20688 - 	CGI_10005319	superfamily	241659	274	341	1.88E-09	53.7471	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#20690 - 	CGI_10005321	superfamily	241659	151	218	9.43E-11	55.2879	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#20692 - 	CGI_10005323	superfamily	244265	149	421	7.93E-126	368.729	cl05973	FAM20_C_like superfamily	 - 	 - 	"C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins; Drosophila Fj is a Golgi kinase that phosphorylates Ser or Thr residues within extracellular cadherin domains of a transmembrane receptor Fat and its ligand, Dachsous (Ds). The Fat signaling pathway regulates growth, gene expression, and planar cell polarity (PCP). Defects from mutation in the Drosophila fj gene include loss of the intermediate leg joint, and a PCP defect in the eye. Fjx1, the murine homologue of Fj, has been shown to be involved in both the Fat and Hippo signaling pathways, these two pathways intersect at multiple points. The Hippo pathway is important in organ size control and in cancer. FAM20B is a xylose kinase that may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. This domain has homology to a kinase-active site, mutation of three conserved Asp residues at the Drosophila Fj putative active site abolished its ability to phosphorylate Ft and Ds cadherin domains. FAM20A may participate in enamel development and gingival homeostasis, FAM20B in proteoglycan production, and FAM20C in bone development. FAM20C, also called Dentin Matrix Protein 4, is abundant in the dentin matrix, and may participate in the differentiation of mesenchymal precursor cells into functional odontoblast-like cells. Mutations in FAM20C are associated with lethal Osteosclerotic Bone Dysplasia (Raine Syndrome), and mutations in FAM20A with Amelogenesis imperfecta (AI) and Gingival Hyperplasia Syndrome. This model includes the FAM20_C domain family, previously known as DUF1193; FAM20_C appears to be homologous to the catalytic domain of the phosphoinositide 3-kinase (PI3K)-like family."
Q#20693 - 	CGI_10005324	superfamily	246925	239	347	4.57E-12	66.2249	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#20694 - 	CGI_10005325	superfamily	245213	740	767	0.000195449	40.3126	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20694 - 	CGI_10005325	superfamily	245213	696	738	0.00265685	36.8458	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20696 - 	CGI_10002704	superfamily	207701	81	198	1.84E-29	114.699	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#20696 - 	CGI_10002704	superfamily	241578	333	473	1.05E-14	73.4033	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20697 - 	CGI_10005672	superfamily	247684	14	183	1.35E-12	64.9175	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#20699 - 	CGI_10005674	superfamily	243179	128	233	1.84E-17	80.6262	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#20699 - 	CGI_10005674	superfamily	241613	1470	1506	2.78E-11	61.0685	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#20699 - 	CGI_10005674	superfamily	241613	1513	1544	2.47E-07	49.5126	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#20699 - 	CGI_10005674	superfamily	214531	680	722	1.69E-13	67.6268	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	723	766	2.54E-11	61.4636	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	767	811	4.71E-10	57.6116	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	457	498	1.19E-09	56.4561	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	916	957	3.92E-09	54.9153	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	958	1000	9.67E-09	53.7597	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	369	409	4.95E-08	51.8337	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	411	450	1.11E-07	50.6781	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	1318	1358	2.37E-07	49.9077	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	638	679	1.38E-05	44.5149	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	215683	1292	1333	2.45E-05	44.0831	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#20699 - 	CGI_10005674	superfamily	214531	1003	1041	4.11E-05	43.3593	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	215683	521	558	7.59E-05	42.5423	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#20699 - 	CGI_10005674	superfamily	214531	813	855	8.99E-05	42.2037	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	1044	1084	0.000109161	41.8185	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20699 - 	CGI_10005674	superfamily	214531	1359	1400	0.00107878	39.1221	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20701 - 	CGI_10005676	superfamily	218453	297	408	7.28E-50	173.184	cl04949	Pep3_Vps18 superfamily	N	 - 	Pep3/Vps18/deep orange family; This region is found in a number of protein identified as involved in golgi function and vacuolar sorting. The molecular function of this region is unknown. The members of this family contain a C-terminal ring finger domain.
Q#20703 - 	CGI_10005678	superfamily	243072	2	109	3.47E-29	107.855	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20705 - 	CGI_10023738	superfamily	241572	51	135	1.60E-11	60.33	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20706 - 	CGI_10023739	superfamily	241572	55	140	2.01E-05	41.8405	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20708 - 	CGI_10023741	superfamily	222424	39	226	2.92E-58	186.626	cl16439	BCIP superfamily	 - 	 - 	"p21-C-terminal region-binding protein; This family of p21-binding proteins is important as a modulator of p21 activity. The domain binds the C-terminal region of p21 in a ternary complex with CDK2, which results in inhibition of the kinase activity of CDK2."
Q#20712 - 	CGI_10023745	superfamily	243065	241	331	1.95E-12	64.7705	cl02516	VWD superfamily	N	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#20712 - 	CGI_10023745	superfamily	244710	378	443	4.79E-12	62.0225	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#20712 - 	CGI_10023745	superfamily	248289	180	238	2.56E-09	53.5819	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#20712 - 	CGI_10023745	superfamily	248289	116	174	6.87E-05	40.8703	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#20713 - 	CGI_10023746	superfamily	214531	139	182	4.05E-07	48.3669	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20713 - 	CGI_10023746	superfamily	241578	286	329	0.000129346	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20713 - 	CGI_10023746	superfamily	214531	450	492	0.00133337	37.9665	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20713 - 	CGI_10023746	superfamily	215683	113	156	0.00137949	37.9199	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#20713 - 	CGI_10023746	superfamily	214531	200	226	0.00538244	36.4257	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20713 - 	CGI_10023746	superfamily	214531	741	776	0.0054625	36.0405	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#20716 - 	CGI_10023749	superfamily	216363	70	156	3.69E-19	78.6662	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#20720 - 	CGI_10023754	superfamily	243199	65	99	1.35E-09	52.5977	cl02808	RT_like superfamily	N	 - 	"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs."
Q#20723 - 	CGI_10023757	superfamily	241593	34	155	2.36E-08	50.7485	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#20723 - 	CGI_10023757	superfamily	243078	152	187	1.73E-05	43.8339	cl02544	VHS_ENTH_ANTH superfamily	N	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#20724 - 	CGI_10023758	superfamily	222006	554	653	4.46E-12	64.1658	cl16182	Hydrolase_like2 superfamily	 - 	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#20724 - 	CGI_10023758	superfamily	215733	191	278	1.58E-11	64.5087	cl02811	E1-E2_ATPase superfamily	C	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#20725 - 	CGI_10023759	superfamily	243306	174	416	2.91E-139	415.773	cl03114	RNase_PH superfamily	 - 	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#20725 - 	CGI_10023759	superfamily	243306	6	181	4.28E-88	281.724	cl03114	RNase_PH superfamily	C	 - 	"RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites."
Q#20725 - 	CGI_10023759	superfamily	242274	536	713	2.29E-10	59.7334	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#20726 - 	CGI_10023760	superfamily	241572	205	294	7.73E-27	102.317	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20726 - 	CGI_10023760	superfamily	241572	303	389	4.39E-09	53.0113	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#20727 - 	CGI_10023761	superfamily	247755	470	604	2.38E-44	156.999	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20729 - 	CGI_10023763	superfamily	247755	4	167	1.91E-33	124.642	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#20730 - 	CGI_10023764	superfamily	241599	301	357	8.79E-15	68.0388	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#20730 - 	CGI_10023764	superfamily	198730	203	272	4.01E-37	129.866	cl02582	Pou superfamily	 - 	 - 	Pou domain - N-terminal to homeobox domain; Pou domain - N-terminal to homeobox domain.  
Q#20731 - 	CGI_10023765	superfamily	244881	329	627	8.66E-142	424.298	cl08267	ISOPREN_C2_like superfamily	 - 	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#20731 - 	CGI_10023765	superfamily	215788	110	199	4.14E-33	123.829	cl08251	A2M superfamily	 - 	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#20731 - 	CGI_10023765	superfamily	203720	734	820	1.14E-23	96.8485	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#20733 - 	CGI_10023767	superfamily	216731	242	330	3.20E-20	87.3143	cl12258	A2M_N superfamily	 - 	 - 	MG2 domain; This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin.
Q#20734 - 	CGI_10023768	superfamily	247743	478	644	6.64E-29	113.395	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#20734 - 	CGI_10023768	superfamily	247743	258	378	2.97E-12	64.8599	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#20738 - 	CGI_10023772	superfamily	216341	206	274	7.95E-21	84.064	cl03125	UPF0016 superfamily	 - 	 - 	Uncharacterized protein family UPF0016; This family contains integral membrane proteins of unknown function. Most members of the family contain two copies of a region that contains an EXGD motif. Each of these regions contains three predicted transmembrane regions.
Q#20738 - 	CGI_10023772	superfamily	216341	68	142	7.56E-19	78.6712	cl03125	UPF0016 superfamily	 - 	 - 	Uncharacterized protein family UPF0016; This family contains integral membrane proteins of unknown function. Most members of the family contain two copies of a region that contains an EXGD motif. Each of these regions contains three predicted transmembrane regions.
Q#20741 - 	CGI_10023775	superfamily	245211	172	736	0	729.341	cl09939	RNR_PFL superfamily	 - 	 - 	"Ribonucleotide reductase and Pyruvate formate lyase; Ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL) are believed to have diverged from a common ancestor. They have a structurally similar ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs use a diiron-tyrosyl radical while Class II RNRs use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. PFL, an essential enzyme in anaerobic bacteria, catalyzes the conversion of pyruvate and CoA to acteylCoA and formate in a mechanism that uses a glycyl radical."
Q#20741 - 	CGI_10023775	superfamily	217585	12	94	6.27E-13	65.7308	cl12279	ATP-cone superfamily	 - 	 - 	ATP cone domain; ATP cone domain.  
Q#20742 - 	CGI_10023776	superfamily	246925	221	369	5.13E-17	80.8625	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#20742 - 	CGI_10023776	superfamily	247856	482	529	0.00123321	37.1421	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#20743 - 	CGI_10023777	superfamily	148145	52	87	0.0082893	33.2416	cl05715	CD34_antigen superfamily	NC	 - 	CD34/Podocalyxin family; This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an anti-adhesin that maintains an open filtration pathway between neighboring foot processes in the glomerular epithelium by charge repulsion.
Q#20744 - 	CGI_10023778	superfamily	244824	23	395	0	544.85	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#20744 - 	CGI_10023778	superfamily	243149	401	469	2.51E-09	54.9365	cl02706	Alpha-amylase_C superfamily	 - 	 - 	"Alpha amylase, C-terminal all-beta domain; Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain."
Q#20745 - 	CGI_10023779	superfamily	216686	1	175	1.85E-45	151.707	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#20747 - 	CGI_10023781	superfamily	244824	57	429	0	534.835	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#20747 - 	CGI_10023781	superfamily	243149	437	506	1.28E-11	61.8701	cl02706	Alpha-amylase_C superfamily	 - 	 - 	"Alpha amylase, C-terminal all-beta domain; Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain."
Q#20748 - 	CGI_10023782	superfamily	246925	138	316	3.07E-13	68.9213	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#20749 - 	CGI_10023783	superfamily	246918	20	73	1.61E-09	49.1223	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#20750 - 	CGI_10023784	superfamily	246918	20	72	0.000120332	35.6403	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#20751 - 	CGI_10023785	superfamily	247723	66	153	4.49E-59	192.818	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#20751 - 	CGI_10023785	superfamily	243034	411	518	1.60E-07	49.3008	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20751 - 	CGI_10023785	superfamily	243034	169	276	2.20E-06	45.834	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20751 - 	CGI_10023785	superfamily	243034	330	435	0.00820528	35.0484	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#20752 - 	CGI_10023786	superfamily	245201	1	128	2.22E-24	96.0663	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#20753 - 	CGI_10023787	superfamily	220394	251	357	3.64E-28	115.634	cl10752	Meckelin superfamily	N	 - 	"Meckelin (Transmembrane protein 67); Members of this family are thought to be related to the ciliary basal body. Defects result in Meckel syndrome type 3, an autosomal recessive disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. Joubert syndrome type 6 is also a manifestation of certain mutations; it is an autosomal recessive congenital malformation of the cerebellar vermis and brainstem with abnormalities of axonal decussation (crossing in the brain) affecting the corticospinal tract and superior cerebellar peduncles. Individuals with Joubert syndrome have motor and behavioral abnormalities, including an inability to walk due to severe clumsiness and 'mirror' movements, and cognitive and behavioural disturbances."
Q#20753 - 	CGI_10023787	superfamily	243521	209	253	2.56E-09	53.7862	cl03759	Alpha_adaptinC2 superfamily	C	 - 	"Adaptin C-terminal domain; Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins."
Q#20757 - 	CGI_10001592	superfamily	241609	712	780	3.85E-20	86.6631	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#20757 - 	CGI_10001592	superfamily	243065	175	329	4.10E-24	100.209	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#20757 - 	CGI_10001592	superfamily	243093	43	119	6.68E-11	59.8514	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#20757 - 	CGI_10001592	superfamily	244710	374	457	0.000864183	38.4756	cl07383	C8 superfamily	 - 	 - 	"C8 domain; This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826."
Q#20758 - 	CGI_10001593	superfamily	221370	55	118	0.00246916	34.6545	cl13441	DUF3497 superfamily	C	 - 	"Domain of unknown function (DUF3497); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with pfam02793, pfam00002, pfam01825. This domain has a single completely conserved residue W that may be functionally important."
Q#20762 - 	CGI_10003854	superfamily	241750	158	462	2.44E-138	405.117	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#20762 - 	CGI_10003854	superfamily	241750	41	90	2.75E-18	84.6314	cl00281	metallo-dependent_hydrolases superfamily	C	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#20762 - 	CGI_10003854	superfamily	219848	1	61	1.31E-13	66.9542	cl07170	A_deaminase_N superfamily	N	 - 	Adenosine/AMP deaminase N-terminal; This domain is found to the N-terminus of the Adenosine/AMP deaminase domain (pfam00962) in metazoan proteins such as the Cat eye syndrome critical region protein 1 and its homologues.
Q#20764 - 	CGI_10003856	superfamily	245205	3	130	4.03E-11	59.6291	cl09930	RPA_2b-aaRSs_OBF_like superfamily	C	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#20765 - 	CGI_10003857	superfamily	242156	85	201	2.63E-45	148.055	cl00869	PTH2_family superfamily	 - 	 - 	"Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes."
Q#20765 - 	CGI_10003857	superfamily	241643	13	50	0.000106955	37.8239	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#20766 - 	CGI_10003858	superfamily	243039	15	158	6.43E-57	177.415	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#20767 - 	CGI_10003859	superfamily	247792	47	85	0.000306714	37.8104	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20767 - 	CGI_10003859	superfamily	190233	186	245	1.24E-13	64.0126	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#20767 - 	CGI_10003859	superfamily	190233	132	187	2.99E-06	43.597	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#20771 - 	CGI_10003546	superfamily	245814	157	218	5.43E-15	68.9727	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20771 - 	CGI_10003546	superfamily	245814	234	336	1.64E-09	54.553	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20772 - 	CGI_10003547	superfamily	245814	184	266	3.44E-08	50.5655	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20772 - 	CGI_10003547	superfamily	245814	378	460	6.26E-07	47.0987	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20772 - 	CGI_10003547	superfamily	245814	88	149	3.83E-13	64.7355	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20772 - 	CGI_10003547	superfamily	245814	285	343	4.74E-13	64.3503	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20774 - 	CGI_10003549	superfamily	219345	87	175	0.00101969	39.4331	cl06326	Phlebovirus_G1 superfamily	C	 - 	Phlebovirus glycoprotein G1; This family consists of several Phlebovirus glycoprotein G1 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi.
Q#20774 - 	CGI_10003549	superfamily	243119	191	222	0.00871188	33.5714	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#20776 - 	CGI_10003197	superfamily	216554	1	67	2.25E-26	95.2389	cl15977	zf-DHHC superfamily	C	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#20777 - 	CGI_10015954	superfamily	248458	191	306	0.00219488	39.2193	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20781 - 	CGI_10015959	superfamily	238012	502	541	2.01E-10	57.7494	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20781 - 	CGI_10015959	superfamily	238012	391	450	1.22E-09	55.4382	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20781 - 	CGI_10015959	superfamily	238012	451	501	2.32E-09	54.6678	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20781 - 	CGI_10015959	superfamily	238012	265	317	3.54E-09	54.2826	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20781 - 	CGI_10015959	superfamily	243198	32	264	1.36E-83	270.152	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#20781 - 	CGI_10015959	superfamily	199166	729	863	5.97E-10	58.878	cl15308	AMN1 superfamily	N	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#20781 - 	CGI_10015959	superfamily	238012	353	381	0.00506461	36.1782	cl11390	EGF_Lam superfamily	N	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20782 - 	CGI_10015960	superfamily	243066	120	213	6.28E-12	58.7185	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20783 - 	CGI_10015961	superfamily	241563	71	115	0.000147476	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20790 - 	CGI_10015968	superfamily	241972	21	88	2.84E-13	60.7936	cl00600	Ribosomal_L7Ae superfamily	C	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#20791 - 	CGI_10015969	superfamily	241972	47	158	1.51E-25	95.8468	cl00600	Ribosomal_L7Ae superfamily	 - 	 - 	"Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118."
Q#20792 - 	CGI_10015970	superfamily	247692	17	443	0	598.762	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#20793 - 	CGI_10015971	superfamily	241609	1	85	6.32E-30	117.094	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#20793 - 	CGI_10015971	superfamily	247038	341	399	1.61E-15	75.5689	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1110	1196	1.83E-14	72.4873	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1705	1793	7.29E-11	62.0869	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1982	2053	1.23E-10	61.3165	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1885	1949	3.38E-10	60.1609	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1371	1425	1.88E-09	57.8497	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1198	1266	1.49E-07	52.0717	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1286	1360	1.04E-06	49.7672	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	1799	1878	2.81E-06	48.2264	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	2056	2140	7.34E-06	47.0641	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	247038	2144	2231	2.48E-05	45.5233	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#20793 - 	CGI_10015971	superfamily	220608	2238	2357	2.48E-34	131.274	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#20793 - 	CGI_10015971	superfamily	220608	3092	3213	1.68E-19	88.1318	cl10859	G8 superfamily	 - 	 - 	G8 domain; This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.
Q#20794 - 	CGI_10015972	superfamily	241563	68	109	1.19E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20794 - 	CGI_10015972	superfamily	241563	28	59	0.00229057	36.3032	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20795 - 	CGI_10015973	superfamily	241705	104	219	5.38E-31	112.77	cl00228	HIT_like superfamily	 - 	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#20795 - 	CGI_10015973	superfamily	245610	2	81	4.29E-48	161.826	cl11424	nitrilase superfamily	N	 - 	"Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy."
Q#20797 - 	CGI_10001778	superfamily	242274	15	191	5.32E-09	52.4146	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#20798 - 	CGI_10001779	superfamily	248097	19	141	6.97E-16	69.2162	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20800 - 	CGI_10001781	superfamily	248097	27	131	8.21E-15	66.1346	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20802 - 	CGI_10005407	superfamily	215754	131	213	1.07E-10	57.6484	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#20802 - 	CGI_10005407	superfamily	215754	63	107	0.000878028	37.2328	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#20805 - 	CGI_10005410	superfamily	215691	240	320	1.25E-07	49.5066	cl15766	Pyr_redox superfamily	 - 	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#20807 - 	CGI_10005412	superfamily	247725	1	113	1.06E-41	143.999	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#20812 - 	CGI_10016282	superfamily	247905	303	430	1.90E-25	101.546	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#20812 - 	CGI_10016282	superfamily	247805	1	133	7.12E-21	88.9336	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#20814 - 	CGI_10016284	superfamily	216301	43	224	1.03E-26	102.342	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#20815 - 	CGI_10016285	superfamily	242156	58	171	1.41E-52	165.389	cl00869	PTH2_family superfamily	 - 	 - 	"Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes."
Q#20816 - 	CGI_10016286	superfamily	245847	23	166	4.46E-17	73.7449	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#20817 - 	CGI_10016287	superfamily	248458	37	390	2.31E-24	103.933	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20817 - 	CGI_10016287	superfamily	197361	554	602	0.00852511	35.0175	cl15254	UBAN superfamily	N	 - 	"polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well."
Q#20818 - 	CGI_10016288	superfamily	197361	525	553	0.0001542	40.4103	cl15254	UBAN superfamily	NC	 - 	"polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well."
Q#20818 - 	CGI_10016288	superfamily	152013	51	118	0.000713732	38.5425	cl13089	NEMO superfamily	 - 	 - 	"NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK."
Q#20819 - 	CGI_10016289	superfamily	128778	19	111	2.27E-05	42.6371	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#20822 - 	CGI_10008668	superfamily	191362	149	202	6.75E-31	109.668	cl05351	zf-nanos superfamily	 - 	 - 	"Nanos RNA binding domain; This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development."
Q#20824 - 	CGI_10008670	superfamily	241750	61	221	2.76E-31	123.838	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#20825 - 	CGI_10008671	superfamily	247856	117	188	5.74E-13	60.6393	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#20825 - 	CGI_10008671	superfamily	247856	81	143	2.15E-12	59.0985	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#20827 - 	CGI_10008673	superfamily	204716	29	223	6.85E-07	48.3907	cl18257	Git3 superfamily	 - 	 - 	"G protein-coupled glucose receptor regulating Gpa2; Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This is the conserved N-terminus of these proteins, and the C-terminal conserved region is now in family Git3_C."
Q#20828 - 	CGI_10008674	superfamily	221441	279	777	1.05E-135	430.401	cl13566	Med12-LCEWAV superfamily	 - 	 - 	"Eukaryotic Mediator 12 subunit domain; This domain is found in eukaryotes, and is typically between 325 and 354 amino acids in length. The function of this particular region of the Mediator subunit Med12 is not known, but there is a conserved sequence motif: LCEWAV, from which the name derives."
Q#20828 - 	CGI_10008674	superfamily	192306	110	157	1.38E-14	71.1215	cl09730	Med12 superfamily	N	 - 	"Transcription mediator complex subunit Med12; Med12 is a negative regulator of the Gli3-dependent sonic hedgehog signalling pathway via its interaction with Gli3 within the RNA polymerase II transcriptional Mediator. A complex is formed between Med12, Med13, CDK8 and CycC which is responsible for suppression of transcription. This subunit forms part of the Kinase section of Mediator."
Q#20829 - 	CGI_10008675	superfamily	110998	10	186	1.37E-63	205.949	cl03422	Glyco_hydro_30 superfamily	N	 - 	O-Glycosyl hydrolase family 30; O-Glycosyl hydrolase family 30.  
Q#20832 - 	CGI_10012973	superfamily	245864	23	457	1.94E-95	298.038	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#20835 - 	CGI_10012976	superfamily	110440	86	110	4.56E-05	37.7725	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20836 - 	CGI_10012977	superfamily	247724	51	364	5.98E-126	368.007	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#20837 - 	CGI_10012978	superfamily	247684	32	331	2.52E-64	213.678	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#20838 - 	CGI_10012979	superfamily	243072	61	191	5.00E-11	61.6306	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20838 - 	CGI_10012979	superfamily	149414	205	267	4.03E-25	100.809	cl07091	TRP_2 superfamily	 - 	 - 	Transient receptor ion channel II; This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023).
Q#20840 - 	CGI_10012981	superfamily	247792	14	64	0.00460105	34.2777	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20841 - 	CGI_10012982	superfamily	216411	23	168	1.30E-20	84.2506	cl15974	MARVEL superfamily	 - 	 - 	"Membrane-associating domain; MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis."
Q#20844 - 	CGI_10002261	superfamily	247723	170	239	2.45E-40	138.554	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#20844 - 	CGI_10002261	superfamily	247723	108	162	2.45E-28	105.931	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#20846 - 	CGI_10002263	superfamily	241645	6	70	6.06E-27	94.4653	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#20847 - 	CGI_10002264	superfamily	241770	42	133	2.63E-16	70.5024	cl00309	PRTases_typeI superfamily	C	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#20849 - 	CGI_10007876	superfamily	199156	398	413	0.00108345	37.4228	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#20852 - 	CGI_10007879	superfamily	243175	65	133	5.43E-14	67.2659	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#20852 - 	CGI_10007879	superfamily	243175	251	382	1.41E-13	66.1104	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#20852 - 	CGI_10007879	superfamily	241832	162	234	1.48E-19	82.2866	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20853 - 	CGI_10007880	superfamily	243175	136	268	1.77E-14	66.8808	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#20853 - 	CGI_10007880	superfamily	241832	45	119	1.43E-12	61.4858	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#20854 - 	CGI_10007881	superfamily	219541	53	102	2.58E-17	72.8863	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#20855 - 	CGI_10007882	superfamily	248097	10	131	1.42E-23	89.6318	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#20856 - 	CGI_10002121	superfamily	246902	197	366	3.32E-53	176.96	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#20856 - 	CGI_10002121	superfamily	246902	15	167	2.53E-49	166.112	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#20857 - 	CGI_10002122	superfamily	241888	1	110	5.98E-43	141.545	cl00473	BI-1-like superfamily	N	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#20858 - 	CGI_10002123	superfamily	241841	13	137	4.99E-60	183.872	cl00399	MoaE superfamily	 - 	 - 	"MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits."
Q#20859 - 	CGI_10002124	superfamily	241719	15	154	1.14E-80	237.445	cl00242	MoaC superfamily	 - 	 - 	"MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis."
Q#20860 - 	CGI_10002125	superfamily	241870	1	62	1.09E-38	126.767	cl00451	MoCF_BD superfamily	N	 - 	"MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin."
Q#20861 - 	CGI_10002126	superfamily	241855	1	105	2.06E-24	93.8657	cl00425	CofD_YvcK superfamily	N	 - 	"Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway.  Both families appear to have a conserved phosphate binding site, but have different substrate binding residues conserved within each family."
Q#20862 - 	CGI_10002127	superfamily	247905	82	204	8.22E-29	108.479	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#20862 - 	CGI_10002127	superfamily	204889	203	246	5.73E-22	86.7149	cl13741	UvrB superfamily	 - 	 - 	"Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00271, pfam02151, pfam04851. There are two conserved sequence motifs: YAD and RRR. This family is the C terminal region of the UvrB protein which conveys mutational resistance against UV light to various different species."
Q#20862 - 	CGI_10002127	superfamily	145355	284	319	0.00118991	36.2256	cl12262	UVR superfamily	 - 	 - 	UvrB/uvrC motif; UvrB/uvrC motif.  
Q#20863 - 	CGI_10002128	superfamily	247757	10	107	3.13E-31	109.418	cl17203	Fer4_NifH superfamily	N	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#20864 - 	CGI_10002130	superfamily	241782	1	181	1.13E-92	277.424	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#20865 - 	CGI_10002132	superfamily	246940	50	249	2.24E-21	89.7001	cl15377	Radical_SAM superfamily	 - 	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#20865 - 	CGI_10002132	superfamily	244315	220	312	5.09E-41	140.309	cl06149	BATS superfamily	 - 	 - 	"Biotin and Thiamin Synthesis associated domain; Biotin synthase (BioB), EC:2.8.1.6, catalyzes the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this family) and form a heterodimer. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers. This domain therefore may be involved in co-factor binding or dimerisation (Finn, RD personal observation)."
Q#20866 - 	CGI_10002135	superfamily	116980	52	110	4.28E-13	65.5009	cl17962	phage_tail_N superfamily	N	 - 	Prophage tail fibre N-terminal; This domain is found at the N-terminus of prophage tail fibre proteins.
Q#20866 - 	CGI_10002135	superfamily	146180	346	383	2.46E-11	58.4602	cl04049	Phage_fiber_2 superfamily	 - 	 - 	Phage tail fibre repeat; This repeat is found in the tail fibres of phage. For example protein K. The repeats are about 40 residues long.
Q#20867 - 	CGI_10002137	superfamily	242762	1	281	6.78E-158	447.546	cl01886	Omptin superfamily	 - 	 - 	Omptin family; The omptin family is a family of serine proteases.
Q#20868 - 	CGI_10002139	superfamily	242667	1	164	2.51E-93	271.385	cl01720	Phage_Nu1 superfamily	 - 	 - 	"Phage DNA packaging protein Nu1; Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA."
Q#20871 - 	CGI_10004752	superfamily	246597	30	307	7.51E-145	422.722	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#20871 - 	CGI_10004752	superfamily	217260	345	506	2.00E-42	149.327	cl03752	5_nucleotid_C superfamily	 - 	 - 	"5'-nucleotidase, C-terminal domain; 5'-nucleotidase, C-terminal domain.  "
Q#20874 - 	CGI_10010726	superfamily	241583	99	285	1.39E-48	170.059	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#20874 - 	CGI_10010726	superfamily	243051	663	818	1.04E-26	107.464	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#20874 - 	CGI_10010726	superfamily	245213	621	656	0.00207251	37.071	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20874 - 	CGI_10010726	superfamily	241571	330	446	0.00301032	37.0067	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#20875 - 	CGI_10010727	superfamily	177822	232	505	3.00E-23	102.306	cl18088	PLN02164 superfamily	 - 	 - 	sulfotransferase
Q#20875 - 	CGI_10010727	superfamily	246921	683	736	1.43E-12	65.0893	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#20875 - 	CGI_10010727	superfamily	246921	613	663	1.87E-05	43.9033	cl15299	FG-GAP superfamily	C	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#20876 - 	CGI_10010728	superfamily	217380	674	956	1.57E-106	338.916	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#20877 - 	CGI_10010729	superfamily	243092	23	308	3.88E-18	85.0792	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20878 - 	CGI_10010730	superfamily	241613	161	192	3.12E-07	46.431	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#20880 - 	CGI_10008311	superfamily	245206	37	291	1.36E-33	126.251	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20881 - 	CGI_10008312	superfamily	247684	32	456	2.76E-110	339.253	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#20883 - 	CGI_10008314	superfamily	243066	2	106	9.18E-22	91.1397	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20883 - 	CGI_10008314	superfamily	198867	120	203	3.84E-19	83.3619	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#20883 - 	CGI_10008314	superfamily	243146	471	512	1.41E-09	54.5898	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20883 - 	CGI_10008314	superfamily	243146	426	468	1.65E-07	48.8118	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20883 - 	CGI_10008314	superfamily	243146	374	421	6.86E-07	46.8858	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20883 - 	CGI_10008314	superfamily	243146	519	571	0.000257276	39.1818	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20884 - 	CGI_10008315	superfamily	241874	47	610	0	717.421	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#20885 - 	CGI_10008316	superfamily	241874	1	175	7.90E-54	181.493	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#20888 - 	CGI_10008319	superfamily	241554	229	364	6.32E-37	136.621	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#20888 - 	CGI_10008319	superfamily	241554	429	571	3.91E-36	134.31	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#20888 - 	CGI_10008319	superfamily	241554	48	185	1.48E-28	112.739	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#20888 - 	CGI_10008319	superfamily	241752	670	918	4.91E-16	77.7559	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#20890 - 	CGI_10008321	superfamily	243035	221	347	3.41E-24	95.3793	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20890 - 	CGI_10008321	superfamily	243051	84	197	1.16E-14	70.0721	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#20891 - 	CGI_10008322	superfamily	114686	27	174	8.35E-06	44.2364	cl11626	UNC-93 superfamily	 - 	 - 	Ion channel regulatory protein UNC-93; This family of proteins is a component of a multi-subunit protein complex which is involved in the coordination of muscle contraction. UNC-93 is most likely an ion channel regulatory protein.
Q#20892 - 	CGI_10008323	superfamily	243035	93	219	1.41E-24	94.9941	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#20893 - 	CGI_10008324	superfamily	248458	299	395	0.00782805	36.9081	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20893 - 	CGI_10008324	superfamily	114686	27	174	0.00821344	35.762	cl11626	UNC-93 superfamily	 - 	 - 	Ion channel regulatory protein UNC-93; This family of proteins is a component of a multi-subunit protein complex which is involved in the coordination of muscle contraction. UNC-93 is most likely an ion channel regulatory protein.
Q#20895 - 	CGI_10008326	superfamily	241974	454	563	1.68E-12	64.185	cl00604	STAS superfamily	C	 - 	"Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation."
Q#20895 - 	CGI_10008326	superfamily	216188	139	393	4.77E-58	197.055	cl18360	Sulfate_transp superfamily	 - 	 - 	Sulfate transporter family; Mutations in human SLC26A2 lead to several human diseases.
Q#20895 - 	CGI_10008326	superfamily	205965	1	56	2.77E-20	85.9271	cl18285	Sulfate_tra_GLY superfamily	N	 - 	"Sulfate transporter N-terminal domain with GLY motif; This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known."
Q#20900 - 	CGI_10017214	superfamily	215827	164	334	1.83E-25	104.858	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#20902 - 	CGI_10017216	superfamily	245306	33	161	7.47E-15	66.4551	cl10465	Peptidase_S24_S26 superfamily	 - 	 - 	"The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases."
Q#20903 - 	CGI_10017217	superfamily	241584	300	374	5.50E-06	44.4095	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#20905 - 	CGI_10017219	superfamily	147395	14	47	1.69E-05	37.9492	cl04973	Dpy-30 superfamily	 - 	 - 	Dpy-30 motif; This motif is found in a wide variety of domain contexts. It is found in the Dpy-30 proteins hence the motifs name. It is about 40 residues long and is probably fomed of two alpha-helices. It may be a dimerisation motif analogous to pfam02197 (Bateman A pers obs).
Q#20906 - 	CGI_10017220	superfamily	218015	1098	1255	9.84E-28	112.609	cl08416	FBA superfamily	 - 	 - 	"F-box associated region; Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. Human FBXO2 is involved in binding to N-glycosylated proteins."
Q#20906 - 	CGI_10017220	superfamily	221187	885	1036	0.000104787	43.049	cl13212	Malectin superfamily	 - 	 - 	"Di-glucose binding within endoplasmic reticulum; Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. It carries a signal peptide from residues 1-26, a C-terminal transmembrane helix from residues 255-274, and a highly conserved central part of approximately 190 residues followed by an acidic, glutamate-rich region. Carbohydrate-binding is mediated by the four aromatic residues, Y67, Y89, Y116, and F117 and the aspartate at D186. NMR-based ligand-screening studies has shown binding of the protein to maltose and related oligosaccharides, on the basis of which the protein has been designated "malectin", and its endogenous ligand is found to be Glc2-high-mannose N-glycan."
Q#20907 - 	CGI_10017221	superfamily	218721	38	401	4.81E-68	226.228	cl05344	TROVE superfamily	 - 	 - 	"TROVE domain; This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding."
Q#20908 - 	CGI_10017222	superfamily	241752	725	841	4.38E-43	152.859	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#20908 - 	CGI_10017222	superfamily	207713	515	592	1.52E-10	58.5053	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#20910 - 	CGI_10017224	superfamily	241900	510	853	4.64E-177	517.241	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#20912 - 	CGI_10017226	superfamily	241783	38	129	1.98E-05	42.9416	cl00322	Ribosomal_L1 superfamily	N	 - 	"Ribosomal protein L1.  The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA.  In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA.  Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity.  L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site."
Q#20913 - 	CGI_10017227	superfamily	247780	246	532	3.11E-106	320.252	cl17226	NAD_bind_amino_acid_DH superfamily	 - 	 - 	"NAD(P) binding domain of amino acid dehydrogenase-like proteins; Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel  domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts."
Q#20913 - 	CGI_10017227	superfamily	202408	96	223	4.87E-61	199.264	cl08368	ELFV_dehydrog_N superfamily	 - 	 - 	"Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Glu/Leu/Phe/Val dehydrogenase, dimerisation domain.  "
Q#20914 - 	CGI_10017228	superfamily	243179	98	215	4.95E-34	120.608	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#20919 - 	CGI_10017233	superfamily	192535	48	329	6.98E-06	45.6646	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#20925 - 	CGI_10001542	superfamily	245670	147	335	2.35E-38	136.171	cl11519	DENN superfamily	C	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#20925 - 	CGI_10001542	superfamily	243635	7	97	1.92E-21	86.6196	cl04085	uDENN superfamily	 - 	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#20926 - 	CGI_10000933	superfamily	243072	9	65	4.07E-09	49.6894	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20928 - 	CGI_10001497	superfamily	241646	40	74	0.000197819	36.6598	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#20929 - 	CGI_10001498	superfamily	244574	11	37	0.00402202	33.132	cl06998	LEM_like superfamily	 - 	 - 	"LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and postmitotic reassembly. Some of the LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are nonmembrane nuclear polypeptides. All LAP2 isoforms contain an N-terminal lamina-associated polypeptide-Emerin-MAN1 (LEM)-domain that is connected to a highly divergent LEM-like domain by an unstructured linker. Both LEM and LEM-like domains share the same structural fold, mainly composed of two large parallel alpha helices. However, their biochemical nature of the solvent-accessible residues is completely different, which indicates the two domains may target different protein surfaces. The LEM domain is responsible for the interaction with the nonspecific DNA binding protein barrier-to-autointegration factor (BAF), and the LEM-like domain is involved in chromosome binding. The family also includes the yeast helix-extension-helix domain-containing proteins, Heh1p (formerly called Src1p) and Heh2p, and their uncharacterized homologs found mainly in fungi and several in bacteria. Heh1p and Heh2p are inner nuclear membrane proteins that might interact with nuclear pore complexes (NPCs). Heh1p is involved in mitosis. It functions at the interface between subtelomeric gene expression and transcription export (TREX)-dependent messenger RNA export through NPCs. The function of Heh2p remains ill-defined. Both Heh1p and Heh2p contain a LEM-like domain (also termed HeH domain), but lack a LEM domain."
Q#20931 - 	CGI_10002215	superfamily	241619	381	430	0.000834707	37.5584	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#20932 - 	CGI_10002216	superfamily	242911	30	290	3.88E-179	498.291	cl02160	Rcd1 superfamily	 - 	 - 	"Cell differentiation family, Rcd1-like; Two of the members in this family have been characterized as being involved in regulation of Ste11 regulated sex genes. Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation."
Q#20935 - 	CGI_10008887	superfamily	247913	124	464	2.74E-47	170.185	cl17359	PTR2 superfamily	 - 	 - 	POT family; The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters.
Q#20937 - 	CGI_10008889	superfamily	243072	5	117	2.57E-22	92.0614	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20937 - 	CGI_10008889	superfamily	247057	414	477	6.59E-09	52.724	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#20938 - 	CGI_10008890	superfamily	241563	68	108	4.04E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20940 - 	CGI_10008892	superfamily	243082	208	521	9.05E-146	442.852	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#20940 - 	CGI_10008892	superfamily	243039	63	198	5.28E-64	213.854	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#20942 - 	CGI_10008894	superfamily	246597	11	272	1.18E-55	190.269	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#20942 - 	CGI_10008894	superfamily	217930	291	455	1.36E-53	182.389	cl04421	Mre11_DNA_bind superfamily	 - 	 - 	"Mre11 DNA-binding presumed domain; The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in combination with Nbs1."
Q#20943 - 	CGI_10008895	superfamily	243058	138	226	0.000579295	39.6052	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#20943 - 	CGI_10008895	superfamily	218299	350	627	1.08E-81	268.363	cl04810	Uso1_p115_head superfamily	 - 	 - 	"Uso1 / p115 like vesicle tethering protein, head region; Also known as General vesicular transport factor, Transcytosis associated protein (TAP) and Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the golgi stack. This family consists of part of the head region. The head region is highly conserved, but its function is unknown. It does not seem to be essential for vesicle tethering. The N-terminal part of the head region, not within this family, contains context-detected Armadillo/beta-catenin-like repeats (pfam00514)."
Q#20943 - 	CGI_10008895	superfamily	218301	888	926	0.00108171	38.7871	cl04811	Uso1_p115_C superfamily	N	 - 	"Uso1 / p115 like vesicle tethering protein, C terminal region; Also known as General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the golgi stack. This family consists of the acidic C-terminus, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another."
Q#20944 - 	CGI_10008896	superfamily	243310	126	329	1.44E-45	157.4	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#20945 - 	CGI_10008897	superfamily	245213	552	592	0.000134058	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20945 - 	CGI_10008897	superfamily	243124	117	230	4.15E-08	52.0441	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#20945 - 	CGI_10008897	superfamily	245213	593	632	1.29E-06	46.188	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20945 - 	CGI_10008897	superfamily	241578	468	504	1.69E-05	45.4536	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#20946 - 	CGI_10008898	superfamily	245612	419	607	8.22E-68	230.662	cl11426	Amidase superfamily	NC	 - 	Amidase; Amidase.  
Q#20946 - 	CGI_10008898	superfamily	245612	15	93	2.54E-29	120.495	cl11426	Amidase superfamily	C	 - 	Amidase; Amidase.  
Q#20947 - 	CGI_10008899	superfamily	248264	338	497	1.12E-41	147.384	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#20947 - 	CGI_10008899	superfamily	243161	3	60	8.40E-05	40.8406	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#20947 - 	CGI_10008899	superfamily	222263	256	342	0.00161186	36.9121	cl16321	DDE_4_2 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#20949 - 	CGI_10007362	superfamily	246676	130	285	4.28E-30	114.364	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#20949 - 	CGI_10007362	superfamily	243146	93	129	0.00559941	34.1247	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20949 - 	CGI_10007362	superfamily	243146	1	41	0.00682918	34.1871	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#20953 - 	CGI_10007366	superfamily	216316	38	259	2.20E-74	239.838	cl10574	CD36 superfamily	C	 - 	CD36 family; The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion.
Q#20955 - 	CGI_10007369	superfamily	243040	42	155	2.70E-54	174.749	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#20955 - 	CGI_10007369	superfamily	243064	168	286	2.94E-09	53.4523	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#20956 - 	CGI_10007370	superfamily	247736	131	196	6.35E-08	47.7094	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#20957 - 	CGI_10004092	superfamily	242173	47	186	3.14E-16	71.5142	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#20958 - 	CGI_10004093	superfamily	110440	472	496	0.0014798	36.6169	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#20958 - 	CGI_10004093	superfamily	128778	88	197	0.00388672	36.4739	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#20958 - 	CGI_10004093	superfamily	241563	43	80	0.00661092	35.0055	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20960 - 	CGI_10004095	superfamily	241563	76	118	1.73E-05	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20960 - 	CGI_10004095	superfamily	128778	125	233	0.000543417	38.7851	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#20962 - 	CGI_10013432	superfamily	238012	139	185	6.00E-07	45.0378	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20962 - 	CGI_10013432	superfamily	238012	53	79	0.000627739	36.5634	cl11390	EGF_Lam superfamily	N	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20965 - 	CGI_10013435	superfamily	238012	4	46	2.06E-06	40.4154	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20965 - 	CGI_10013435	superfamily	238012	50	81	0.00493651	31.1706	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#20966 - 	CGI_10013436	superfamily	243100	164	239	1.65E-08	50.6403	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#20968 - 	CGI_10013438	superfamily	147395	55	96	1.98E-16	67.6096	cl04973	Dpy-30 superfamily	 - 	 - 	Dpy-30 motif; This motif is found in a wide variety of domain contexts. It is found in the Dpy-30 proteins hence the motifs name. It is about 40 residues long and is probably fomed of two alpha-helices. It may be a dimerisation motif analogous to pfam02197 (Bateman A pers obs).
Q#20969 - 	CGI_10013439	superfamily	202715	115	213	2.97E-30	108.82	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#20970 - 	CGI_10013440	superfamily	202715	93	193	3.01E-30	108.434	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#20971 - 	CGI_10013441	superfamily	241699	40	127	6.38E-18	79.1577	cl00221	ACBP superfamily	 - 	 - 	Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Q#20972 - 	CGI_10013442	superfamily	247905	1114	1242	5.69E-17	79.5892	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#20972 - 	CGI_10013442	superfamily	247792	1042	1087	1.13E-10	58.9964	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#20972 - 	CGI_10013442	superfamily	247805	759	867	2.43E-07	50.7988	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#20972 - 	CGI_10013442	superfamily	244719	44	134	3.14E-25	102.439	cl07418	HIRAN superfamily	 - 	 - 	"HIRAN domain; The HIRAN domain (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. The HIRAN domain is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes. It has been predicted that this domain functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks"
Q#20973 - 	CGI_10013443	superfamily	248458	98	457	3.65E-08	53.8569	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20974 - 	CGI_10013444	superfamily	248458	83	437	1.30E-09	58.0941	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20975 - 	CGI_10013445	superfamily	248458	84	432	6.30E-14	71.5761	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20976 - 	CGI_10013446	superfamily	245596	64	287	4.24E-92	275.615	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#20977 - 	CGI_10013447	superfamily	243092	207	491	1.97E-70	228.759	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#20977 - 	CGI_10013447	superfamily	199091	43	82	7.89E-19	80.2202	cl13550	Beta-TrCP_D superfamily	 - 	 - 	"D domain of beta-TrCP; This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found associated with pfam00646, pfam00400. The protein that contains this domain functions as a ubiquitin ligase. Ubiquitination is required to direct proteins towards the proteasome for degradation. This protein is part of the WD40 class of F box proteins. The D domain of these F box proteins is involved in mediating the dimerisation of the protein. Dimerisation is necessary to polyubiquitinate substrates so this D domain is vital in directing substrates towards the proteasome for degradation."
Q#20977 - 	CGI_10013447	superfamily	243074	86	133	9.61E-08	49.0421	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#20978 - 	CGI_10013448	superfamily	241599	105	162	1.31E-18	76.5132	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#20979 - 	CGI_10013449	superfamily	242274	149	352	1.17E-60	201.96	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#20979 - 	CGI_10013449	superfamily	242274	21	133	5.19E-23	97.186	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#20981 - 	CGI_10013451	superfamily	248458	18	332	6.37E-10	58.4793	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20984 - 	CGI_10013454	superfamily	245213	485	521	8.85E-09	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	638	675	3.30E-08	52.2538	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	1208	1243	8.10E-08	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	715	752	1.72E-07	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	1246	1282	1.94E-07	49.9426	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	1170	1206	2.58E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	1284	1320	2.60E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	523	558	2.64E-07	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	409	445	6.58E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	561	598	6.66E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	447	483	6.99E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	830	865	8.62E-07	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	868	904	2.26E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	755	791	3.22E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	372	407	8.62E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	677	713	9.08E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	600	636	2.04E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245213	793	828	4.23E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20984 - 	CGI_10013454	superfamily	245814	1356	1429	0.00389038	37.6136	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#20985 - 	CGI_10013455	superfamily	245213	671	707	2.44E-12	63.4246	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20985 - 	CGI_10013455	superfamily	245213	709	746	1.20E-11	61.4986	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20985 - 	CGI_10013455	superfamily	245213	748	783	2.27E-10	57.6466	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20985 - 	CGI_10013455	superfamily	245213	633	669	4.43E-10	56.8762	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20985 - 	CGI_10013455	superfamily	248458	863	1077	1.55E-09	59.6349	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#20985 - 	CGI_10013455	superfamily	245213	786	821	2.09E-08	52.2538	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20985 - 	CGI_10013455	superfamily	245213	596	631	5.24E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#20985 - 	CGI_10013455	superfamily	243060	330	419	4.15E-07	49.2996	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#20987 - 	CGI_10013457	superfamily	243072	6	86	2.47E-11	60.8602	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#20987 - 	CGI_10013457	superfamily	243066	116	212	8.31E-15	70.0272	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20987 - 	CGI_10013457	superfamily	243066	270	368	2.24E-14	69.1833	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#20988 - 	CGI_10013458	superfamily	245596	253	490	1.52E-58	195.097	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#20988 - 	CGI_10013458	superfamily	248046	33	234	2.72E-56	187.715	cl17492	DUF2064 superfamily	 - 	 - 	Uncharacterized protein conserved in bacteria (DUF2064); This family has structural similarity to proteins in the nucleotide-diphospho-sugar transferases superfamily. The similarity suggests that it is an enzyme with a sugar substrate.
Q#20989 - 	CGI_10013459	superfamily	245206	23	257	1.57E-131	375.088	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#20991 - 	CGI_10013461	superfamily	241563	61	95	6.80E-05	40.7336	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#20991 - 	CGI_10013461	superfamily	128778	105	211	0.00109254	38.0147	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#20992 - 	CGI_10005969	superfamily	221316	973	1076	7.64E-32	121.669	cl13375	DUF3441 superfamily	 - 	 - 	"Domain of unknown function (DUF3441); This presumed domain is functionally uncharacterized. This domain is found in archaea and eukaryotes. This domain is typically between 104 to 119 amino acids in length. This domain is found associated with pfam05833, pfam05670. This domain has two conserved residues (P and G) that may be functionally important."
Q#20992 - 	CGI_10005969	superfamily	218683	504	602	1.13E-27	108.834	cl05307	DUF814 superfamily	 - 	 - 	"Domain of unknown function (DUF814); This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from B. subtilis yloA, where the N-terminal region is involved in this activity. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important."
Q#20995 - 	CGI_10005972	superfamily	110998	163	625	2.55E-172	504.094	cl03422	Glyco_hydro_30 superfamily	 - 	 - 	O-Glycosyl hydrolase family 30; O-Glycosyl hydrolase family 30.  
Q#20996 - 	CGI_10005973	superfamily	241868	99	210	1.05E-39	140.065	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#20996 - 	CGI_10005973	superfamily	191168	21	96	7.09E-30	110.803	cl04894	DCP2 superfamily	 - 	 - 	"Dcp2, box A domain; This domain is always found to the amino terminal side of pfam00293. This domain is specific to mRNA decapping protein 2 and this region has been termed Box A. Removal of the cap structure is catalyzed by the Dcp1-Dcp2 complex."
Q#20997 - 	CGI_10005974	superfamily	241758	21	163	2.78E-19	79.3362	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#20998 - 	CGI_10005975	superfamily	241758	26	123	3.94E-16	69.7062	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#20999 - 	CGI_10005976	superfamily	241758	2	129	1.88E-16	74.3286	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#20999 - 	CGI_10005976	superfamily	241758	129	239	1.03E-07	49.2906	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#21000 - 	CGI_10005977	superfamily	241578	219	381	9.74E-45	154.752	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21000 - 	CGI_10005977	superfamily	241578	7	182	5.89E-41	144.838	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21001 - 	CGI_10005978	superfamily	241578	162	324	4.51E-38	137.423	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21001 - 	CGI_10005978	superfamily	241578	2	93	1.54E-18	83.9735	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21001 - 	CGI_10005978	superfamily	241578	364	504	3.87E-05	43.212	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21004 - 	CGI_10015365	superfamily	248020	25	352	1.76E-50	176.501	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#21007 - 	CGI_10015368	superfamily	248020	25	352	6.68E-50	174.96	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#21008 - 	CGI_10015369	superfamily	248020	25	353	2.07E-50	176.116	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#21009 - 	CGI_10015370	superfamily	241578	464	626	9.95E-11	60.6574	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21010 - 	CGI_10015371	superfamily	221476	1634	1976	3.74E-57	213.003	cl13644	Rav1p_C superfamily	N	 - 	"RAVE protein 1 C terminal; This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits."
Q#21010 - 	CGI_10015371	superfamily	243092	3047	3314	5.44E-30	123.599	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21014 - 	CGI_10015375	superfamily	217020	27	112	0.0092667	33.337	cl03574	Seryl_tRNA_N superfamily	N	 - 	Seryl-tRNA synthetase N-terminal domain; This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Q#21020 - 	CGI_10015381	superfamily	241640	42	266	5.90E-91	271.842	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#21021 - 	CGI_10015382	superfamily	243100	75	125	2.71E-11	54.9273	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#21024 - 	CGI_10006460	superfamily	241563	107	148	2.70E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21024 - 	CGI_10006460	superfamily	241563	67	98	0.0023617	36.3032	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21027 - 	CGI_10006463	superfamily	241563	68	109	9.55E-06	43.2368	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21029 - 	CGI_10006465	superfamily	243540	914	1140	1.71E-29	118.119	cl03831	HlyIII superfamily	 - 	 - 	"Haemolysin-III related; Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea."
Q#21029 - 	CGI_10006465	superfamily	241563	59	95	1.53E-05	43.8651	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21029 - 	CGI_10006465	superfamily	221533	115	208	6.64E-05	42.2988	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#21030 - 	CGI_10011953	superfamily	247724	274	434	0.000186416	40.9028	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21030 - 	CGI_10011953	superfamily	242902	69	219	3.17E-16	75.361	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#21031 - 	CGI_10011954	superfamily	247724	89	249	0.000177283	40.1324	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21033 - 	CGI_10011956	superfamily	202224	244	344	2.01E-14	70.7875	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#21033 - 	CGI_10011956	superfamily	247999	9	55	6.53E-10	56.0662	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#21033 - 	CGI_10011956	superfamily	214721	205	272	1.66E-07	49.1728	cl18313	JmjC superfamily	 - 	 - 	"A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press)."
Q#21036 - 	CGI_10011959	superfamily	246748	358	592	4.10E-104	321.464	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#21036 - 	CGI_10011959	superfamily	244870	132	348	1.66E-73	238.729	cl08238	PA superfamily	 - 	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#21036 - 	CGI_10011959	superfamily	202944	592	683	4.28E-29	112.749	cl07854	TFR_dimer superfamily	N	 - 	Transferrin receptor-like dimerisation domain; This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
Q#21036 - 	CGI_10011959	superfamily	246748	72	126	6.39E-10	59.5285	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#21039 - 	CGI_10011962	superfamily	247856	48	101	2.49E-05	38.6829	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21040 - 	CGI_10011963	superfamily	247856	22	78	0.000306656	36.7569	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21040 - 	CGI_10011963	superfamily	247856	58	102	0.000655986	35.9865	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21040 - 	CGI_10011963	superfamily	150838	136	177	0.00700218	34.7474	cl10913	DUF2216 superfamily	NC	 - 	"Uncharacterized conserved proteins (DUF2216); This is the conserved N-terminal half of a proteins which are found from worms to humans. some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed."
Q#21042 - 	CGI_10000259	superfamily	243609	1	109	4.01E-32	112.313	cl04000	Cornichon superfamily	N	 - 	Cornichon protein; Cornichon protein.  
Q#21046 - 	CGI_10018692	superfamily	248097	3	118	1.58E-21	83.8538	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21048 - 	CGI_10018694	superfamily	222150	553	578	6.67E-05	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21048 - 	CGI_10018694	superfamily	222150	526	549	0.000159763	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21048 - 	CGI_10018694	superfamily	222150	434	458	0.000231843	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21050 - 	CGI_10018696	superfamily	248054	187	359	1.04E-05	44.9859	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#21051 - 	CGI_10018697	superfamily	243034	296	394	7.91E-14	68.1756	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21051 - 	CGI_10018697	superfamily	243034	160	258	5.37E-12	62.7828	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21051 - 	CGI_10018697	superfamily	243034	92	191	3.29E-09	54.6936	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21052 - 	CGI_10018698	superfamily	245864	1	162	1.33E-46	158.981	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#21053 - 	CGI_10018699	superfamily	245864	1	219	8.23E-31	117.765	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#21055 - 	CGI_10018701	superfamily	241571	114	226	1.05E-30	117.128	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#21055 - 	CGI_10018701	superfamily	241613	378	411	1.01E-06	46.431	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21055 - 	CGI_10018701	superfamily	241571	250	339	2.13E-06	46.6367	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#21056 - 	CGI_10018702	superfamily	202894	65	130	5.98E-14	63.0086	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#21057 - 	CGI_10018703	superfamily	241733	572	658	2.22E-43	151.223	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#21057 - 	CGI_10018703	superfamily	241571	166	276	9.00E-09	53.9554	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#21057 - 	CGI_10018703	superfamily	241613	419	447	1.64E-05	42.9642	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21057 - 	CGI_10018703	superfamily	241613	476	511	7.04E-05	41.0382	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21060 - 	CGI_10018706	superfamily	247724	171	326	1.92E-40	143.699	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21061 - 	CGI_10018707	superfamily	247724	165	324	5.44E-40	142.158	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21062 - 	CGI_10018708	superfamily	241600	1	166	2.45E-79	237.138	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#21063 - 	CGI_10018709	superfamily	241600	20	230	1.35E-95	281.051	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#21066 - 	CGI_10018712	superfamily	245814	607	679	3.36E-27	107.328	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21066 - 	CGI_10018712	superfamily	245814	691	771	1.17E-13	68.686	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21066 - 	CGI_10018712	superfamily	245814	486	586	1.39E-06	47.858	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21066 - 	CGI_10018712	superfamily	214507	431	479	7.51E-06	45.1136	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#21066 - 	CGI_10018712	superfamily	246925	61	189	0.000104844	44.2686	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#21066 - 	CGI_10018712	superfamily	243030	28	54	0.00972076	35.3711	cl02423	LRRNT superfamily	C	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#21067 - 	CGI_10018713	superfamily	245864	43	502	4.02E-84	269.918	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#21068 - 	CGI_10018714	superfamily	214531	194	235	2.39E-06	44.9001	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21068 - 	CGI_10018714	superfamily	214531	149	192	1.52E-05	42.5889	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21075 - 	CGI_10010794	superfamily	245847	131	279	0.000894975	37.5362	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#21076 - 	CGI_10010795	superfamily	243104	28	71	9.65E-06	40.6061	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#21078 - 	CGI_10010798	superfamily	111397	111	184	2.76E-08	51.9582	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#21078 - 	CGI_10010798	superfamily	241611	296	430	9.18E-06	45.072	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#21081 - 	CGI_10001126	superfamily	207654	119	184	4.00E-28	103.677	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#21081 - 	CGI_10001126	superfamily	207654	48	112	3.29E-22	87.4982	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#21081 - 	CGI_10001126	superfamily	207654	203	268	6.61E-21	83.6462	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#21083 - 	CGI_10008025	superfamily	247941	147	286	1.21E-14	69.2868	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#21084 - 	CGI_10008026	superfamily	241619	770	807	8.35E-05	42.0717	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#21084 - 	CGI_10008026	superfamily	241619	838	909	1.08E-05	44.8805	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#21085 - 	CGI_10008027	superfamily	247724	22	180	1.54E-84	249.031	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21089 - 	CGI_10008031	superfamily	243161	5	64	4.33E-11	54.7077	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#21091 - 	CGI_10001364	superfamily	247746	156	213	0.00471534	36.0822	cl17192	ATP-synt_B superfamily	N	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#21094 - 	CGI_10001350	superfamily	245814	29	92	8.29E-07	43.9348	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21094 - 	CGI_10001350	superfamily	245814	113	190	0.00289342	34.4033	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21095 - 	CGI_10003473	superfamily	243072	1	83	2.22E-13	62.7862	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21095 - 	CGI_10003473	superfamily	243073	112	145	2.82E-07	43.6129	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#21096 - 	CGI_10003474	superfamily	243072	80	189	3.39E-19	79.735	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21097 - 	CGI_10003475	superfamily	241866	15	346	3.53E-169	489.97	cl00445	Iso_dh superfamily	 - 	 - 	Isocitrate/isopropylmalate dehydrogenase; Isocitrate/isopropylmalate dehydrogenase.  
Q#21098 - 	CGI_10003476	superfamily	241563	71	109	3.07E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21098 - 	CGI_10003476	superfamily	241563	28	59	0.000803123	37.844	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21099 - 	CGI_10005574	superfamily	241600	2	164	2.54E-54	172.81	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#21100 - 	CGI_10005575	superfamily	241600	1	206	6.98E-95	278.355	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#21102 - 	CGI_10005577	superfamily	241600	1	205	3.90E-94	276.429	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#21103 - 	CGI_10005578	superfamily	243064	68	224	5.21E-05	41.6322	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#21104 - 	CGI_10005579	superfamily	243064	1	119	5.19E-12	59.3514	cl02512	NTR_like superfamily	N	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#21105 - 	CGI_10005580	superfamily	245201	7	261	1.76E-106	321.37	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21106 - 	CGI_10001524	superfamily	247743	429	552	1.24E-07	50.2223	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21106 - 	CGI_10001524	superfamily	205451	136	228	0.00175584	37.1727	cl16203	DUF4062 superfamily	 - 	 - 	"Domain of unknown function (DUF4062); This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif."
Q#21109 - 	CGI_10011210	superfamily	247739	88	300	1.20E-91	280.261	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#21109 - 	CGI_10011210	superfamily	247856	405	465	1.36E-11	60.2541	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21109 - 	CGI_10011210	superfamily	247856	329	389	1.97E-06	45.2313	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21110 - 	CGI_10011211	superfamily	245201	25	217	6.77E-33	121.96	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21111 - 	CGI_10011212	superfamily	241754	918	1244	1.54E-173	519.821	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21112 - 	CGI_10011213	superfamily	241613	189	218	5.42E-08	49.1274	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21112 - 	CGI_10011213	superfamily	241571	26	136	4.00E-07	47.7923	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#21113 - 	CGI_10011214	superfamily	241858	152	265	2.64E-18	79.2516	cl00429	SNARE_assoc superfamily	 - 	 - 	SNARE associated Golgi protein; This is a family of SNARE associated Golgi proteins. The yeast member of this family localises with the t-SNARE Tlg2.
Q#21116 - 	CGI_10011217	superfamily	247725	51	65	0.00862844	32.5612	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#21120 - 	CGI_10011221	superfamily	243648	27	141	1.24E-11	64.2346	cl04109	Methyltransf_7 superfamily	C	 - 	"SAM dependent carboxyl methyltransferase; This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesised through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyzes the second step to produce theobromine."
Q#21120 - 	CGI_10011221	superfamily	243648	292	397	3.29E-09	56.9158	cl04109	Methyltransf_7 superfamily	C	 - 	"SAM dependent carboxyl methyltransferase; This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesised through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyzes the second step to produce theobromine."
Q#21121 - 	CGI_10011222	superfamily	215754	23	107	1.37E-26	103.872	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21121 - 	CGI_10011222	superfamily	215754	121	204	1.40E-14	69.9748	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21121 - 	CGI_10011222	superfamily	215754	211	256	9.11E-05	41.0848	cl02813	Mito_carr superfamily	C	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21123 - 	CGI_10011224	superfamily	245206	2	232	6.63E-75	229.046	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#21125 - 	CGI_10001851	superfamily	241753	87	619	0	722.939	cl00285	Aconitase superfamily	 - 	 - 	"Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Aconitase catalytic domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle.  Cis-aconitate is formed as an intermediate product during the course of the reaction. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. Aconitase, in its active form, contains a 4Fe-4S  iron-sulfur cluster; three cysteine residues have been shown to be ligands of the 4Fe-4S cluster. This is the Aconitase core domain, including structural domains 1, 2 and 3, which binds the Fe-S cluster. The aconitase family also contains the following proteins: - Iron-responsive  element binding protein (IRE-BP), a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in  the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of  transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the  alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid."
Q#21125 - 	CGI_10001851	superfamily	241693	723	892	1.74E-103	321.533	cl00215	Aconitase_swivel superfamily	 - 	 - 	"Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive  element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid."
Q#21128 - 	CGI_10001394	superfamily	246680	7	103	4.19E-33	118.822	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#21129 - 	CGI_10001427	superfamily	245814	148	197	5.91E-08	47.4016	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21130 - 	CGI_10001453	superfamily	236795	117	163	0.000541097	37.7682	cl15947	PRK10920 superfamily	C	 - 	putative uroporphyrinogen III C-methyltransferase; Provisional
Q#21131 - 	CGI_10018226	superfamily	241623	3575	3866	2.49E-115	369.341	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#21131 - 	CGI_10018226	superfamily	219733	1687	2091	3.30E-114	372.551	cl06971	NUC194 superfamily	 - 	 - 	NUC194 domain; This is domain B in the catalytic subunit of DNA-dependent protein kinases.
Q#21132 - 	CGI_10018227	superfamily	241622	5	87	2.72E-16	69.5178	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#21133 - 	CGI_10018228	superfamily	243034	2250	2337	9.35E-06	46.6044	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21133 - 	CGI_10018228	superfamily	243034	2161	2212	0.000450226	41.2116	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21133 - 	CGI_10018228	superfamily	222150	1809	1831	0.00294307	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21133 - 	CGI_10018228	superfamily	222150	1836	1859	0.00909525	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21134 - 	CGI_10018229	superfamily	219592	650	810	3.54E-43	161.851	cl06720	WAPL superfamily	C	 - 	"Wings apart-like protein regulation of heterochromatin; This family contains sequences expressed in eukaryotic organisms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure. hWAPL, the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death."
Q#21134 - 	CGI_10018229	superfamily	219592	882	960	5.36E-27	113.315	cl06720	WAPL superfamily	C	 - 	"Wings apart-like protein regulation of heterochromatin; This family contains sequences expressed in eukaryotic organisms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure. hWAPL, the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death."
Q#21135 - 	CGI_10018230	superfamily	219592	2	265	5.56E-54	186.118	cl06720	WAPL superfamily	N	 - 	"Wings apart-like protein regulation of heterochromatin; This family contains sequences expressed in eukaryotic organisms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure. hWAPL, the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death."
Q#21136 - 	CGI_10018231	superfamily	243036	303	598	4.32E-89	281.161	cl02434	CNH superfamily	 - 	 - 	"CNH domain; Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations."
Q#21140 - 	CGI_10018235	superfamily	247856	103	131	0.000271486	35.6484	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21142 - 	CGI_10018237	superfamily	246975	39	60	0.00521454	32.7041	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#21143 - 	CGI_10018238	superfamily	244824	1	368	1.49E-107	328.935	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#21144 - 	CGI_10018239	superfamily	245201	21	350	8.41E-141	420.339	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21151 - 	CGI_10018246	superfamily	242406	2	122	2.31E-20	83.4097	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#21154 - 	CGI_10002800	superfamily	217410	246	422	1.02E-16	78.1647	cl18409	DDE_1 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere."
Q#21158 - 	CGI_10003130	superfamily	248369	85	261	2.41E-07	48.5834	cl17815	Yip1 superfamily	 - 	 - 	Yip1 domain; The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterized by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases.
Q#21161 - 	CGI_10003133	superfamily	218482	73	163	4.13E-19	83.0801	cl04969	Kri1 superfamily	 - 	 - 	KRI1-like family; The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus.
Q#21161 - 	CGI_10003133	superfamily	193409	262	330	1.99E-18	80.7077	cl15178	Kri1_C superfamily	N	 - 	KRI1-like family C-terminal; The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus. This is the C-terminal domain of the family.
Q#21162 - 	CGI_10003134	superfamily	248012	445	581	2.41E-28	112.367	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#21162 - 	CGI_10003134	superfamily	245213	309	338	0.00334075	36.7261	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21165 - 	CGI_10002119	superfamily	242274	9	90	0.000287212	36.5384	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#21167 - 	CGI_10002543	superfamily	216456	442	534	7.76E-07	48.4738	cl03182	RYDR_ITPR superfamily	C	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#21167 - 	CGI_10002543	superfamily	197746	95	137	0.00400138	35.7799	cl02624	MIR superfamily	C	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#21168 - 	CGI_10003028	superfamily	221683	61	102	5.31E-08	47.2635	cl15002	UPF0489 superfamily	C	 - 	UPF0489 domain; This family is probably an enzyme which is related to the Arginase family.
Q#21169 - 	CGI_10003029	superfamily	245847	26	120	1.47E-16	71.0485	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#21172 - 	CGI_10004196	superfamily	201831	3	27	0.00481962	32.136	cl03238	Vault superfamily	N	 - 	Major Vault Protein repeat; The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeat found in the amino terminal half of the major vault protein.
Q#21176 - 	CGI_10003710	superfamily	247856	10	72	1.87E-06	42.9201	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21177 - 	CGI_10003711	superfamily	246918	63	119	5.31E-05	39.1071	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21179 - 	CGI_10005631	superfamily	243051	1	100	6.33E-12	58.9013	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#21180 - 	CGI_10004724	superfamily	241783	33	239	3.21E-51	167.746	cl00322	Ribosomal_L1 superfamily	 - 	 - 	"Ribosomal protein L1.  The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA.  In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA.  Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity.  L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site."
Q#21181 - 	CGI_10004725	superfamily	243082	223	571	8.07E-113	358.108	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#21182 - 	CGI_10004726	superfamily	216981	35	73	4.20E-05	37.5122	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#21183 - 	CGI_10008967	superfamily	219542	29	142	1.66E-39	140.84	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#21183 - 	CGI_10008967	superfamily	219541	429	603	9.03E-26	103.317	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#21183 - 	CGI_10008967	superfamily	215896	152	342	1.99E-12	65.0088	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#21185 - 	CGI_10008969	superfamily	219542	99	211	5.14E-41	148.544	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#21185 - 	CGI_10008969	superfamily	219541	736	892	8.62E-28	111.021	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#21185 - 	CGI_10008969	superfamily	215896	533	632	5.89E-22	94.6692	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#21185 - 	CGI_10008969	superfamily	113452	284	369	0.00902412	38.5613	cl04672	BAF1_ABF1 superfamily	NC	 - 	"BAF1 / ABF1 chromatin reorganising factor; ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 S. cerevisiae). The N-terminal two thirds of the protein are necessary for DNA binding, and the N-terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure."
Q#21186 - 	CGI_10008970	superfamily	241574	78	209	6.06E-44	147.755	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21187 - 	CGI_10008971	superfamily	245864	65	484	1.24E-67	226.391	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#21188 - 	CGI_10008972	superfamily	245864	56	490	8.96E-76	248.732	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#21189 - 	CGI_10008973	superfamily	217324	27	136	3.64E-09	51.2954	cl03844	Folate_rec superfamily	 - 	 - 	Folate receptor family; This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anchor. The proteins contain 16 conserved cysteines that form eight disulphide bridges.
Q#21190 - 	CGI_10008974	superfamily	244083	303	391	2.82E-34	125.492	cl05417	PLA2_like superfamily	 - 	 - 	"PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers."
Q#21190 - 	CGI_10008974	superfamily	217740	25	242	1.73E-76	244.578	cl18427	Scramblase superfamily	 - 	 - 	Scramblase; Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury.
Q#21190 - 	CGI_10008974	superfamily	217252	482	577	1.17E-20	88.0055	cl08372	Pyr_redox_dim superfamily	 - 	 - 	"Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases."
Q#21192 - 	CGI_10011852	superfamily	243061	55	155	8.63E-41	134.392	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#21192 - 	CGI_10011852	superfamily	243061	2	52	1.21E-16	71.219	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#21193 - 	CGI_10011853	superfamily	242274	48	136	0.000299658	38.5474	cl01053	SGNH_hydrolase superfamily	NC	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#21196 - 	CGI_10011856	superfamily	243035	28	85	1.98E-14	64.2395	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#21198 - 	CGI_10011858	superfamily	245819	110	284	2.09E-70	219.373	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#21198 - 	CGI_10011858	superfamily	219526	1	97	7.12E-24	96.9194	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#21202 - 	CGI_10003915	superfamily	215647	167	210	7.96E-11	59.9297	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#21203 - 	CGI_10003916	superfamily	215647	2	37	1.46E-07	45.6773	cl18338	7tm_2 superfamily	N	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#21205 - 	CGI_10020653	superfamily	247736	175	231	0.00342663	35.3293	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#21205 - 	CGI_10020653	superfamily	247736	34	91	0.000684335	37.5464	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#21206 - 	CGI_10020655	superfamily	245604	1	64	1.83E-19	82.0671	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#21206 - 	CGI_10020655	superfamily	215782	211	414	4.36E-75	235.137	cl18344	2-oxoacid_dh superfamily	 - 	 - 	2-oxoacid dehydrogenases acyltransferase (catalytic domain); These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain.
Q#21206 - 	CGI_10020655	superfamily	202412	104	142	1.86E-07	47.4169	cl03729	E3_binding superfamily	 - 	 - 	e3 binding domain; This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit.
Q#21207 - 	CGI_10020656	superfamily	241614	11	138	4.86E-41	135.471	cl00105	LMWPc superfamily	 - 	 - 	Low molecular weight phosphatase family;
Q#21208 - 	CGI_10020657	superfamily	245849	155	235	2.63E-12	61.1042	cl12045	Ubiq_cyt_C_chap superfamily	C	 - 	Ubiquinol-cytochrome C chaperone; Ubiquinol-cytochrome C chaperone.  
Q#21210 - 	CGI_10020659	superfamily	244881	134	187	4.48E-15	72.2256	cl08267	ISOPREN_C2_like superfamily	NC	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#21210 - 	CGI_10020659	superfamily	203720	188	230	7.28E-07	45.617	cl08457	A2M_recep superfamily	N	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#21211 - 	CGI_10020660	superfamily	243072	48	163	3.73E-24	98.995	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21211 - 	CGI_10020660	superfamily	245814	387	449	0.00608777	35.5589	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21212 - 	CGI_10020661	superfamily	243072	60	178	7.98E-26	100.151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21212 - 	CGI_10020661	superfamily	243072	1	113	1.54E-24	96.6838	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21213 - 	CGI_10020662	superfamily	247794	16	421	0	768.159	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#21215 - 	CGI_10020664	superfamily	245814	105	194	1.31E-13	65.5446	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21215 - 	CGI_10020664	superfamily	245814	204	281	4.77E-12	61.4172	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21216 - 	CGI_10020665	superfamily	201590	31	187	1.61E-93	274.475	cl03090	HH_signal superfamily	 - 	 - 	"Hedgehog amino-terminal signalling domain; For the carboxyl Hint module, see pfam01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation."
Q#21216 - 	CGI_10020665	superfamily	247996	200	230	0.000338923	37.6348	cl17442	Hint superfamily	C	 - 	"Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here."
Q#21217 - 	CGI_10020666	superfamily	248097	54	169	6.07E-21	83.8538	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21218 - 	CGI_10020667	superfamily	247684	176	330	0.00717299	37.9536	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#21218 - 	CGI_10020667	superfamily	248383	668	1035	8.70E-92	300.633	cl17829	DUF917 superfamily	 - 	 - 	Protein of unknown function (DUF917); This family consists of hypothetical bacterial and archaeal proteins of unknown function.
Q#21218 - 	CGI_10020667	superfamily	218571	11	184	7.15E-31	121.207	cl05110	Hydant_A_N superfamily	 - 	 - 	Hydantoinase/oxoprolinase N-terminal region; This family is found at the N-terminus of the pfam01968 family.
Q#21218 - 	CGI_10020667	superfamily	248097	1125	1241	1.80E-20	89.6318	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21219 - 	CGI_10020668	superfamily	248458	31	204	3.11E-05	44.6121	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21219 - 	CGI_10020668	superfamily	248458	282	408	0.000706861	40.3749	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21220 - 	CGI_10020669	superfamily	243096	305	487	6.66E-20	89.2792	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#21221 - 	CGI_10020670	superfamily	241752	130	292	2.77E-24	98.1714	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#21222 - 	CGI_10020671	superfamily	247743	3	43	6.72E-07	45.2147	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21224 - 	CGI_10020673	superfamily	241572	196	285	1.48E-23	93.4572	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#21224 - 	CGI_10020673	superfamily	241572	295	379	9.06E-17	74.9676	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#21225 - 	CGI_10020674	superfamily	244962	60	250	2.88E-27	106.852	cl08452	SKA1_N superfamily	 - 	 - 	"Spindle and kinetochore-associated protein 1, N-terminal domain; SKA1 is a component of the SKA complex, which is formed by the association of three subunits (SKA1, SKA2, annd SKA3). The SKA complex is essential for accurate cell division. It functions with the Ndc80 network to establish stable kinetochore-microtubule interactions, which are crucial for the highly orchestrated chromosome movements during mitosis. The biological unit is a W-shaped homodimer of the three-subunit complex. This model represents the N-terminal domain of SKA1, which is involved in interactions with SKA2 and SKA3 to form the SKA complex. The C-terminal portion of SKA1 is involved in creating a microtubule-binding surface."
Q#21226 - 	CGI_10020675	superfamily	245841	692	1055	1.51E-124	392.655	cl12025	PolY superfamily	 - 	 - 	"Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions.  Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity.  They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases.  Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria.  In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion.  Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention."
Q#21226 - 	CGI_10020675	superfamily	128973	1345	1370	0.00117248	38.3574	cl02765	ZnF_Rad18 superfamily	 - 	 - 	Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Q#21227 - 	CGI_10020676	superfamily	247725	33	129	1.15E-57	190.157	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#21227 - 	CGI_10020676	superfamily	246681	367	599	9.23E-123	365.125	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#21228 - 	CGI_10020677	superfamily	241578	409	592	3.78E-14	71.443	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21228 - 	CGI_10020677	superfamily	115363	758	817	1.34E-12	64.7005	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#21228 - 	CGI_10020677	superfamily	115363	686	744	1.83E-12	64.3153	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#21229 - 	CGI_10020678	superfamily	241578	167	329	4.78E-11	61.4278	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21231 - 	CGI_10020680	superfamily	242165	4	260	0	515.635	cl00880	Ribosomal_S8e_like superfamily	 - 	 - 	"Eukaryotic/archaeal ribosomal protein S8e and similar proteins; This family contains the eukaryotic/archaeal ribosomal protein S8, a component of the small ribosomal subunits, as well as the NSA2 gene product."
Q#21232 - 	CGI_10020681	superfamily	243072	473	595	8.02E-34	127.115	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21232 - 	CGI_10020681	superfamily	243072	637	758	3.41E-29	114.018	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21232 - 	CGI_10020681	superfamily	241760	87	131	3.90E-18	79.8099	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#21232 - 	CGI_10020681	superfamily	115363	13	78	7.01E-15	70.8637	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#21232 - 	CGI_10020681	superfamily	115363	159	222	3.61E-11	60.0781	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#21234 - 	CGI_10020683	superfamily	222557	26	201	2.01E-75	227.864	cl16634	DUF4291 superfamily	 - 	 - 	Domain of unknown function (DUF4291); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 190 and 214 amino acids in length. There are two conserved sequence motifs: VYQAY and RMTW.
Q#21235 - 	CGI_10020684	superfamily	241570	65	165	8.15E-14	67.351	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#21235 - 	CGI_10020684	superfamily	241570	205	319	1.14E-07	49.2466	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#21237 - 	CGI_10020686	superfamily	245863	69	359	2.69E-110	326.608	cl12077	Methyltrn_RNA_3 superfamily	 - 	 - 	"Putative RNA methyltransferase; This family has a TIM barrel-like fold with a deep C-terminal trefoil knot. The arrangement of its hydrophilic and hydrophobic surfaces are opposite to that of the classic TIM barrel proteins. It is likely to bind RNA, and may function as a methyltransferase."
Q#21238 - 	CGI_10020687	superfamily	243092	183	496	1.08E-57	203.721	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21238 - 	CGI_10020687	superfamily	243084	1179	1294	8.15E-30	117.438	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21238 - 	CGI_10020687	superfamily	243084	1359	1471	1.27E-47	168.405	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21239 - 	CGI_10020688	superfamily	241707	28	251	9.88E-109	319.198	cl00230	CIS_IPPS superfamily	 - 	 - 	"Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity."
Q#21242 - 	CGI_10020195	superfamily	217518	254	356	1.90E-36	129.277	cl08388	CBM_21 superfamily	 - 	 - 	"Putative phosphatase regulatory subunit; This family consists of several eukaryotic proteins that are thought to be involved in the regulation of glycogen metabolism. For instance, the mouse PTG protein has been shown to interact with glycogen synthase, phosphorylase kinase, phosphorylase a: these three enzymes have key roles in the regulation of glycogen metabolism. PTG also binds the catalytic subunit of protein phosphatase 1 (PP1C) and localises it to glycogen. Subsets of similar interactions have been observed with several other members of this family, such as the yeast PIG1, PIG2, GAC1 and GIP2 proteins. While the precise function of these proteins is not known, they may serve a scaffold function, bringing together the key enzymes in glycogen metabolism. This family is a carbohydrate binding domain."
Q#21243 - 	CGI_10020196	superfamily	247724	6	92	1.06E-09	51.3724	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21244 - 	CGI_10020197	superfamily	220692	2	257	3.07E-08	52.5917	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#21247 - 	CGI_10020200	superfamily	217293	26	217	1.53E-30	116.578	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#21249 - 	CGI_10020202	superfamily	243034	348	443	3.00E-10	59.316	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21249 - 	CGI_10020202	superfamily	243034	155	260	0.000534598	40.4412	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21249 - 	CGI_10020202	superfamily	202224	1034	1142	8.54E-36	133.96	cl18224	JmjC superfamily	 - 	 - 	"JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation."
Q#21249 - 	CGI_10020202	superfamily	214721	1000	1064	1.58E-06	47.632	cl18313	JmjC superfamily	 - 	 - 	"A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press)."
Q#21249 - 	CGI_10020202	superfamily	242988	1447	1585	0.00249573	39.9116	cl02331	Intg_mem_TP0381 superfamily	N	 - 	"Integral membrane protein (intg_mem_TP0381); This entry represents a family of hydrophobic proteins with seven predicted transmembrane alpha helices. Members are found in Bacillus subtilis (ywaF), TP0381 from Treponema pallidum (TP0381), Streptococcus pyogenes, Rhodococcus erythropolis, etc."
Q#21251 - 	CGI_10020204	superfamily	247725	44	92	9.39E-18	74.9439	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#21253 - 	CGI_10020206	superfamily	242251	49	103	4.26E-13	61.5315	cl01015	FUN14 superfamily	C	 - 	FUN14 family; This family of short proteins are found in eukaryotes and some archaea. Although the function of these proteins is not known they may contain transmembrane helices.
Q#21255 - 	CGI_10020208	superfamily	243034	460	525	2.08E-08	52.3824	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21255 - 	CGI_10020208	superfamily	243034	349	447	3.09E-07	48.5304	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21255 - 	CGI_10020208	superfamily	243034	291	378	3.42E-05	42.3672	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21259 - 	CGI_10020212	superfamily	217888	474	782	4.19E-95	302.261	cl04396	Sec15 superfamily	 - 	 - 	Exocyst complex subunit Sec15-like; Exocyst complex subunit Sec15-like.  
Q#21260 - 	CGI_10020213	superfamily	245206	9	237	4.40E-63	199.435	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#21261 - 	CGI_10020214	superfamily	247723	29	58	1.78E-05	43.366	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21263 - 	CGI_10020216	superfamily	241570	27	87	0.00191635	34.609	cl00047	CAP_ED superfamily	N	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#21265 - 	CGI_10020218	superfamily	241874	644	1162	2.42E-161	495.463	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#21265 - 	CGI_10020218	superfamily	241874	1	499	8.30E-156	480.825	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#21266 - 	CGI_10020219	superfamily	241874	1	64	4.20E-14	66.7358	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#21270 - 	CGI_10020223	superfamily	242406	22	105	3.20E-09	51.4381	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#21272 - 	CGI_10013812	superfamily	241618	1	35	2.06E-06	41.5527	cl00111	PAH superfamily	 - 	 - 	"Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers"
Q#21275 - 	CGI_10013816	superfamily	241563	62	102	0.000144869	39.77	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21276 - 	CGI_10013817	superfamily	241563	62	102	0.000106305	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21276 - 	CGI_10013817	superfamily	110440	493	517	0.00647422	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#21276 - 	CGI_10013817	superfamily	220631	576	612	0.0094989	34.7606	cl10899	MRP-S32 superfamily	N	 - 	"Mitochondrial 28S ribosomal protein S32; This entry is of a family of short, approximately 100 amino acid residues, proteins which are mitochondrial 28S ribosomal proteins named as MRP-S32. Their exact function could not be confirmed."
Q#21277 - 	CGI_10013818	superfamily	241563	132	172	0.000114162	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21277 - 	CGI_10013818	superfamily	242730	231	372	0.000584894	39.1667	cl01825	Phage_Mu_Gam superfamily	 - 	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#21278 - 	CGI_10013819	superfamily	191362	217	269	2.08E-26	98.8822	cl05351	zf-nanos superfamily	 - 	 - 	"Nanos RNA binding domain; This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development."
Q#21279 - 	CGI_10013820	superfamily	215859	429	631	1.06E-33	127.718	cl18347	Peptidase_S9 superfamily	 - 	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#21280 - 	CGI_10013821	superfamily	241563	59	98	6.60E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21281 - 	CGI_10013822	superfamily	241563	67	104	0.000186504	39.3848	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21282 - 	CGI_10013823	superfamily	247746	41	98	0.00747019	35.3118	cl17192	ATP-synt_B superfamily	N	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#21288 - 	CGI_10013829	superfamily	241600	411	616	7.36E-45	158.943	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#21289 - 	CGI_10013830	superfamily	149409	182	725	2.27E-119	372.109	cl18037	Plexin_cytopl superfamily	 - 	 - 	"Plexin cytoplasmic RasGAP domain; This family features the C-terminal regions of various plexins. Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels. The cytoplasmic region, which has been called a SEX domain in some members of this family, is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins. This domain acts as a RasGAP domain."
Q#21290 - 	CGI_10018247	superfamily	247684	249	452	6.47E-21	94.6515	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#21290 - 	CGI_10018247	superfamily	245847	11	171	0.000243186	40.6178	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#21290 - 	CGI_10018247	superfamily	110440	691	717	0.00636305	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#21291 - 	CGI_10018248	superfamily	214531	79	120	1.38E-06	43.7445	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21291 - 	CGI_10018248	superfamily	214531	34	77	5.89E-06	42.2037	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21291 - 	CGI_10018248	superfamily	215683	8	51	0.00696546	33.2975	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#21293 - 	CGI_10018250	superfamily	245213	198	233	0.000576304	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21293 - 	CGI_10018250	superfamily	245213	240	275	0.0026518	36.0754	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21293 - 	CGI_10018250	superfamily	222083	406	472	0.00493131	36.4334	cl16258	DUF2407_C superfamily	C	 - 	DUF2407 C-terminal domain; This is a family of proteins found in fungi. The function is not known. There is a characteristic GFDRL sequence motif.
Q#21294 - 	CGI_10018251	superfamily	218520	31	211	3.28E-69	212.909	cl05007	EBP superfamily	 - 	 - 	"Emopamil binding protein; Emopamil binding protein (EBP) is as a gene that encodes a non-glycosylated type I integral membrane protein of endoplasmic reticulum and shows high level expression in epithelial tissues. The EBP protein has emopamil binding domains, including the sterol acceptor site and the catalytic centre, which show Delta8-Delta7 sterol isomerase activity. Human sterol isomerase, a homologue of mouse EBP, is suggested not only to play a role in cholesterol biosynthesis, but also to affect lipoprotein internalisation. In humans, mutations of EBP are known to cause the genetic disorder of X-linked dominant chondrodysplasia punctata (CDPX2). This syndrome of humans is lethal in most males, and affected females display asymmetric hyperkeratotic skin and skeletal abnormalities."
Q#21296 - 	CGI_10018253	superfamily	243166	61	253	5.06E-16	73.4818	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#21297 - 	CGI_10018254	superfamily	243051	80	164	0.00115298	36.587	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#21299 - 	CGI_10018256	superfamily	243106	1085	1204	7.42E-54	187.021	cl02608	BAH superfamily	 - 	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#21299 - 	CGI_10018256	superfamily	243084	231	341	8.82E-48	169.436	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21299 - 	CGI_10018256	superfamily	243084	907	1019	3.19E-46	164.848	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21299 - 	CGI_10018256	superfamily	241597	1390	1452	9.30E-16	75.3479	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#21299 - 	CGI_10018256	superfamily	243084	386	485	5.72E-35	132.178	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21299 - 	CGI_10018256	superfamily	243084	556	652	4.53E-30	117.825	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21299 - 	CGI_10018256	superfamily	243084	811	893	5.83E-30	117.791	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21299 - 	CGI_10018256	superfamily	243106	1247	1314	5.92E-12	65.6835	cl02608	BAH superfamily	C	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#21299 - 	CGI_10018256	superfamily	243084	737	776	1.72E-11	64.0038	cl02556	Bromodomain superfamily	N	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#21299 - 	CGI_10018256	superfamily	241563	1817	1852	0.00196121	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21301 - 	CGI_10018258	superfamily	248458	67	230	7.77E-26	108.17	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21301 - 	CGI_10018258	superfamily	248458	298	364	0.000919184	40.3749	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21301 - 	CGI_10018258	superfamily	248458	471	556	0.0049336	38.0637	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21302 - 	CGI_10018259	superfamily	217228	113	407	4.45E-167	473.766	cl07843	G6PD_C superfamily	 - 	 - 	"Glucose-6-phosphate dehydrogenase, C-terminal domain; Glucose-6-phosphate dehydrogenase, C-terminal domain.  "
Q#21302 - 	CGI_10018259	superfamily	215937	1	111	1.77E-54	180.776	cl02877	G6PD_N superfamily	N	 - 	"Glucose-6-phosphate dehydrogenase, NAD binding domain; Glucose-6-phosphate dehydrogenase, NAD binding domain.  "
Q#21303 - 	CGI_10008625	superfamily	216686	180	364	1.14E-34	128.21	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#21304 - 	CGI_10008626	superfamily	243035	368	490	6.58E-18	79.5861	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#21304 - 	CGI_10008626	superfamily	246918	124	175	2.58E-14	67.9971	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21304 - 	CGI_10008626	superfamily	246918	181	220	2.94E-06	44.8851	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21305 - 	CGI_10008627	superfamily	246918	168	220	8.53E-12	61.0635	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21305 - 	CGI_10008627	superfamily	246918	288	335	4.01E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21305 - 	CGI_10008627	superfamily	246918	54	106	8.60E-11	58.3671	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21305 - 	CGI_10008627	superfamily	246918	111	163	1.15E-10	57.9819	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21305 - 	CGI_10008627	superfamily	246918	3	49	3.17E-08	50.6631	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21305 - 	CGI_10008627	superfamily	246918	346	385	2.34E-07	48.3519	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	432	484	5.45E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	716	768	8.34E-10	56.0559	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	659	711	1.44E-09	55.2855	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	773	825	5.12E-09	53.7447	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	602	654	1.25E-08	52.5891	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	260	307	1.34E-08	52.5891	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	67	113	5.39E-08	51.0483	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	119	170	1.04E-07	49.8927	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	545	597	1.23E-07	49.8927	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	830	882	4.32E-07	48.3519	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	318	368	7.39E-06	44.4999	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21306 - 	CGI_10008628	superfamily	246918	204	254	3.13E-05	42.5739	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21308 - 	CGI_10008630	superfamily	217925	45	90	4.27E-11	55.5901	cl04417	Ctr superfamily	N	 - 	"Ctr copper transporter family; The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport."
Q#21309 - 	CGI_10008631	superfamily	241571	244	355	2.28E-14	69.3634	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#21309 - 	CGI_10008631	superfamily	241584	154	241	2.96E-08	51.3431	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21309 - 	CGI_10008631	superfamily	241583	14	109	8.84E-38	136.932	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#21312 - 	CGI_10014772	superfamily	247085	728	817	0.000357997	40.9519	cl15820	RICIN superfamily	N	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#21312 - 	CGI_10014772	superfamily	241645	519	615	0.000863927	39.5488	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#21312 - 	CGI_10014772	superfamily	241645	207	272	0.00980552	36.082	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#21313 - 	CGI_10014773	superfamily	243146	19	57	0.00210017	34.9447	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#21314 - 	CGI_10014774	superfamily	241568	880	911	0.00663557	36.2868	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21314 - 	CGI_10014774	superfamily	214531	695	737	2.98E-10	57.6116	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21314 - 	CGI_10014774	superfamily	215683	670	712	3.44E-08	51.7871	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#21314 - 	CGI_10014774	superfamily	214531	70	112	1.48E-07	49.9077	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21314 - 	CGI_10014774	superfamily	214531	26	69	2.34E-06	46.4409	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21314 - 	CGI_10014774	superfamily	241578	182	214	0.00151473	40.0608	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21316 - 	CGI_10014776	superfamily	191378	53	102	0.000437215	37.4876	cl05416	PSP94 superfamily	NC	 - 	"Beta-microseminoprotein (PSP-94); This family consists of the mammalian specific protein beta-microseminoprotein. Prostatic secretory protein of 94 amino acids (PSP94), also called beta-microseminoprotein, is a small, nonglycosylated protein, rich in cysteine residues. It was first isolated as a major protein from human seminal plasma. The exact function of this protein is unknown."
Q#21318 - 	CGI_10014778	superfamily	247042	41	154	1.36E-09	55.7998	cl15693	Sema superfamily	C	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#21319 - 	CGI_10014779	superfamily	157570	1	31	0.00955277	32.6875	cl07019	SHR3_chaperone superfamily	N	 - 	"ER membrane protein SH3; This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER."
Q#21321 - 	CGI_10014781	superfamily	217293	30	234	1.53E-65	213.263	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#21321 - 	CGI_10014781	superfamily	202474	241	491	2.06E-29	114.673	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#21322 - 	CGI_10014782	superfamily	241812	37	100	0.000616695	37.0156	cl00356	Ribosomal_L17 superfamily	C	 - 	Ribosomal protein L17; Ribosomal protein L17.  
Q#21323 - 	CGI_10014783	superfamily	217293	3	182	2.57E-30	115.808	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#21323 - 	CGI_10014783	superfamily	202474	212	288	4.49E-09	54.9673	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#21325 - 	CGI_10014785	superfamily	246710	82	194	1.64E-06	45.8372	cl14783	DOMON_like superfamily	N	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#21327 - 	CGI_10014787	superfamily	243072	33	149	2.67E-19	85.513	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21327 - 	CGI_10014787	superfamily	245814	178	231	0.00933124	35.1575	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21327 - 	CGI_10014787	superfamily	245814	406	463	0.00171365	37.6626	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21327 - 	CGI_10014787	superfamily	245814	542	607	0.00260013	37.0714	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21329 - 	CGI_10014790	superfamily	247999	98	143	0.00146205	34.1098	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#21333 - 	CGI_10006564	superfamily	177822	18	299	1.84E-22	94.2165	cl18088	PLN02164 superfamily	 - 	 - 	sulfotransferase
Q#21334 - 	CGI_10006565	superfamily	177822	82	292	4.28E-20	87.2829	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#21335 - 	CGI_10006566	superfamily	177822	34	291	1.69E-21	91.1349	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#21337 - 	CGI_10006568	superfamily	243066	23	124	7.39E-13	65.3313	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#21338 - 	CGI_10006569	superfamily	247677	940	1087	1.83E-43	155.52	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#21338 - 	CGI_10006569	superfamily	243128	271	493	5.99E-47	167.892	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#21338 - 	CGI_10006569	superfamily	241899	15	169	3.50E-11	62.946	cl00489	60KD_IMP superfamily	C	 - 	60Kd inner membrane protein; 60Kd inner membrane protein.  
Q#21338 - 	CGI_10006569	superfamily	243129	758	863	1.47E-05	44.543	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#21339 - 	CGI_10006570	superfamily	241574	325	559	4.68E-100	305.664	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21341 - 	CGI_10006572	superfamily	218663	4	380	1.62E-114	340.785	cl05280	PAXNEB superfamily	 - 	 - 	"PAXNEB protein; PAXNEB or PAX6 neighbor is found in several eukaryotic organisms. PAXNED is an RNA polymerase II Elongator protein subunit. It is part of the HAP subcomplex of Elongator, which is a six-subunit component of the RNA polymerase II holoenzyme. The HAP subcomplex is required for Elongator structural integrity and histone acetyltransferase activity. This protein family has a P-loop motif. However its sequence has degraded in many members of the family."
Q#21343 - 	CGI_10006574	superfamily	202184	10	87	5.30E-18	73.0822	cl03509	UCR_14kD superfamily	N	 - 	"Ubiquinol-cytochrome C reductase complex 14kD subunit; The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex."
Q#21344 - 	CGI_10006575	superfamily	192997	659	782	4.55E-51	178.544	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#21347 - 	CGI_10010843	superfamily	241584	278	361	0.000602883	37.8611	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21350 - 	CGI_10010846	superfamily	219276	371	535	8.02E-61	200.434	cl06189	Mic1 superfamily	 - 	 - 	Colon cancer-associated protein Mic1-like; This family represents the C-terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Q#21352 - 	CGI_10010848	superfamily	218549	76	234	1.31E-07	49.7507	cl18461	Mito_fiss_reg superfamily	C	 - 	"Mitochondrial fission regulator; In eukaryotes, this family of proteins induces mitochondrial fission."
Q#21355 - 	CGI_10010851	superfamily	247856	372	434	0.00363135	35.9865	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21356 - 	CGI_10010852	superfamily	241563	286	326	9.42E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21357 - 	CGI_10010853	superfamily	241574	168	395	1.55E-92	280.626	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21358 - 	CGI_10010854	superfamily	215724	41	334	1.12E-111	329.965	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#21360 - 	CGI_10010856	superfamily	192535	43	334	0.000534109	39.8866	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#21361 - 	CGI_10010857	superfamily	243053	404	634	6.24E-52	180.141	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#21361 - 	CGI_10010857	superfamily	243067	248	373	1.87E-15	73.6007	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#21362 - 	CGI_10010858	superfamily	247743	2016	2156	0.000940959	41.3627	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21362 - 	CGI_10010858	superfamily	193256	2342	2611	3.79E-64	223.286	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#21362 - 	CGI_10010858	superfamily	193257	2995	3218	2.53E-46	170.166	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#21362 - 	CGI_10010858	superfamily	193253	2624	2968	1.45E-38	150.958	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#21362 - 	CGI_10010858	superfamily	247743	1646	1789	8.97E-06	47.29	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21365 - 	CGI_10010861	superfamily	192535	50	148	0.000290818	39.8866	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#21367 - 	CGI_10010863	superfamily	241868	19	154	4.78E-44	144.254	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#21368 - 	CGI_10010864	superfamily	241868	1	90	7.90E-29	102.653	cl00447	Nudix_Hydrolase superfamily	N	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#21369 - 	CGI_10010865	superfamily	247792	39	82	0.00116984	36.2696	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#21369 - 	CGI_10010865	superfamily	190233	102	151	0.00065749	37.0486	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#21371 - 	CGI_10010867	superfamily	215647	2	152	0.000606618	39.1289	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#21372 - 	CGI_10005565	superfamily	241752	27	146	1.17E-36	123.969	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#21373 - 	CGI_10005566	superfamily	247684	9	78	4.57E-13	66.5319	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#21373 - 	CGI_10005566	superfamily	247684	66	102	3.37E-05	43.0348	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#21374 - 	CGI_10005567	superfamily	243035	115	186	5.07E-16	70.7965	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#21376 - 	CGI_10005569	superfamily	217473	105	144	0.00388722	38.115	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#21377 - 	CGI_10005570	superfamily	215647	716	929	7.27E-38	142.748	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#21377 - 	CGI_10005570	superfamily	243086	628	674	3.01E-10	57.385	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#21378 - 	CGI_10005571	superfamily	220695	99	292	0.000126435	42.5659	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#21380 - 	CGI_10005573	superfamily	241646	8	51	6.78E-07	42.4378	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#21381 - 	CGI_10005892	superfamily	220782	53	253	2.27E-33	122.103	cl11134	Stk19 superfamily	 - 	 - 	"Serine-threonine protein kinase 19; This serine-threonine protein kinase number 19 is expressed from the MHC and predominantly in the nucleus. Protein kinases are involved in signal transduction pathways and play fundamental roles in the regulation of cell functions. This is a novel Ser/Thr protein kinase, that has Mn2+-dependent protein kinase activity that phosphorylates alpha -casein at Ser/Thr residues and histone at Ser residues. It can be covalently modified by the reactive ATP analogue 5'-p-fluorosulfonylbenzoyladenosine in the absence of ATP, and this modification is prevented in the presence of 1 mM ATP, indicating that the kinase domain of is capable of binding ATP."
Q#21382 - 	CGI_10005893	superfamily	204014	245	310	5.08E-20	83.0329	cl07321	RAI1 superfamily	 - 	 - 	"RAI1 like PD-(D/E)XK nuclease; RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z and binds to a nuclear exoribonuclease. It is required for 5.8S rRNA processing. Profile-profile comparison tools demonstrate this to be a PD-(D/E)XK nuclease, with a full set of canonical active site signature motifs characteristic to the PD-(D/E)XK nuclease superfamily."
Q#21383 - 	CGI_10005894	superfamily	247804	196	244	0.000810329	37.1698	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#21383 - 	CGI_10005894	superfamily	241760	371	419	1.87E-12	62.0655	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#21393 - 	CGI_10007216	superfamily	243082	317	580	2.35E-102	320.809	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#21393 - 	CGI_10007216	superfamily	241643	677	710	2.50E-11	60.1655	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#21393 - 	CGI_10007216	superfamily	241643	609	647	4.15E-08	50.5355	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#21393 - 	CGI_10007216	superfamily	243082	736	793	1.94E-25	107.409	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#21393 - 	CGI_10007216	superfamily	245220	189	262	3.81E-20	85.9194	cl09957	zf-UBP superfamily	 - 	 - 	Zn-finger in ubiquitin-hydrolases and other protein; Zn-finger in ubiquitin-hydrolases and other protein.  
Q#21394 - 	CGI_10007217	superfamily	247725	89	234	2.30E-48	166	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#21395 - 	CGI_10007218	superfamily	246908	70	164	4.33E-19	79.3934	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#21398 - 	CGI_10007221	superfamily	241874	73	418	4.37E-123	374.125	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#21398 - 	CGI_10007221	superfamily	241874	20	87	1.43E-28	117.967	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#21399 - 	CGI_10007222	superfamily	241644	1	127	1.12E-57	177.78	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#21400 - 	CGI_10007223	superfamily	241607	383	421	7.94E-10	55.3538	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#21401 - 	CGI_10008423	superfamily	248318	262	314	9.68E-22	86.3357	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#21402 - 	CGI_10008424	superfamily	247750	8	147	2.75E-51	170.164	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#21402 - 	CGI_10008424	superfamily	247750	266	317	6.45E-15	70.7823	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#21404 - 	CGI_10008426	superfamily	247755	132	234	7.07E-61	193.196	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#21404 - 	CGI_10008426	superfamily	217962	24	96	0.006145	35.314	cl09558	TPD52 superfamily	C	 - 	"Tumour protein D52 family; The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other."
Q#21409 - 	CGI_10008431	superfamily	243310	27	265	3.23E-77	236.751	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#21410 - 	CGI_10008432	superfamily	245602	183	375	3.27E-37	139.684	cl11402	GH31 superfamily	N	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#21410 - 	CGI_10008432	superfamily	245602	109	193	0.00531776	36.8099	cl11402	GH31 superfamily	C	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#21413 - 	CGI_10008435	superfamily	243555	2	148	1.65E-09	55.0898	cl03871	Chitin_bind_3 superfamily	N	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#21417 - 	CGI_10005546	superfamily	192604	70	136	1.01E-16	70.4058	cl11135	PACT_coil_coil superfamily	C	 - 	"Pericentrin-AKAP-450 domain of centrosomal targeting protein; This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly."
Q#21419 - 	CGI_10005548	superfamily	245201	1	172	5.68E-37	134.163	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21419 - 	CGI_10005548	superfamily	242406	200	292	8.55E-31	114.226	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#21422 - 	CGI_10018731	superfamily	220131	17	212	8.36E-46	156.282	cl11721	DUF1943 superfamily	C	 - 	"Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined."
Q#21430 - 	CGI_10018739	superfamily	242113	1	186	5.57E-42	143.236	cl00814	Cyclase superfamily	N	 - 	Putative cyclase; Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.
Q#21431 - 	CGI_10018740	superfamily	242113	5	121	3.44E-28	104.716	cl00814	Cyclase superfamily	N	 - 	Putative cyclase; Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.
Q#21432 - 	CGI_10018741	superfamily	242113	1	186	3.31E-44	149.014	cl00814	Cyclase superfamily	N	 - 	Putative cyclase; Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.
Q#21436 - 	CGI_10018746	superfamily	248054	75	130	3.99E-06	44.7704	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#21437 - 	CGI_10018747	superfamily	248054	28	80	0.00049581	38.222	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#21440 - 	CGI_10024508	superfamily	245226	2	132	8.21E-13	61.1625	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#21442 - 	CGI_10024510	superfamily	216363	28	96	3.29E-07	43.613	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#21444 - 	CGI_10024512	superfamily	221154	26	191	1.07E-09	57.4104	cl13144	TAN superfamily	 - 	 - 	"Telomere-length maintenance and DNA damage repair; ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage. It is classified as an EC:2.7.11.1."
Q#21449 - 	CGI_10024517	superfamily	242485	35	99	7.66E-10	50.7399	cl01407	Rdx superfamily	 - 	 - 	"Rdx family; This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown. Selenoprotein W contains selenium as selenocysteine in the primary protein structure and levels of this selenoprotein are affected by selenium."
Q#21450 - 	CGI_10024518	superfamily	220074	22	301	1.64E-144	411.683	cl07499	DUF1907 superfamily	 - 	 - 	"Domain of Unknown Function (DUF1907); The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an HxHxxxxxxxxxH motif that coordinates a zinc ion, and an acetate anion at a site that likely supports the enzymatic activity of an ester hydrolase."
Q#21451 - 	CGI_10024519	superfamily	243072	49	188	6.01E-08	50.845	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21452 - 	CGI_10024520	superfamily	245201	150	400	1.57E-70	227.403	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21453 - 	CGI_10024521	superfamily	248097	123	250	7.55E-21	85.0094	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21454 - 	CGI_10024522	superfamily	248097	201	327	3.47E-23	92.7134	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21455 - 	CGI_10024523	superfamily	245201	55	321	4.35E-66	216.334	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21456 - 	CGI_10024524	superfamily	241704	337	462	1.86E-23	96.2884	cl00227	PEBP superfamily	 - 	 - 	"PhosphatidylEthanolamine-Binding Protein (PEBP) domain; PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer)."
Q#21456 - 	CGI_10024524	superfamily	241704	118	250	2.22E-08	52.3756	cl00227	PEBP superfamily	 - 	 - 	"PhosphatidylEthanolamine-Binding Protein (PEBP) domain; PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer)."
Q#21458 - 	CGI_10024526	superfamily	247743	40	174	3.30E-22	90.6683	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21458 - 	CGI_10024526	superfamily	203973	245	333	2.91E-29	108.748	cl16006	Rep_fac_C superfamily	 - 	 - 	"Replication factor C C-terminal domain; This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A."
Q#21459 - 	CGI_10024527	superfamily	217868	156	331	9.61E-59	192.457	cl04384	DUF383 superfamily	 - 	 - 	Domain of unknown function (DUF383); Domain of unknown function (DUF383).  
Q#21459 - 	CGI_10024527	superfamily	190851	336	393	2.75E-14	67.2738	cl04385	DUF384 superfamily	 - 	 - 	Domain of unknown function (DUF384); Domain of unknown function (DUF384).  
Q#21461 - 	CGI_10024529	superfamily	247805	283	425	2.11E-27	110.12	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#21461 - 	CGI_10024529	superfamily	219532	918	1020	8.65E-22	92.7626	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#21461 - 	CGI_10024529	superfamily	243778	743	835	5.27E-13	66.8639	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#21461 - 	CGI_10024529	superfamily	247905	596	645	1.16E-06	47.9769	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#21463 - 	CGI_10024531	superfamily	245213	69	102	6.38E-06	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21463 - 	CGI_10024531	superfamily	245213	212	254	6.92E-05	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21463 - 	CGI_10024531	superfamily	245213	29	64	0.000537414	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21463 - 	CGI_10024531	superfamily	245213	169	201	0.00189042	35.305	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21463 - 	CGI_10024531	superfamily	201391	132	169	1.79E-06	44.2446	cl02926	TB superfamily	 - 	 - 	TB domain; This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Q#21463 - 	CGI_10024531	superfamily	245213	255	295	0.00263404	35.0172	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21465 - 	CGI_10024533	superfamily	248097	468	587	4.94E-21	89.6318	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21465 - 	CGI_10024533	superfamily	248097	193	310	2.04E-15	73.4534	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21465 - 	CGI_10024533	superfamily	248097	362	447	1.20E-06	47.2969	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21465 - 	CGI_10024533	superfamily	248097	92	176	5.72E-06	44.9486	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21467 - 	CGI_10024535	superfamily	246918	263	307	1.40E-09	54.5151	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21467 - 	CGI_10024535	superfamily	246918	116	164	4.58E-09	52.9743	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21467 - 	CGI_10024535	superfamily	246918	62	110	3.93E-06	44.4999	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21467 - 	CGI_10024535	superfamily	246918	310	355	6.45E-06	44.1147	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21469 - 	CGI_10024537	superfamily	246918	284	332	4.08E-11	57.5967	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21469 - 	CGI_10024537	superfamily	246918	176	224	4.66E-09	51.8187	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21469 - 	CGI_10024537	superfamily	246918	122	170	2.67E-07	46.8111	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21469 - 	CGI_10024537	superfamily	246918	230	277	0.000168085	38.7219	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21470 - 	CGI_10024538	superfamily	246918	21	73	2.57E-10	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#21472 - 	CGI_10024540	superfamily	241913	19	112	1.71E-05	39.3706	cl00509	hot_dog superfamily	C	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#21473 - 	CGI_10024541	superfamily	247858	673	862	5.45E-33	125.963	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#21473 - 	CGI_10024541	superfamily	203913	347	515	4.77E-13	67.2421	cl07084	P4Ha_N superfamily	 - 	 - 	"Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known."
Q#21473 - 	CGI_10024541	superfamily	247799	146	196	0.000679137	38.8156	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#21474 - 	CGI_10024542	superfamily	245596	135	249	6.73E-47	167.485	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#21474 - 	CGI_10024542	superfamily	245814	415	481	5.86E-07	48.2705	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21474 - 	CGI_10024542	superfamily	247775	279	369	0.00105473	40.6982	cl17221	ArsB_NhaD_permease superfamily	NC	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#21474 - 	CGI_10024542	superfamily	245814	512	566	0.00267949	37.0328	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21475 - 	CGI_10024543	superfamily	247858	377	568	7.10E-31	118.259	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#21475 - 	CGI_10024543	superfamily	203913	73	239	3.14E-12	64.1605	cl07084	P4Ha_N superfamily	 - 	 - 	"Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known."
Q#21476 - 	CGI_10024544	superfamily	209898	138	157	4.11E-05	38.8607	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#21476 - 	CGI_10024544	superfamily	209898	115	135	0.00602048	32.7606	cl14787	MORN superfamily	 - 	 - 	MORN repeat; The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Q#21477 - 	CGI_10024545	superfamily	245604	49	123	2.63E-27	104.023	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#21477 - 	CGI_10024545	superfamily	215782	271	484	8.35E-94	285.983	cl18344	2-oxoacid_dh superfamily	 - 	 - 	2-oxoacid dehydrogenases acyltransferase (catalytic domain); These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain.
Q#21477 - 	CGI_10024545	superfamily	202412	200	238	1.41E-07	48.1873	cl03729	E3_binding superfamily	 - 	 - 	e3 binding domain; This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit.
Q#21478 - 	CGI_10024546	superfamily	241580	65	160	2.45E-17	76.8903	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#21479 - 	CGI_10024547	superfamily	222436	231	367	3.49E-23	96.1844	cl16454	DUF4203 superfamily	N	 - 	Domain of unknown function (DUF4203); This is the N-terminal region of 7tm proteins. The function is not known.
Q#21480 - 	CGI_10024548	superfamily	247740	262	474	4.59E-54	182.376	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#21480 - 	CGI_10024548	superfamily	241770	76	182	2.25E-17	78.5916	cl00309	PRTases_typeI superfamily	 - 	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#21481 - 	CGI_10024549	superfamily	241997	27	125	1.71E-26	97.4227	cl00638	RNA_pol_Rpb4 superfamily	 - 	 - 	RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II.
Q#21483 - 	CGI_10024551	superfamily	246676	340	494	3.43E-24	99.7265	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#21483 - 	CGI_10024551	superfamily	243146	58	115	0.000453051	38.4243	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#21483 - 	CGI_10024551	superfamily	243146	177	228	0.00814102	34.5723	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#21486 - 	CGI_10024554	superfamily	241807	38	190	3.16E-77	230.742	cl00351	Ribosomal_S17 superfamily	 - 	 - 	Ribosomal protein S17; Ribosomal protein S17.  
Q#21487 - 	CGI_10024555	superfamily	243066	129	220	1.02E-19	82.2801	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#21487 - 	CGI_10024555	superfamily	243179	1	69	1.11E-06	45.9867	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#21489 - 	CGI_10024557	superfamily	243179	1	107	1.79E-17	74.4915	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#21490 - 	CGI_10024558	superfamily	243066	2	95	4.81E-20	80.3541	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#21491 - 	CGI_10024559	superfamily	246902	283	399	0.000255032	39.2484	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#21492 - 	CGI_10008676	superfamily	241574	165	383	1.57E-87	267.53	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21493 - 	CGI_10008677	superfamily	241574	16	183	4.44E-46	154.281	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21494 - 	CGI_10008678	superfamily	241574	146	360	1.31E-87	282.167	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21494 - 	CGI_10008678	superfamily	241574	553	638	1.48E-17	83.0189	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21495 - 	CGI_10008679	superfamily	241574	234	446	3.94E-37	136.562	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21500 - 	CGI_10008684	superfamily	243092	964	1250	2.18E-23	102.028	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21502 - 	CGI_10003647	superfamily	245213	284	320	4.87E-07	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21502 - 	CGI_10003647	superfamily	245213	171	207	1.91E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21502 - 	CGI_10003647	superfamily	245213	210	245	2.12E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21502 - 	CGI_10003647	superfamily	245213	95	131	2.63E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21502 - 	CGI_10003647	superfamily	245213	133	169	4.12E-05	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21502 - 	CGI_10003647	superfamily	245213	362	395	5.83E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21502 - 	CGI_10003647	superfamily	245213	251	282	0.000756301	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21502 - 	CGI_10003647	superfamily	245213	327	358	0.00159591	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21504 - 	CGI_10003649	superfamily	215866	7	164	4.81E-36	130.523	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#21504 - 	CGI_10003649	superfamily	243212	187	356	4.28E-19	83.1621	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#21506 - 	CGI_10003651	superfamily	220384	133	282	3.02E-40	142.48	cl10738	Arb2 superfamily	 - 	 - 	"Arb2 domain; A second fission yeast Argonaute complex (Argonaute siRNA chaperone, ARC) that contains two previously uncharacterized proteins, Arb1 and Arb2, both of which are required for histone H3 Lys9 (H3-K9) methylation, heterochromatin assembly and siRNA generation. This family includes a region found in Arb2 and the Hda1 protein."
Q#21507 - 	CGI_10003652	superfamily	245201	103	359	2.98E-77	254.769	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21507 - 	CGI_10003652	superfamily	247683	18	74	8.74E-28	107.93	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#21510 - 	CGI_10010439	superfamily	197448	2950	3103	4.39E-58	200.917	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	796	944	2.80E-53	187.049	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	1161	1302	4.90E-48	172.027	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	1865	2011	3.60E-46	166.634	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	246671	59	173	3.43E-12	67.0628	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#21510 - 	CGI_10010439	superfamily	197448	1668	1835	2.05E-54	191.276	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	2229	2393	2.15E-50	178.937	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	3585	3737	1.35E-49	176.91	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	1504	1659	9.91E-49	174.236	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	2401	2557	3.05E-46	167.005	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	3372	3544	7.52E-46	166.552	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	2593	2740	1.81E-45	164.623	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	3109	3281	1.39E-44	163.085	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	950	1116	2.43E-42	156.232	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	2020	2192	4.00E-38	143.664	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	1313	1468	1.73E-34	133.792	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	611	757	4.54E-33	128.824	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	197	323	2.87E-31	123.735	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	2752	2911	4.34E-25	105.915	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	3306	3366	2.22E-18	86.1272	cl15240	Reelin_subrepeat_like superfamily	N	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	504	643	1.22E-12	68.7932	cl15240	Reelin_subrepeat_like superfamily	 - 	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	197448	443	494	0.000921727	41.2598	cl15240	Reelin_subrepeat_like superfamily	C	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#21510 - 	CGI_10010439	superfamily	219677	3547	3572	0.00387278	38.1876	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#21510 - 	CGI_10010439	superfamily	219677	2564	2586	0.0062057	37.8024	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#21511 - 	CGI_10010440	superfamily	243119	49	87	0.000409856	37.0382	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21513 - 	CGI_10010442	superfamily	247743	19	165	1.63E-11	61.4468	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21514 - 	CGI_10010443	superfamily	241600	71	144	2.23E-26	101.933	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#21514 - 	CGI_10010443	superfamily	220647	145	192	8.82E-18	77.3679	cl18565	L_HGMIC_fpl superfamily	N	 - 	"Lipoma HMGIC fusion partner-like protein; This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines."
Q#21515 - 	CGI_10010444	superfamily	241609	31	108	6.56E-28	98.9894	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#21516 - 	CGI_10010445	superfamily	247041	292	556	9.78E-78	249.156	cl15692	CE4_SF superfamily	 - 	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#21516 - 	CGI_10010445	superfamily	247041	7	227	1.22E-44	159.79	cl15692	CE4_SF superfamily	 - 	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#21517 - 	CGI_10010446	superfamily	190614	30	113	2.32E-28	109.958	cl15647	YEATS superfamily	 - 	 - 	"YEATS family; We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity"
Q#21518 - 	CGI_10010447	superfamily	243072	51	145	5.12E-23	89.365	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21519 - 	CGI_10010448	superfamily	247724	5	149	9.08E-42	138.831	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21520 - 	CGI_10010449	superfamily	247724	5	152	3.76E-42	139.986	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21521 - 	CGI_10010450	superfamily	222269	692	979	5.91E-62	211.028	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#21521 - 	CGI_10010450	superfamily	222269	224	504	1.27E-60	207.561	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#21522 - 	CGI_10010451	superfamily	222269	20	305	6.21E-67	212.569	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#21523 - 	CGI_10010452	superfamily	241754	6	558	0	583.073	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21524 - 	CGI_10010453	superfamily	245596	635	871	3.19E-73	246.065	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#21524 - 	CGI_10010453	superfamily	248458	897	1038	6.39E-06	48.8493	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21524 - 	CGI_10010453	superfamily	241754	1	96	2.20E-14	76.9207	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21524 - 	CGI_10010453	superfamily	245596	512	598	2.73E-05	46.1468	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#21525 - 	CGI_10010454	superfamily	241754	6	57	9.60E-15	68.4463	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21526 - 	CGI_10010455	superfamily	241754	3	220	8.85E-61	205.192	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21527 - 	CGI_10010456	superfamily	241754	1	96	3.42E-15	72.2983	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21530 - 	CGI_10003478	superfamily	218713	13	62	1.63E-19	78.1528	cl05332	MRG superfamily	N	 - 	"MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif."
Q#21536 - 	CGI_10007372	superfamily	217869	352	505	0.00978679	36.4962	cl12286	Not3 superfamily	C	 - 	"Not1 N-terminal domain, CCR4-Not complex component; Not1 N-terminal domain, CCR4-Not complex component.  "
Q#21538 - 	CGI_10007374	superfamily	248097	46	170	3.69E-21	84.239	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21539 - 	CGI_10007376	superfamily	248097	256	380	1.23E-21	88.8614	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21540 - 	CGI_10007377	superfamily	220097	27	102	1.49E-07	45.0873	cl08518	Phospholip_A2_3 superfamily	N	 - 	"Prokaryotic phospholipase A2; The prokaryotic phospholipase A2 domain is predominantly found in bacterial and fungal phospholipases, as well as various hypothetical and putative proteins. It enables the liberation of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments."
Q#21541 - 	CGI_10007378	superfamily	207609	15	115	2.52E-19	77.9044	cl02481	NGF superfamily	 - 	 - 	Nerve growth factor family; Nerve growth factor family.  
Q#21543 - 	CGI_10007380	superfamily	241596	216	256	3.16E-07	46.8235	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#21543 - 	CGI_10007380	superfamily	245721	171	200	5.80E-09	52.4864	cl11603	Basic superfamily	N	 - 	Myogenic Basic domain; This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding. With 12 residues of the basic domain involved in DNA binding. The basic domain forms an extended alpha helix in the structure.
Q#21545 - 	CGI_10007382	superfamily	243034	10	121	0.000693331	37.7448	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21547 - 	CGI_10011192	superfamily	241754	185	546	2.04E-164	499.916	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21547 - 	CGI_10011192	superfamily	241581	638	734	1.19E-11	63.5594	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#21549 - 	CGI_10011194	superfamily	241563	68	109	1.90E-06	45.548	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21549 - 	CGI_10011194	superfamily	241563	28	59	0.000784212	37.844	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21550 - 	CGI_10011195	superfamily	243604	12	389	1.44E-122	363.153	cl03994	Trp_dioxygenase superfamily	 - 	 - 	"Tryptophan 2,3-dioxygenase; Tryptophan 2,3-dioxygenase.  "
Q#21551 - 	CGI_10011196	superfamily	247757	48	193	6.07E-71	219.1	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#21551 - 	CGI_10011196	superfamily	150200	17	60	1.61E-05	41.8909	cl09685	VMA21 superfamily	C	 - 	VMA21-like domain; This presumed short domain appears to contain two potential transmembrane helices. VMA21 is localised in the ER where it is needed as an accessory factor for assembly of the V0 component of the vacuolar ATPase.
Q#21551 - 	CGI_10011196	superfamily	247724	171	246	0.00027665	39.7152	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21553 - 	CGI_10011198	superfamily	241563	18	50	0.00162157	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21555 - 	CGI_10011200	superfamily	241750	201	581	2.30E-142	420.447	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#21555 - 	CGI_10011200	superfamily	203031	16	73	9.04E-08	49.634	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#21556 - 	CGI_10011201	superfamily	203031	6	63	3.68E-07	44.6264	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#21557 - 	CGI_10011202	superfamily	203136	42	170	5.91E-11	56.9692	cl04867	LRAT superfamily	 - 	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#21560 - 	CGI_10011205	superfamily	241613	1223	1258	4.10E-11	60.6833	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21560 - 	CGI_10011205	superfamily	241613	1182	1218	2.33E-10	58.7574	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21560 - 	CGI_10011205	superfamily	241584	1428	1519	1.64E-09	57.5063	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21560 - 	CGI_10011205	superfamily	241613	1378	1413	5.50E-09	54.5202	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21560 - 	CGI_10011205	superfamily	241613	1331	1368	1.12E-07	51.0534	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21560 - 	CGI_10011205	superfamily	241613	1064	1098	1.48E-06	47.5866	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21560 - 	CGI_10011205	superfamily	241613	1283	1314	0.000227532	41.0382	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#21560 - 	CGI_10011205	superfamily	241584	1604	1672	0.000566991	40.5575	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21560 - 	CGI_10011205	superfamily	241584	1904	1986	0.00792425	37.0907	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21560 - 	CGI_10011205	superfamily	214531	789	829	2.61E-09	55.6857	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21560 - 	CGI_10011205	superfamily	214531	876	919	6.82E-08	51.4485	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#21560 - 	CGI_10011205	superfamily	215683	851	893	8.51E-07	48.3203	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#21563 - 	CGI_10003698	superfamily	247741	47	70	0.00862582	32.0801	cl17187	Aldolase_Class_I superfamily	C	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#21564 - 	CGI_10003699	superfamily	218312	120	217	1.86E-37	132.154	cl04824	Cwf_Cwc_15 superfamily	N	 - 	"Cwf15/Cwc15 cell cycle control protein; This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing."
Q#21564 - 	CGI_10003699	superfamily	218312	1	51	1.20E-16	74.7594	cl04824	Cwf_Cwc_15 superfamily	C	 - 	"Cwf15/Cwc15 cell cycle control protein; This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing."
Q#21565 - 	CGI_10003700	superfamily	245201	356	640	8.35E-144	422.208	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21565 - 	CGI_10003700	superfamily	243115	64	196	3.24E-40	143.253	cl02623	WIF superfamily	 - 	 - 	"WIF domain; The WIF domain is found in the RYK tyrosine kinase receptors and WIF, the Wnt-inhibitory- factor. The domain is extracellular and contains two conserved cysteines that may form a disulphide bridge. This domain is Wnt binding in WIF, and it has been suggested that RYK may also bind to Wnt. The WIF domain is a member of the immunoglobulin superfamily, and it comprises nine beta-strands and two alpha-helices, with two of the beta-strands (6 and 9) interrupted by four and six residues of irregular secondary structure, respectively. Considering that the activity of Wnts depends on the presence of a palmitoylated cysteine residue in their amino-terminal polypeptide segment, Wnt proteins are lipid-modified and can act as stem cell growth factors, it is likely that the WIF domain recognises and binds to Wnts that have been activated by palmitoylation and that the recognition of palmitoylated Wnts by WIF-1 is effected by its WIF domain rather than by its EGF domains. A strong binding affinity for palmitoylated cysteine residues would further explain the remarkably high affinity of human WIF-1 not only for mammalian Wnts, but also for Wnts from Xenopus and Drosophila."
Q#21566 - 	CGI_10003701	superfamily	217473	121	344	1.66E-27	112.073	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#21567 - 	CGI_10004874	superfamily	248232	229	443	1.48E-40	153.991	cl17678	MRS6 superfamily	C	 - 	"RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational modification, protein turnover, chaperones]"
Q#21567 - 	CGI_10004874	superfamily	248232	4	66	2.44E-12	68.2728	cl17678	MRS6 superfamily	C	 - 	"RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational modification, protein turnover, chaperones]"
Q#21568 - 	CGI_10004875	superfamily	222150	397	422	0.00506328	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21568 - 	CGI_10004875	superfamily	222150	425	448	0.00586633	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21568 - 	CGI_10004875	superfamily	218108	527	694	0.0061117	37.5629	cl04540	CITED superfamily	C	 - 	"CITED; CITED, CBP/p300-interacting transactivator with ED-rich tail, are characterized by a conserved 32-amino acid sequence at the C-terminus. CITED proteins do not bind DNA directly and are thought to function as transcriptional co-activators."
Q#21570 - 	CGI_10004877	superfamily	245847	16	81	0.000751628	34.4546	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#21571 - 	CGI_10004879	superfamily	245213	19	47	0.000633511	36.0754	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21571 - 	CGI_10004879	superfamily	245847	55	175	3.42E-10	55.2553	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#21572 - 	CGI_10001615	superfamily	217574	1	131	1.86E-43	148.91	cl04089	eRF1_1 superfamily	 - 	 - 	"eRF1 domain 1; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#21572 - 	CGI_10001615	superfamily	217575	136	268	2.22E-37	132.783	cl04090	eRF1_2 superfamily	 - 	 - 	"eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#21572 - 	CGI_10001615	superfamily	146221	271	370	1.43E-36	129.595	cl04091	eRF1_3 superfamily	 - 	 - 	"eRF1 domain 3; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#21573 - 	CGI_10001616	superfamily	243091	141	259	1.88E-10	58.4999	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#21573 - 	CGI_10001616	superfamily	222150	394	418	3.87E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21573 - 	CGI_10001616	superfamily	222150	365	389	0.000145543	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21573 - 	CGI_10001616	superfamily	246975	352	373	0.00404293	35.4005	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#21574 - 	CGI_10015975	superfamily	241574	320	548	1.78E-98	302.197	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21575 - 	CGI_10015976	superfamily	247858	18	150	2.35E-19	80.5098	cl17304	2OG-FeII_Oxy_3 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#21577 - 	CGI_10015978	superfamily	247755	1106	1333	1.20E-145	448.142	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#21577 - 	CGI_10015978	superfamily	247755	469	706	2.53E-145	446.986	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#21577 - 	CGI_10015978	superfamily	216049	216	422	1.86E-53	190.575	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#21577 - 	CGI_10015978	superfamily	216049	790	1059	3.19E-46	169.389	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#21577 - 	CGI_10015978	superfamily	190308	1403	1531	5.43E-08	54.2471	cl18163	Fringe superfamily	C	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#21580 - 	CGI_10015981	superfamily	247769	46	102	1.05E-09	53.4973	cl17215	HDc superfamily	C	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#21581 - 	CGI_10015982	superfamily	241619	85	121	0.00300041	36.2602	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#21582 - 	CGI_10015983	superfamily	242406	14	88	5.99E-08	47.2009	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#21584 - 	CGI_10015985	superfamily	243082	647	782	1.88E-31	124.133	cl02553	Peptidase_C19 superfamily	N	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#21584 - 	CGI_10015985	superfamily	243082	477	564	1.92E-06	48.6335	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#21584 - 	CGI_10015985	superfamily	243082	292	404	2.72E-06	48.8111	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#21585 - 	CGI_10015986	superfamily	241900	19	177	1.22E-11	63.39	cl00490	EEP superfamily	C	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#21586 - 	CGI_10015987	superfamily	217249	192	335	3.28E-80	243.683	cl03742	Prp18 superfamily	 - 	 - 	"Prp18 domain; The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles."
Q#21586 - 	CGI_10015987	superfamily	207680	85	114	1.15E-08	50.4343	cl02632	PRP4 superfamily	 - 	 - 	pre-mRNA processing factor 4 (PRP4) like; This small domain is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing.
Q#21587 - 	CGI_10015988	superfamily	217473	172	342	8.76E-26	104.754	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#21589 - 	CGI_10015990	superfamily	245852	95	289	1.20E-32	125.927	cl12050	TraB superfamily	C	 - 	"TraB family; pAD1 is a hemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans, suggesting that members of the TraB family have some more general function. This family also includes the bacterial GumN protein. The family has a conserved GXXH motif close to the N-terminus, a conserved glutamate and a conserved arginine that may be catalytic. The family also includes a second conserved GXXH motif near the C-terminus."
Q#21591 - 	CGI_10015992	superfamily	218118	40	120	5.85E-16	73.032	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#21592 - 	CGI_10015993	superfamily	241758	15	167	5.76E-27	99.7518	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#21594 - 	CGI_10003268	superfamily	150423	11	129	1.24E-49	156.639	cl10732	Med10 superfamily	 - 	 - 	"Transcription factor subunit Med10 of Mediator complex; Med10 is one of the protein subunits of the Mediator complex, tethered to Rgr1 protein. The Mediator complex is required for the transcription of most RNA polymerase II (Pol II)-transcribed genes. Med10 specifically mediates basal-level HIS4 transcription via Gcn4, and, additionally, there is a putative requirement for Med10 in Bas2-mediated transcription. Med10 is part of the middle region of Mediator."
Q#21595 - 	CGI_10003269	superfamily	116878	112	222	1.25E-26	100.829	cl17958	TIM21 superfamily	N	 - 	TIM21; TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane.
Q#21596 - 	CGI_10003270	superfamily	241606	21	128	5.40E-45	153.986	cl00096	IRF superfamily	 - 	 - 	Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
Q#21596 - 	CGI_10003270	superfamily	220732	254	414	4.32E-24	98.4993	cl11061	IRF-3 superfamily	 - 	 - 	"Interferon-regulatory factor 3; This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein. These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1). Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection."
Q#21597 - 	CGI_10003271	superfamily	245596	54	283	2.07E-44	155.717	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#21600 - 	CGI_10002254	superfamily	216653	142	230	5.12E-20	83.0302	cl08331	Na_Ca_ex superfamily	C	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#21602 - 	CGI_10002256	superfamily	241754	5	156	2.51E-46	157.473	cl00286	Motor_domain superfamily	NC	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#21603 - 	CGI_10004906	superfamily	245847	335	474	7.25E-08	51.3492	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#21604 - 	CGI_10004907	superfamily	248097	34	163	8.98E-13	61.127	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21605 - 	CGI_10004908	superfamily	248097	30	159	3.39E-13	62.2826	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21606 - 	CGI_10004909	superfamily	241568	40	76	3.32E-07	46.6872	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21607 - 	CGI_10004910	superfamily	243051	1	70	1.53E-06	45.0614	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#21609 - 	CGI_10004912	superfamily	247856	93	142	0.000113654	37.1421	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21610 - 	CGI_10011113	superfamily	215872	8	86	1.99E-11	54.8922	cl08261	Ribosomal_L6 superfamily	 - 	 - 	Ribosomal protein L6; Ribosomal protein L6.  
Q#21614 - 	CGI_10011117	superfamily	242268	136	598	3.13E-176	510.321	cl01046	Glyco_hydro_1 superfamily	 - 	 - 	Glycosyl hydrolase family 1; Glycosyl hydrolase family 1.  
Q#21614 - 	CGI_10011117	superfamily	242268	2	111	5.99E-34	133.211	cl01046	Glyco_hydro_1 superfamily	N	 - 	Glycosyl hydrolase family 1; Glycosyl hydrolase family 1.  
Q#21615 - 	CGI_10011118	superfamily	243119	78	129	4.73E-08	45.8876	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21615 - 	CGI_10011118	superfamily	243119	21	69	1.26E-05	39.3393	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21616 - 	CGI_10011119	superfamily	243119	72	121	0.000214425	36.653	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21617 - 	CGI_10011120	superfamily	243119	25	73	2.13E-06	40.505	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21618 - 	CGI_10011121	superfamily	241703	5	308	2.98E-116	340.776	cl00226	nuc_hydro superfamily	 - 	 - 	"nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity.  This group contains eukaryotic, bacterial and archeal proteins similar to the inosine-uridine preferring nucleoside hydrolase from Crithidia fasciculata,  the xanthosine-inosine-uridine-adenosine-preferring nucleoside hydrolase RihC from Salmonella enterica serovar Typhimurium, the purine-specific  inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax and, pyrimidine-specific uridine-cytidine preferring nucleoside hydrolases such as URH1 from Saccharomyces cerevisiae, RihA and RihB from Escherichia coli. Nucleoside hydrolases are of interest as a target for antiprotozoan drugs as, no nucleoside hydrolase activity or genes encoding these enzymes have been detected in humans and, parasitic protozoans lack de novo purine synthesis relying on nucleoside hydrolase to scavenge purine and/or pyrimidines from the environment."
Q#21620 - 	CGI_10001460	superfamily	241563	75	115	2.44E-08	50.9408	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21621 - 	CGI_10001461	superfamily	241563	72	112	1.73E-07	48.2444	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21622 - 	CGI_10022265	superfamily	241563	96	136	0.000945709	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21625 - 	CGI_10022268	superfamily	241622	1073	1114	0.00740493	36.2028	cl00117	PDZ superfamily	N	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#21626 - 	CGI_10022269	superfamily	247809	659	859	1.03E-29	117.762	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#21628 - 	CGI_10022271	superfamily	246669	772	871	2.02E-12	65.5511	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#21628 - 	CGI_10022271	superfamily	204692	615	724	7.83E-33	124.763	cl13124	DUF3250 superfamily	 - 	 - 	Protein of unknown function (DUF3250); This family of proteins represents a protein with unknown function. It may be the C2 domain from KIAA1005 however this cannot be confirmed.
Q#21629 - 	CGI_10022272	superfamily	247724	40	407	7.80E-172	486.264	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21631 - 	CGI_10022274	superfamily	243238	105	570	1.35E-136	414.743	cl02915	Voltage_gated_ClC superfamily	 - 	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#21631 - 	CGI_10022274	superfamily	246936	687	743	1.15E-18	82.6852	cl15354	CBS_pair superfamily	N	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#21632 - 	CGI_10022275	superfamily	242664	179	257	0.00841561	35.9932	cl01709	PBP2_NikA_DppA_OppA_like superfamily	NC	 - 	"The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis.  Similar to the ABC-type dipeptide and oligopeptide import systems, nickel transporter is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, which is the initial nickel receptor that controls the chemotactic response away from nickel.  Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine.  The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.  Besides transport proteins, the PBP2 superfamily includes the ligand binding domains of ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction."
Q#21633 - 	CGI_10022276	superfamily	244888	37	338	1.40E-73	233.501	cl08282	Acyl_transf_1 superfamily	 - 	 - 	Acyl transferase domain; Acyl transferase domain.  
Q#21634 - 	CGI_10022277	superfamily	221056	1	943	0	628.765	cl12819	Med24_N superfamily	 - 	 - 	"Mediator complex subunit 24 N-terminal; This subunit of the Mediator complex appears to be conserved only from insects to humans. It is essential for correct retinal development in fish. Subunit composition of the mediator contributes to the control of differentiation in the vertebrate CNS as there are divergent functions of the mediator subunits Crsp34/Med27, Trap100/Med24, and Crsp150/Med14."
Q#21636 - 	CGI_10022279	superfamily	245814	40	126	0.00393971	34.7216	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21639 - 	CGI_10022282	superfamily	245306	92	186	2.79E-19	79.1667	cl10465	Peptidase_S24_S26 superfamily	 - 	 - 	"The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases."
Q#21640 - 	CGI_10022283	superfamily	247792	18	66	1.53E-08	52.0628	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#21640 - 	CGI_10022283	superfamily	248097	371	406	0.000171684	40.7114	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21641 - 	CGI_10022284	superfamily	219502	227	431	4.93E-65	212.305	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#21641 - 	CGI_10022284	superfamily	219507	129	208	4.18E-06	44.9227	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#21641 - 	CGI_10022284	superfamily	201962	61	115	0.00237932	36.1996	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#21642 - 	CGI_10022285	superfamily	247792	18	66	7.28E-06	42.4328	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#21643 - 	CGI_10022286	superfamily	247736	85	157	0.0030132	34.2274	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#21644 - 	CGI_10022287	superfamily	192997	25	171	4.84E-27	107.282	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#21645 - 	CGI_10022288	superfamily	242406	1	71	1.47E-07	45.2749	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#21647 - 	CGI_10022290	superfamily	247692	47	540	4.36E-45	166.256	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#21649 - 	CGI_10002477	superfamily	217473	4	284	8.90E-27	110.147	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#21650 - 	CGI_10002478	superfamily	241792	92	178	8.08E-24	91.7641	cl00332	Ribosomal_S11 superfamily	 - 	 - 	Ribosomal protein S11; Ribosomal protein S11.  
Q#21652 - 	CGI_10001664	superfamily	241563	15	59	0.000585486	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21654 - 	CGI_10001868	superfamily	220635	24	504	4.88E-161	477.026	cl12380	DUF2151 superfamily	N	 - 	"Cell cycle and development regulator; This is a set of proteins conserved from worms to humans. The proteins are a PAN GU kinase substrate, Mat89Bb, essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells."
Q#21655 - 	CGI_10001869	superfamily	247724	221	381	9.93E-06	44.3696	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21655 - 	CGI_10001869	superfamily	242902	25	104	6.88E-15	71.509	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#21656 - 	CGI_10008643	superfamily	243035	13	76	6.61E-15	64.5633	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#21657 - 	CGI_10008644	superfamily	243035	282	390	2.04E-26	101.928	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#21657 - 	CGI_10008644	superfamily	241568	213	265	0.00234481	35.9016	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21657 - 	CGI_10008644	superfamily	216533	105	152	0.000142482	39.5344	cl09264	HTH_Tnp_Tc3_2 superfamily	C	 - 	"Transposase; Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements."
Q#21659 - 	CGI_10008646	superfamily	243051	307	467	6.39E-27	105.538	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#21659 - 	CGI_10008646	superfamily	245213	31	64	0.000358664	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21659 - 	CGI_10008646	superfamily	245213	267	299	0.00521983	34.9198	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21661 - 	CGI_10008648	superfamily	216347	206	623	3.15E-128	388.047	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#21662 - 	CGI_10008649	superfamily	217473	96	216	1.52E-09	57.7601	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#21663 - 	CGI_10007059	superfamily	246031	218	336	5.81E-41	144.605	cl12567	Beta-Casp superfamily	 - 	 - 	Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.
Q#21663 - 	CGI_10007059	superfamily	203663	349	390	2.52E-10	56.7291	cl06522	RMMBL superfamily	 - 	 - 	RNA-metabolising metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism.
Q#21663 - 	CGI_10007059	superfamily	241867	34	157	4.16E-09	55.2522	cl00446	Lactamase_B superfamily	C	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#21664 - 	CGI_10007060	superfamily	218375	51	355	2.45E-92	284.762	cl09349	IFRD superfamily	 - 	 - 	"Interferon-related developmental regulator (IFRD); Interferon-related developmental regulator (IFRD1) is the human homologue of the rat early response protein PC4 and its murine homologue TIS7. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary to muscle differentiation and that it might have a role in signal transduction. This family also contains IFRD2 and its murine equivalent SKMc15 which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis."
Q#21664 - 	CGI_10007060	superfamily	203103	400	451	2.39E-14	67.8005	cl04790	IFRD_C superfamily	 - 	 - 	Interferon-related protein conserved region; Family of proteins thought to be involved in regulating gene activity in the proliferative and/or differentiative pathways induced by NGF.
Q#21665 - 	CGI_10007061	superfamily	245201	688	935	7.11E-116	358.772	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21665 - 	CGI_10007061	superfamily	247038	257	340	1.15E-11	62.4721	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#21665 - 	CGI_10007061	superfamily	247038	350	426	8.70E-10	56.8489	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#21665 - 	CGI_10007061	superfamily	247042	77	214	0.00346089	39.6509	cl15693	Sema superfamily	N	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#21666 - 	CGI_10007062	superfamily	245201	525	781	1.10E-118	362.561	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21666 - 	CGI_10007062	superfamily	247042	32	229	4.55E-16	79.6822	cl15693	Sema superfamily	C	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#21666 - 	CGI_10007062	superfamily	243104	276	317	4.13E-09	53.7029	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#21668 - 	CGI_10007064	superfamily	245847	4	71	0.00011107	36.3264	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#21669 - 	CGI_10002466	superfamily	245213	117	151	0.00273852	34.9198	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21671 - 	CGI_10013211	superfamily	191128	16	117	5.90E-17	71.0308	cl04846	Ninjurin superfamily	 - 	 - 	Ninjurin; Ninjurin (nerve injury-induced protein) is involved in nerve regeneration and in the formation and function in some tissues.
Q#21673 - 	CGI_10013213	superfamily	241599	12	69	7.06E-17	71.8908	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#21674 - 	CGI_10013214	superfamily	243119	110	160	7.70E-05	39.7346	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21674 - 	CGI_10013214	superfamily	243119	248	300	0.00060644	37.0382	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21674 - 	CGI_10013214	superfamily	243119	186	225	0.000991093	36.2678	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#21675 - 	CGI_10013215	superfamily	221135	186	344	1.06E-13	68.5526	cl13079	PI31_Prot_N superfamily	 - 	 - 	PI31 proteasome regulator N-terminal; PI31 is a regulatory subunit of the immuno-proteasome which is an inhibitor of the 20 S proteasome in vitro.PI31 is also an F-box protein Fbxo7.Skp1 binding partner which requires an N terminal FP domain in both proteins for the interaction to occur via the FP beta sheets. The structure of PI31 FP domain contains a novel alpha/beta-fold and two intermolecular contact surfaces. This is the N-terminal domain of the members.
Q#21675 - 	CGI_10013215	superfamily	243074	360	405	1.97E-08	50.9681	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#21677 - 	CGI_10013217	superfamily	241648	213	263	1.48E-16	74.3314	cl00158	ZnF_GATA superfamily	 - 	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#21677 - 	CGI_10013217	superfamily	241648	267	300	3.17E-12	62.005	cl00158	ZnF_GATA superfamily	C	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#21679 - 	CGI_10013220	superfamily	246669	269	372	1.84E-23	94.0558	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#21679 - 	CGI_10013220	superfamily	246669	121	245	1.22E-24	97.7109	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#21680 - 	CGI_10013221	superfamily	215869	75	459	4.10E-84	265.145	cl10564	SecY superfamily	 - 	 - 	SecY translocase; SecY translocase.  
Q#21680 - 	CGI_10013221	superfamily	204513	40	74	1.82E-13	64.7519	cl11188	Plug_translocon superfamily	 - 	 - 	Plug domain of Sec61p; The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74.
Q#21681 - 	CGI_10013222	superfamily	247743	40	123	7.47E-08	50.6075	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21683 - 	CGI_10013224	superfamily	245201	2	140	7.93E-18	77.5768	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21684 - 	CGI_10013225	superfamily	218109	257	289	6.98E-09	52.7129	cl12292	Gly_transf_sug superfamily	N	 - 	"Glycosyltransferase sugar-binding region containing DXD motif; The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases."
Q#21685 - 	CGI_10013226	superfamily	246597	3	262	1.26E-169	487.879	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#21686 - 	CGI_10013227	superfamily	241574	449	515	6.28E-30	116.531	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21687 - 	CGI_10013228	superfamily	241574	1	105	1.12E-34	129.628	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21687 - 	CGI_10013228	superfamily	241574	170	342	5.84E-12	64.1441	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21688 - 	CGI_10013229	superfamily	241574	485	713	2.15E-98	311.057	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21688 - 	CGI_10013229	superfamily	241574	778	976	1.27E-17	83.0189	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21695 - 	CGI_10023882	superfamily	245864	57	504	2.01E-126	379.7	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#21699 - 	CGI_10023886	superfamily	247684	83	251	2.10E-07	49.5095	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#21699 - 	CGI_10023886	superfamily	202746	225	460	3.57E-60	198.673	cl08402	Hexokinase_2 superfamily	 - 	 - 	Hexokinase; Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains.
Q#21700 - 	CGI_10023887	superfamily	241640	28	302	2.89E-65	207.129	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#21701 - 	CGI_10023888	superfamily	248097	103	226	1.70E-15	69.6014	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21702 - 	CGI_10023889	superfamily	248097	163	277	2.12E-17	75.7646	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21703 - 	CGI_10023890	superfamily	247792	18	68	1.23E-06	46.2848	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#21704 - 	CGI_10023891	superfamily	245201	8	307	0	562.197	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21707 - 	CGI_10023894	superfamily	245213	292	329	1.25E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21707 - 	CGI_10023894	superfamily	245213	139	176	1.91E-05	43.009	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21707 - 	CGI_10023894	superfamily	245213	178	214	5.96E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21707 - 	CGI_10023894	superfamily	245213	570	599	0.000126817	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21707 - 	CGI_10023894	superfamily	245213	216	252	0.00134056	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21708 - 	CGI_10023895	superfamily	247723	16	88	3.15E-46	155.917	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21708 - 	CGI_10023895	superfamily	217936	221	359	3.65E-07	48.826	cl18432	Arv1 superfamily	N	 - 	Arv1-like family; Arv1 is a transmembrane protein with potential zinc-binding motifs. ARV1 is a novel mediator of eukaryotic sterol homeostasis.
Q#21709 - 	CGI_10023896	superfamily	242025	69	160	6.65E-26	96.5177	cl00682	Alba superfamily	 - 	 - 	Alba; Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.
Q#21710 - 	CGI_10023897	superfamily	245213	257	292	2.13E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	332	367	2.28E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	178	216	6.62E-06	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	512	547	7.71E-06	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	703	739	1.39E-05	43.7794	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	294	329	4.13E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	632	663	5.16E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	226	254	6.43E-05	41.8534	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	407	443	8.82E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	665	700	0.000137297	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	372	405	0.000169943	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	245213	550	586	0.000829362	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21710 - 	CGI_10023897	superfamily	214565	751	822	7.54E-07	48.3277	cl18312	VWC_out superfamily	 - 	 - 	von Willebrand factor (vWF) type C domain; von Willebrand factor (vWF) type C domain.  
Q#21711 - 	CGI_10023898	superfamily	247856	101	157	1.17E-16	74.8917	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21711 - 	CGI_10023898	superfamily	247856	193	255	1.67E-14	68.7285	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21711 - 	CGI_10023898	superfamily	247856	28	89	8.47E-14	66.8025	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21711 - 	CGI_10023898	superfamily	247856	305	366	1.70E-12	62.9505	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21711 - 	CGI_10023898	superfamily	247856	361	423	2.91E-11	59.4837	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21711 - 	CGI_10023898	superfamily	247856	435	490	1.17E-07	49.0833	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21711 - 	CGI_10023898	superfamily	247856	269	325	1.95E-07	48.3129	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21712 - 	CGI_10023899	superfamily	215754	27	119	1.92E-23	91.9312	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21712 - 	CGI_10023899	superfamily	215754	130	224	2.87E-23	91.546	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21712 - 	CGI_10023899	superfamily	215754	227	288	1.65E-12	61.8856	cl02813	Mito_carr superfamily	C	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21714 - 	CGI_10023901	superfamily	247856	98	159	7.23E-07	43.3053	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21714 - 	CGI_10023901	superfamily	247856	19	82	7.65E-05	37.9125	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21715 - 	CGI_10023902	superfamily	243053	229	462	1.39E-71	234.454	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#21715 - 	CGI_10023902	superfamily	241566	577	626	4.60E-16	73.6803	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#21715 - 	CGI_10023902	superfamily	243067	75	195	3.44E-09	55.1112	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#21715 - 	CGI_10023902	superfamily	247856	509	559	5.08E-06	44.8461	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21717 - 	CGI_10023904	superfamily	243095	54	249	1.03E-55	193.457	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#21718 - 	CGI_10023905	superfamily	242876	1	122	1.12E-57	177.546	cl02092	Clat_adaptor_s superfamily	 - 	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#21719 - 	CGI_10023906	superfamily	245605	47	332	6.52E-179	505.976	cl11409	RNAP_RPB11_RPB3 superfamily	 - 	 - 	"RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts."
Q#21719 - 	CGI_10023906	superfamily	245814	379	436	6.86E-08	49.7951	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21720 - 	CGI_10023907	superfamily	245814	33	93	3.14E-09	55.1879	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21720 - 	CGI_10023907	superfamily	245814	416	481	4.56E-08	51.7211	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21720 - 	CGI_10023907	superfamily	245814	130	181	0.004084	36.6983	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21720 - 	CGI_10023907	superfamily	245201	696	972	2.85E-113	352.537	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21720 - 	CGI_10023907	superfamily	245814	494	574	8.74E-14	68.686	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21720 - 	CGI_10023907	superfamily	245814	309	395	1.86E-11	62.0273	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21720 - 	CGI_10023907	superfamily	245814	235	291	0.000109647	41.6117	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21721 - 	CGI_10023908	superfamily	247743	285	451	2.12E-20	88.3571	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21721 - 	CGI_10023908	superfamily	199226	26	58	0.000108301	40.1104	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#21722 - 	CGI_10023909	superfamily	243072	83	205	2.68E-30	109.781	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21723 - 	CGI_10023910	superfamily	222500	110	320	3.03E-06	46.2165	cl16546	DUF4239 superfamily	 - 	 - 	Protein of unknown function (DUF4239); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 254 and 270 amino acids in length.
Q#21724 - 	CGI_10023911	superfamily	245814	160	212	0.000209456	40.1651	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21724 - 	CGI_10023911	superfamily	216981	314	469	1.03E-14	71.795	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#21725 - 	CGI_10023912	superfamily	247723	173	265	1.28E-44	153.577	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21725 - 	CGI_10023912	superfamily	207717	83	159	2.59E-43	149.355	cl02755	LAM superfamily	 - 	 - 	"LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes."
Q#21725 - 	CGI_10023912	superfamily	193374	526	544	0.000470813	38.3012	cl15152	SUZ-C superfamily	N	 - 	SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.
Q#21727 - 	CGI_10023914	superfamily	222269	74	293	4.83E-36	133.603	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#21728 - 	CGI_10023915	superfamily	238191	26	498	2.32E-123	373.591	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#21732 - 	CGI_10023919	superfamily	241599	117	175	2.03E-18	76.128	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#21734 - 	CGI_10023921	superfamily	247684	164	608	0	549.201	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#21735 - 	CGI_10023922	superfamily	247725	355	462	2.32E-39	139.777	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#21735 - 	CGI_10023922	superfamily	247725	183	300	3.79E-39	139.504	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#21741 - 	CGI_10011506	superfamily	243161	3	60	4.23E-12	63.9525	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#21743 - 	CGI_10011508	superfamily	217293	22	120	5.78E-16	71.8951	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#21743 - 	CGI_10011508	superfamily	202474	127	190	0.000303357	38.7889	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#21744 - 	CGI_10011509	superfamily	207662	173	255	7.84E-36	128.439	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#21744 - 	CGI_10011509	superfamily	245599	326	491	5.98E-23	95.3674	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#21745 - 	CGI_10011510	superfamily	241574	76	139	1.38E-11	57.6792	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21746 - 	CGI_10011511	superfamily	241758	5	199	4.78E-82	247.075	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#21747 - 	CGI_10011512	superfamily	216371	21	369	2.42E-93	288.183	cl18365	ERG4_ERG24 superfamily	 - 	 - 	Ergosterol biosynthesis ERG4/ERG24 family; Ergosterol biosynthesis ERG4/ERG24 family.  
Q#21748 - 	CGI_10011513	superfamily	241564	224	290	3.27E-26	99.6475	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#21748 - 	CGI_10011513	superfamily	241564	42	108	1.41E-16	73.4539	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#21748 - 	CGI_10011513	superfamily	247792	328	373	1.22E-11	59.3156	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#21751 - 	CGI_10003379	superfamily	243077	58	106	9.83E-11	57.1701	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#21751 - 	CGI_10003379	superfamily	244850	210	274	7.02E-17	74.9563	cl08096	DUF1992 superfamily	 - 	 - 	Domain of unknown function (DUF1992); This family of proteins are functionally uncharacterized.
Q#21752 - 	CGI_10003380	superfamily	245815	77	553	0	749.646	cl11961	ALDH-SF superfamily	 - 	 - 	"NAD(P)+-dependent aldehyde dehydrogenase superfamily; The aldehyde dehydrogenase superfamily (ALDH-SF) of  NAD(P)+-dependent enzymes, in general, oxidize a wide range of  endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an  important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase.  Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group."
Q#21753 - 	CGI_10003381	superfamily	243092	11	360	6.88E-25	105.11	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21753 - 	CGI_10003381	superfamily	243092	502	749	3.33E-16	78.5308	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21754 - 	CGI_10002829	superfamily	241596	188	244	5.49E-10	53.3719	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#21757 - 	CGI_10018961	superfamily	241563	86	126	2.33E-06	45.1628	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21757 - 	CGI_10018961	superfamily	241563	32	77	0.000392874	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21757 - 	CGI_10018961	superfamily	110440	548	575	0.00705548	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#21758 - 	CGI_10018962	superfamily	243092	13	217	2.15E-32	119.747	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21759 - 	CGI_10018963	superfamily	245835	85	207	0.000391002	40.3143	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#21759 - 	CGI_10018963	superfamily	241563	18	50	0.000464865	37.7019	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21760 - 	CGI_10018964	superfamily	247805	499	657	2.90E-19	87.3928	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#21760 - 	CGI_10018964	superfamily	247805	1291	1438	2.75E-17	81.6148	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#21760 - 	CGI_10018964	superfamily	247905	686	872	4.03E-11	63.0256	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#21760 - 	CGI_10018964	superfamily	247905	1560	1658	5.40E-07	50.3141	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#21760 - 	CGI_10018964	superfamily	214946	1765	2077	1.69E-86	287.718	cl15345	Sec63 superfamily	 - 	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#21760 - 	CGI_10018964	superfamily	214946	1064	1233	1.10E-37	146.349	cl15345	Sec63 superfamily	N	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#21760 - 	CGI_10018964	superfamily	214946	983	1058	2.12E-17	84.3323	cl15345	Sec63 superfamily	C	 - 	"Sec63 Brl domain; This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases."
Q#21765 - 	CGI_10018969	superfamily	247805	299	503	2.72E-93	292.466	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#21765 - 	CGI_10018969	superfamily	247905	514	645	1.34E-36	134.673	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#21766 - 	CGI_10018970	superfamily	245716	120	141	1.96E-06	44.5425	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#21766 - 	CGI_10018970	superfamily	245716	24	44	0.000197459	38.7645	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#21766 - 	CGI_10018970	superfamily	245674	212	262	0.00327344	35.3426	cl11531	DUF904 superfamily	 - 	 - 	Protein of unknown function (DUF904); This family consists of several bacterial and archaeal hypothetical proteins of unknown function.
Q#21767 - 	CGI_10018971	superfamily	247792	15	63	1.81E-06	45.5144	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#21767 - 	CGI_10018971	superfamily	243054	193	309	0.00115292	39.3512	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#21767 - 	CGI_10018971	superfamily	241563	164	195	0.00393077	35.7759	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21768 - 	CGI_10018972	superfamily	245819	94	263	4.39E-66	206.276	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#21768 - 	CGI_10018972	superfamily	219526	38	81	0.000892447	38.3691	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#21769 - 	CGI_10018973	superfamily	217473	1	130	2.31E-20	90.1169	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#21770 - 	CGI_10018974	superfamily	248097	86	193	1.55E-23	91.5578	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#21775 - 	CGI_10018979	superfamily	192535	63	342	6.99E-08	51.8278	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#21776 - 	CGI_10018980	superfamily	246031	1	73	3.70E-10	52.9272	cl12567	Beta-Casp superfamily	C	 - 	Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.
Q#21779 - 	CGI_10019489	superfamily	247684	17	201	6.23E-17	78.0143	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#21781 - 	CGI_10019491	superfamily	243058	463	577	3.90E-12	65.7987	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#21781 - 	CGI_10019491	superfamily	220736	1159	1282	2.37E-41	150.923	cl11068	PTEN_C2 superfamily	 - 	 - 	"C2 domain of PTEN tumour-suppressor protein; This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane."
Q#21781 - 	CGI_10019491	superfamily	246908	1940	2010	9.18E-28	111.365	cl15255	SH2 superfamily	C	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#21781 - 	CGI_10019491	superfamily	243689	21	101	1.29E-07	51.0901	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#21781 - 	CGI_10019491	superfamily	241574	1051	1120	3.28E-06	47.7387	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21781 - 	CGI_10019491	superfamily	243689	132	199	6.08E-05	43.3861	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#21782 - 	CGI_10019492	superfamily	221788	505	668	3.77E-57	197.409	cl15106	Vps8 superfamily	 - 	 - 	"Golgi CORVET complex core vacuolar protein 8; Vps8 is one of the Golgi complex components necessary for vacuolar sorting. Eukaryotic cells contain a highly dynamic endo-membrane system, in which individual organelles keep their identity despite continuous vesicle generation and fusion. Vesicles that bud from a donor membrane are targeted and delivered to each individual organelle, where they release their cargo after fusion with the acceptor membrane. Vps8 is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering). Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8 is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes. Late endosomes form intralumenal vesicles, and the resulting multivesicular bodies fuse with the vacuole to release their cargoes."
Q#21782 - 	CGI_10019492	superfamily	243092	86	166	2.30E-06	49.6408	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21783 - 	CGI_10019493	superfamily	207654	268	328	9.15E-20	84.0314	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#21783 - 	CGI_10019493	superfamily	207654	335	406	1.42E-16	75.1718	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#21783 - 	CGI_10019493	superfamily	207654	528	593	1.48E-14	69.3938	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#21783 - 	CGI_10019493	superfamily	207654	452	518	1.54E-08	52.0598	cl02574	Annexin superfamily	 - 	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#21785 - 	CGI_10019495	superfamily	241584	583	677	1.24E-18	83.6999	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21785 - 	CGI_10019495	superfamily	245814	496	560	1.14E-12	65.9735	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21785 - 	CGI_10019495	superfamily	241584	817	906	2.40E-12	65.5955	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21785 - 	CGI_10019495	superfamily	245814	90	187	1.34E-30	118.8	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21785 - 	CGI_10019495	superfamily	245814	197	279	1.21E-20	89.3764	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21785 - 	CGI_10019495	superfamily	245814	300	368	3.92E-20	87.4621	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21785 - 	CGI_10019495	superfamily	245814	387	468	1.16E-12	66.115	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#21785 - 	CGI_10019495	superfamily	241584	712	789	8.64E-07	48.9595	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#21794 - 	CGI_10019504	superfamily	243069	3	46	0.000101796	37.1267	cl02525	Band_7 superfamily	N	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#21797 - 	CGI_10019507	superfamily	241568	763	817	2.85E-11	62.0952	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1938	1992	2.29E-10	59.3988	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1004	1057	2.50E-10	59.3988	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1178	1231	7.90E-10	57.858	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	2347	2401	9.20E-10	57.858	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	2056	2109	2.02E-09	56.7024	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1120	1174	2.19E-09	56.7024	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1294	1347	2.29E-09	56.7024	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	2289	2343	5.22E-09	55.5468	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	2114	2168	5.40E-09	55.5468	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1582	1636	6.82E-09	55.1616	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1817	1874	1.23E-08	54.3912	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1062	1115	2.44E-08	53.6208	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	2172	2226	3.25E-08	53.2356	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1414	1464	3.81E-08	52.8504	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1532	1577	5.05E-08	52.4652	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1352	1407	6.81E-08	52.08	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1996	2051	8.02E-08	52.08	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	945	999	2.33E-07	50.5392	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1236	1289	2.51E-07	50.5392	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	821	877	3.58E-07	50.154	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	2230	2277	3.70E-07	50.154	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	245213	463	499	1.23E-06	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21797 - 	CGI_10019507	superfamily	241568	1879	1934	1.54E-06	48.228	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1652	1694	2.65E-06	47.4576	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	245213	388	423	3.58E-06	46.861	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21797 - 	CGI_10019507	superfamily	241568	1755	1812	3.82E-06	47.0724	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	245213	425	461	6.08E-06	46.0906	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21797 - 	CGI_10019507	superfamily	241568	882	941	8.34E-06	45.9168	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1698	1751	1.03E-05	45.9168	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	245213	313	347	0.000121686	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21797 - 	CGI_10019507	superfamily	245213	349	384	0.000223677	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21797 - 	CGI_10019507	superfamily	241568	705	758	0.000316855	41.2944	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	245213	282	309	0.000746827	39.9274	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21797 - 	CGI_10019507	superfamily	241568	2463	2515	0.00128467	39.3684	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	1484	1516	0.00175112	38.9832	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241568	2418	2459	0.00544905	37.4424	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21797 - 	CGI_10019507	superfamily	241611	508	692	5.92E-39	147.03	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#21797 - 	CGI_10019507	superfamily	219525	98	145	4.14E-10	58.5845	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#21797 - 	CGI_10019507	superfamily	219525	152	199	1.11E-07	51.2657	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#21797 - 	CGI_10019507	superfamily	219525	206	253	1.23E-06	48.1841	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#21798 - 	CGI_10019508	superfamily	241578	76	232	1.62E-36	136.267	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21798 - 	CGI_10019508	superfamily	241568	441	497	4.03E-12	62.8656	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21798 - 	CGI_10019508	superfamily	241568	381	437	1.66E-09	55.5468	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21798 - 	CGI_10019508	superfamily	241568	501	555	6.70E-07	47.8428	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21798 - 	CGI_10019508	superfamily	111397	648	725	9.53E-15	71.2182	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#21798 - 	CGI_10019508	superfamily	111397	565	646	9.52E-10	56.5806	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#21798 - 	CGI_10019508	superfamily	219525	313	362	0.000204454	40.095	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#21800 - 	CGI_10019510	superfamily	245201	11	278	6.39E-86	264.36	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21801 - 	CGI_10019511	superfamily	245201	6	262	1.41E-71	225.455	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21803 - 	CGI_10019513	superfamily	241777	204	349	6.91E-37	137.059	cl00316	Cation_efflux superfamily	N	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#21803 - 	CGI_10019513	superfamily	241777	10	110	7.03E-30	117.028	cl00316	Cation_efflux superfamily	C	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#21804 - 	CGI_10019514	superfamily	247725	62	192	1.04E-79	254.197	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#21804 - 	CGI_10019514	superfamily	216381	326	645	6.54E-101	318.38	cl03136	Oxysterol_BP superfamily	 - 	 - 	Oxysterol-binding protein; Oxysterol-binding protein.  
Q#21806 - 	CGI_10019516	superfamily	241599	356	405	1.19E-07	48.3937	cl00084	homeodomain superfamily	C	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#21807 - 	CGI_10019517	superfamily	243034	451	562	6.14E-12	62.7828	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21807 - 	CGI_10019517	superfamily	243034	343	442	7.68E-08	50.8416	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21807 - 	CGI_10019517	superfamily	243034	165	243	3.17E-07	48.9156	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21807 - 	CGI_10019517	superfamily	243034	531	637	0.000202052	40.056	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21807 - 	CGI_10019517	superfamily	243034	101	194	0.00344488	36.5892	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#21808 - 	CGI_10019518	superfamily	241599	297	353	1.67E-11	59.1793	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#21810 - 	CGI_10019520	superfamily	247068	1148	1235	2.69E-11	62.3309	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21810 - 	CGI_10019520	superfamily	247068	849	924	2.11E-08	53.4714	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21810 - 	CGI_10019520	superfamily	247068	1066	1139	3.98E-07	49.6194	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21810 - 	CGI_10019520	superfamily	247068	229	307	3.64E-06	46.923	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21810 - 	CGI_10019520	superfamily	247068	429	517	0.0004598	40.3746	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21810 - 	CGI_10019520	superfamily	247068	332	417	0.00434701	37.293	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21810 - 	CGI_10019520	superfamily	247068	729	823	0.0098531	36.1374	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21812 - 	CGI_10019522	superfamily	247723	11	90	1.68E-52	173.104	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21812 - 	CGI_10019522	superfamily	247723	96	171	2.01E-48	161.95	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21812 - 	CGI_10019522	superfamily	247723	293	370	1.66E-45	154.314	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21812 - 	CGI_10019522	superfamily	247723	189	269	5.31E-39	136.55	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21813 - 	CGI_10019523	superfamily	247724	3	105	1.43E-25	99.9171	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21814 - 	CGI_10004774	superfamily	243051	90	221	6.83E-16	71.6129	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#21814 - 	CGI_10004774	superfamily	241583	29	81	9.52E-08	49.7778	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#21815 - 	CGI_10004776	superfamily	248264	112	281	8.13E-22	91.5297	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#21821 - 	CGI_10006785	superfamily	247856	428	492	0.00700723	34.8309	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21824 - 	CGI_10006246	superfamily	247038	408	494	1.77E-15	73.7977	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#21824 - 	CGI_10006246	superfamily	247038	311	407	8.12E-15	71.9631	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#21824 - 	CGI_10006246	superfamily	215686	693	793	7.83E-10	58.1976	cl18340	Lipocalin superfamily	N	 - 	"Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel."
Q#21824 - 	CGI_10006246	superfamily	215686	901	1048	3.67E-08	52.8048	cl18340	Lipocalin superfamily	 - 	 - 	"Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel."
Q#21824 - 	CGI_10006246	superfamily	215686	783	865	9.23E-07	48.5677	cl18340	Lipocalin superfamily	N	 - 	"Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel."
Q#21824 - 	CGI_10006246	superfamily	215686	650	718	4.67E-06	46.2565	cl18340	Lipocalin superfamily	N	 - 	"Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel."
Q#21824 - 	CGI_10006246	superfamily	247038	496	564	4.46E-05	43.1745	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#21824 - 	CGI_10006246	superfamily	243104	266	309	9.92E-05	41.3848	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#21824 - 	CGI_10006246	superfamily	243104	96	126	0.00305426	37.1393	cl02601	PSI superfamily	C	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#21825 - 	CGI_10006247	superfamily	247856	65	123	1.82E-10	52.5501	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21825 - 	CGI_10006247	superfamily	247856	7	50	1.87E-07	44.0757	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21826 - 	CGI_10006248	superfamily	224772	99	275	5.41E-39	142.086	cl15312	KptA superfamily	 - 	 - 	"RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]"
Q#21827 - 	CGI_10006249	superfamily	242611	166	435	4.70E-147	438.116	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#21827 - 	CGI_10006249	superfamily	245606	552	758	4.34E-46	163.461	cl11410	TPP_enzyme_PYR superfamily	 - 	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#21828 - 	CGI_10004126	superfamily	245213	63	99	5.81E-09	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21828 - 	CGI_10004126	superfamily	245213	32	61	5.49E-08	44.935	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#21830 - 	CGI_10008516	superfamily	242907	95	157	4.18E-13	61.9322	cl02154	YL1_C superfamily	N	 - 	YL1 nuclear protein C-terminal domain; This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins.
Q#21832 - 	CGI_10008518	superfamily	243092	9	300	2.16E-18	82.768	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21837 - 	CGI_10008523	superfamily	244658	85	233	8.83E-45	150.222	cl07248	CDC37_M superfamily	 - 	 - 	"Cdc37 Hsp90 binding domain; Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the Hsp90 chaperone (Heat shocked protein 90) binding domain of Cdc37. It is found between the N terminal Cdc37 domain pfam03234, which is predominantly involved in kinase binding, and the C terminal domain of Cdc37 pfam08564 whose function is unclear."
Q#21839 - 	CGI_10003277	superfamily	241779	125	329	3.91E-64	205.495	cl00318	YjeF_N superfamily	 - 	 - 	"YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions."
Q#21839 - 	CGI_10003277	superfamily	241874	87	155	4.12E-07	49.9763	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#21841 - 	CGI_10003279	superfamily	216554	93	216	1.29E-22	91.7721	cl15977	zf-DHHC superfamily	N	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#21842 - 	CGI_10004825	superfamily	248264	1	138	1.12E-08	52.2394	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#21843 - 	CGI_10004826	superfamily	244881	605	765	2.26E-33	131.161	cl08267	ISOPREN_C2_like superfamily	N	 - 	"This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds.  The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system."
Q#21843 - 	CGI_10004826	superfamily	203720	853	935	2.59E-15	72.9662	cl08457	A2M_recep superfamily	 - 	 - 	A-macroglobulin receptor; This family includes the receptor domain region of the alpha-2-macroglobulin family.
Q#21843 - 	CGI_10004826	superfamily	215788	584	621	0.000106527	41.7811	cl08251	A2M superfamily	N	 - 	Alpha-2-macroglobulin family; This family includes the C-terminal region of the alpha-2-macroglobulin family.
Q#21843 - 	CGI_10004826	superfamily	219677	229	254	0.00582962	35.8764	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#21844 - 	CGI_10004827	superfamily	244339	2	183	2.60E-16	75.2629	cl06253	VDE superfamily	NC	 - 	"Violaxanthin de-epoxidase (VDE); This family represents a conserved region approximately 150 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage."
Q#21845 - 	CGI_10004828	superfamily	243035	23	97	3.59E-10	56.8593	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#21847 - 	CGI_10012639	superfamily	242406	3	121	1.10E-15	69.5425	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#21850 - 	CGI_10012642	superfamily	245201	2	66	1.21E-20	83.0549	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21850 - 	CGI_10012642	superfamily	245201	40	108	0.000383225	37.2949	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21851 - 	CGI_10012643	superfamily	247792	7	79	1.51E-31	107.227	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#21853 - 	CGI_10012645	superfamily	217293	33	232	8.11E-44	154.328	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#21853 - 	CGI_10012645	superfamily	202474	240	460	2.38E-17	80.0053	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#21855 - 	CGI_10012647	superfamily	245835	26	267	4.74E-131	377.887	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#21855 - 	CGI_10012647	superfamily	247683	319	370	7.75E-27	101.21	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#21856 - 	CGI_10012648	superfamily	241640	36	271	2.90E-86	259.516	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#21858 - 	CGI_10012650	superfamily	241647	189	219	2.31E-05	40.2038	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#21860 - 	CGI_10012652	superfamily	243072	45	169	1.73E-26	100.921	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21862 - 	CGI_10010378	superfamily	241581	26	117	2.30E-13	68.567	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#21863 - 	CGI_10010379	superfamily	248458	46	211	6.57E-11	61.9461	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21864 - 	CGI_10010380	superfamily	203016	5	135	7.25E-72	217.415	cl15994	Thg1 superfamily	 - 	 - 	"tRNAHis guanylyltransferase; The Thg1 protein from Saccharomyces cerevisiae is responsible for adding a GMP residue to the 5' end of tRNA His. The catalytic domain Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases, diguanylate cyclases (GGDEF domain) and the predicted polymerase of the CRISPR system. Thg1 possesses an active site with three acidic residues that chelate Mg++ cations. Thg1 catalyzes polymerization similar to the 5'-3' polymerases."
Q#21864 - 	CGI_10010380	superfamily	222741	137	218	2.92E-41	138.196	cl16863	Thg1C superfamily	C	 - 	"Thg1 C terminal domain; Thg1 polymerases contain an additional region of conservation C-terminal to the core palm domain that comprise of 5 helices and two strands. This region has several well-conserved charged residues including a basic residue found towards the end of the first helix of this unit might contribute to the Thg1-specific active site. This C-terminal module of Thg1 is predicted to form a helical bundle that functions equivalently to the fingers of the other nucleic acid polymerases, probably in interacting with the template HtRNA."
Q#21865 - 	CGI_10010381	superfamily	243072	7	114	3.06E-26	105.543	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21865 - 	CGI_10010381	superfamily	246680	750	827	0.00143676	37.7002	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#21866 - 	CGI_10010382	superfamily	247068	64	149	6.20E-06	44.6118	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#21866 - 	CGI_10010382	superfamily	216152	257	610	2.65E-65	219.878	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#21870 - 	CGI_10010386	superfamily	243179	271	358	2.38E-05	42.9051	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#21870 - 	CGI_10010386	superfamily	131187	54	163	0.00809283	36.3441	cl11779	phaR_Bmeg superfamily	N	 - 	"polyhydroxyalkanoic acid synthase, PhaR subunit; This model describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit."
Q#21873 - 	CGI_10010389	superfamily	220415	68	146	1.56E-19	79.3631	cl10782	MRP-L27 superfamily	N	 - 	Mitochondrial ribosomal protein L27; Members of this family of proteins are components of the mitochondrial ribosome large subunit. They are also involved in apoptosis and cell cycle regulation.
Q#21874 - 	CGI_10010390	superfamily	243058	386	502	0.00148803	38.0644	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#21875 - 	CGI_10010391	superfamily	243179	21	102	5.47E-07	43.6755	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#21876 - 	CGI_10010392	superfamily	243179	41	161	1.18E-15	69.8691	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#21877 - 	CGI_10010393	superfamily	241629	90	224	4.85E-57	180.099	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#21878 - 	CGI_10010394	superfamily	131388	42	255	4.53E-05	44.1201	cl17985	hydr_PhnA superfamily	C	 - 	"phosphonoacetate hydrolase; This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile that the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for pther specific phosphonatases."
Q#21879 - 	CGI_10010395	superfamily	243179	29	142	4.27E-15	67.5579	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#21880 - 	CGI_10012779	superfamily	243090	295	416	5.92E-63	201.313	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#21880 - 	CGI_10012779	superfamily	243038	31	86	7.79E-18	78.1009	cl02442	DEP superfamily	N	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#21880 - 	CGI_10012779	superfamily	241587	240	276	9.30E-10	54.6026	cl00069	GGL superfamily	N	 - 	"G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors"
Q#21881 - 	CGI_10012780	superfamily	241563	134	166	3.96E-05	41.504	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21881 - 	CGI_10012780	superfamily	220764	161	272	0.00368309	37.1693	cl11102	DUF2458 superfamily	C	 - 	Protein of unknown function (DUF2458); This a is family of uncharacterized proteins.
Q#21883 - 	CGI_10012782	superfamily	177822	42	232	1.04E-19	84.9717	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#21884 - 	CGI_10012783	superfamily	244837	57	83	0.00833994	33.9765	cl07971	Glyco_hydro_3 superfamily	NC	 - 	Glycosyl hydrolase family 3 N terminal domain; Glycosyl hydrolase family 3 N terminal domain.  
Q#21885 - 	CGI_10012784	superfamily	245206	5	229	7.46E-47	159.362	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#21886 - 	CGI_10012785	superfamily	218028	660	713	0.000150028	41.144	cl04479	AAA_4 superfamily	C	 - 	"Divergent AAA domain; This family is related to the pfam00004 family, and presumably has the same function (ATP-binding)."
Q#21886 - 	CGI_10012785	superfamily	243058	365	468	0.00332276	36.9088	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#21889 - 	CGI_10012788	superfamily	245602	259	561	2.89E-148	452.825	cl11402	GH31 superfamily	 - 	 - 	"The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed.  Most characterized GH31 enzymes are alpha-glucosidases.  In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively."
Q#21889 - 	CGI_10012788	superfamily	207662	909	991	5.88E-51	176.106	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#21889 - 	CGI_10012788	superfamily	245599	1098	1260	6.60E-41	150.069	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#21892 - 	CGI_10014107	superfamily	243050	441	508	5.03E-42	145.301	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#21892 - 	CGI_10014107	superfamily	243050	381	440	1.09E-36	129.972	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#21892 - 	CGI_10014107	superfamily	243050	321	374	3.36E-22	90.1553	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#21893 - 	CGI_10014108	superfamily	221564	32	105	2.27E-26	97.6675	cl13797	P5-ATPase superfamily	C	 - 	"P5-type ATPase cation transporter; This domain family is found in eukaryotes, and is typically between 110 and 126 amino acids in length. The family is found in association with pfam00122, pfam00702. P-type ATPases comprise a large superfamily of proteins, present in both prokaryotes and eukaryotes, that transport inorganic cations and other substrates across cell membranes."
Q#21894 - 	CGI_10014109	superfamily	215733	116	345	3.25E-36	138.082	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#21894 - 	CGI_10014109	superfamily	247756	707	757	8.57E-05	43.7626	cl17202	HAD superfamily	N	 - 	haloacid dehalogenase-like hydrolase; haloacid dehalogenase-like hydrolase.  
Q#21894 - 	CGI_10014109	superfamily	222006	469	511	0.000747832	39.1278	cl16182	Hydrolase_like2 superfamily	N	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#21896 - 	CGI_10014111	superfamily	245202	42	110	6.85E-25	90.6744	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#21897 - 	CGI_10014112	superfamily	245202	6	74	5.60E-21	83.7822	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#21899 - 	CGI_10014114	superfamily	216152	257	552	3.48E-64	215.641	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#21899 - 	CGI_10014114	superfamily	216152	12	254	2.08E-49	175.58	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#21900 - 	CGI_10014115	superfamily	216152	58	360	5.87E-65	212.944	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#21901 - 	CGI_10014116	superfamily	215647	619	735	4.11E-05	44.5217	cl18338	7tm_2 superfamily	NC	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#21903 - 	CGI_10014118	superfamily	222150	93	120	0.00106894	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21903 - 	CGI_10014118	superfamily	246975	80	101	0.00263367	34.6301	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#21904 - 	CGI_10014119	superfamily	246671	26	164	8.26E-25	96.7232	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#21906 - 	CGI_10014121	superfamily	245201	34	289	9.87E-145	413.701	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21906 - 	CGI_10014121	superfamily	247683	276	345	2.91E-05	41.3697	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#21907 - 	CGI_10014122	superfamily	222150	1484	1508	0.00978524	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#21909 - 	CGI_10014124	superfamily	241578	94	140	1.64E-05	46.6092	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21909 - 	CGI_10014124	superfamily	241578	395	434	0.000141956	43.5276	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21909 - 	CGI_10014124	superfamily	241578	353	390	0.000278274	42.7572	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21909 - 	CGI_10014124	superfamily	241578	225	264	0.00186449	40.446	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21909 - 	CGI_10014124	superfamily	241578	179	224	0.00188606	40.446	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#21910 - 	CGI_10014125	superfamily	247743	312	471	1.19E-05	45.9851	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#21910 - 	CGI_10014125	superfamily	243092	1169	1351	0.00256761	40.396	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21911 - 	CGI_10014126	superfamily	247057	6	64	8.18E-22	91.872	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#21911 - 	CGI_10014126	superfamily	245201	198	445	1.18E-121	382.885	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21911 - 	CGI_10014126	superfamily	247683	457	509	8.09E-05	42.5042	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#21912 - 	CGI_10014127	superfamily	221585	82	195	4.78E-25	97.1448	cl13842	hSac2 superfamily	 - 	 - 	"Inositol phosphatase; This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam02383. hSac2 functions as an inositol polyphosphate 5-phosphatase."
Q#21913 - 	CGI_10014128	superfamily	247095	14	465	6.31E-152	442.095	cl15837	alkPPc superfamily	 - 	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#21914 - 	CGI_10014129	superfamily	241607	156	195	1.14E-09	51.1166	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#21914 - 	CGI_10014129	superfamily	241607	73	107	0.0004052	36.479	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#21915 - 	CGI_10014130	superfamily	247095	28	477	1.21E-158	459.044	cl15837	alkPPc superfamily	 - 	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#21916 - 	CGI_10014131	superfamily	247095	452	790	6.85E-124	380.463	cl15837	alkPPc superfamily	N	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#21916 - 	CGI_10014131	superfamily	247095	1	215	6.35E-54	192.67	cl15837	alkPPc superfamily	C	 - 	"Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity."
Q#21919 - 	CGI_10012423	superfamily	241858	81	202	9.98E-09	51.132	cl00429	SNARE_assoc superfamily	 - 	 - 	SNARE associated Golgi protein; This is a family of SNARE associated Golgi proteins. The yeast member of this family localises with the t-SNARE Tlg2.
Q#21922 - 	CGI_10012426	superfamily	243035	59	163	2.10E-10	54.163	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#21925 - 	CGI_10012429	superfamily	243072	181	354	6.82E-24	100.536	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21925 - 	CGI_10012429	superfamily	243072	86	241	4.43E-23	98.2246	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#21925 - 	CGI_10012429	superfamily	245201	2118	2378	6.99E-137	430.101	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21927 - 	CGI_10012431	superfamily	245670	146	340	2.48E-49	175.462	cl11519	DENN superfamily	 - 	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#21927 - 	CGI_10012431	superfamily	243635	6	96	5.42E-21	90.4716	cl04085	uDENN superfamily	 - 	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#21927 - 	CGI_10012431	superfamily	208095	417	485	3.64E-09	55.3738	cl04084	dDENN superfamily	 - 	 - 	dDENN domain; This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
Q#21928 - 	CGI_10012432	superfamily	243040	29	168	2.48E-44	157.914	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#21928 - 	CGI_10012432	superfamily	215647	211	348	0.00111597	40.6697	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#21929 - 	CGI_10012433	superfamily	245244	102	195	1.25E-20	83.091	cl10045	tRNA_int_endo superfamily	 - 	 - 	"tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9."
Q#21929 - 	CGI_10012433	superfamily	217225	45	92	0.00690317	33.3655	cl03709	tRNA_int_endo_N superfamily	 - 	 - 	"tRNA intron endonuclease, N-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9."
Q#21931 - 	CGI_10012435	superfamily	243092	59	352	5.65E-37	137.466	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21931 - 	CGI_10012435	superfamily	217935	353	440	1.80E-30	112.754	cl04424	Sof1 superfamily	 - 	 - 	Sof1-like domain; Sof1 is essential for cell growth and is a component of the nucleolar rRNA processing machinery.
Q#21932 - 	CGI_10012436	superfamily	247727	8	105	1.57E-13	63.2178	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#21933 - 	CGI_10000090	superfamily	243092	38	280	3.10E-13	68.1304	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21934 - 	CGI_10006288	superfamily	246669	408	545	3.18E-83	257.682	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#21934 - 	CGI_10006288	superfamily	246669	252	375	6.02E-34	124.661	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#21936 - 	CGI_10006290	superfamily	220107	488	754	1.35E-60	206.116	cl07638	MIF4G_like_2 superfamily	 - 	 - 	"MIF4G like; Members of this family are involved in mediating U snRNA export from the nucleus. They adopt a highly helical structure, wherein the polypeptide chain forms a right-handed solenoid. At the tertiary level, the domain is composed of a superhelical arrangement of successive antiparallel pairs of helices."
Q#21936 - 	CGI_10006290	superfamily	149958	307	474	1.75E-58	197.624	cl07636	MIF4G_like superfamily	 - 	 - 	"MIF4G like; Members of this family are involved in mediating U snRNA export from the nucleus. They adopt a highly helical structure, wherein the polypeptide chain forms a right-handed solenoid. At the tertiary level, the domain is composed of a superhelical arrangement of successive antiparallel pairs of helices."
Q#21936 - 	CGI_10006290	superfamily	243128	31	243	1.37E-24	102.824	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#21937 - 	CGI_10006291	superfamily	219626	69	108	3.29E-14	61.8127	cl12354	DUF1674 superfamily	 - 	 - 	Protein of unknown function (DUF1674); The members of this family are sequences derived from hypothetical eukaryotic and bacterial proteins. The region in question is approximately 60 residues long.
Q#21939 - 	CGI_10006294	superfamily	241802	187	296	7.88E-28	109.499	cl00342	Trp-synth-beta_II superfamily	N	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#21939 - 	CGI_10006294	superfamily	245874	21	64	7.42E-05	40.1022	cl12111	TNFR superfamily	NC	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#21940 - 	CGI_10006295	superfamily	216939	34	86	0.00506249	33.4053	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#21942 - 	CGI_10006297	superfamily	248458	50	110	1.66E-05	44.6121	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#21942 - 	CGI_10006297	superfamily	242406	137	275	4.55E-21	87.2617	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#21945 - 	CGI_10001341	superfamily	243179	112	217	7.10E-19	78.7002	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#21946 - 	CGI_10010295	superfamily	247057	767	834	2.19E-38	137.919	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#21946 - 	CGI_10010295	superfamily	247744	2	45	2.33E-07	50.6893	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#21946 - 	CGI_10010295	superfamily	247744	42	74	0.00345046	38.3629	cl17190	NK superfamily	N	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#21947 - 	CGI_10010296	superfamily	245342	424	526	1.35E-13	69.2998	cl10594	ERCC4 superfamily	 - 	 - 	ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Q#21947 - 	CGI_10010296	superfamily	241563	239	288	0.00222887	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#21949 - 	CGI_10010298	superfamily	247724	3	177	3.32E-131	368.432	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#21950 - 	CGI_10010299	superfamily	247856	47	105	1.43E-10	54.0909	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#21951 - 	CGI_10010300	superfamily	245819	284	431	0.00195876	38.3291	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#21951 - 	CGI_10010300	superfamily	245201	1	180	1.09E-23	100.304	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21952 - 	CGI_10010301	superfamily	247850	11	90	1.23E-10	57.0671	cl17296	PBP_like_2 superfamily	C	 - 	PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
Q#21953 - 	CGI_10010302	superfamily	245819	704	851	0.0016311	39.0995	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#21953 - 	CGI_10010302	superfamily	245201	370	600	4.74E-35	135.357	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#21953 - 	CGI_10010302	superfamily	247850	7	224	3.83E-26	110.225	cl17296	PBP_like_2 superfamily	N	 - 	PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
Q#21954 - 	CGI_10010303	superfamily	247850	14	104	0.000952721	35.5735	cl17296	PBP_like_2 superfamily	C	 - 	PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
Q#21955 - 	CGI_10010304	superfamily	247850	7	45	0.00347807	34.0327	cl17296	PBP_like_2 superfamily	C	 - 	PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
Q#21956 - 	CGI_10010305	superfamily	241884	18	205	6.66E-111	318.4	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#21957 - 	CGI_10010306	superfamily	241622	15	88	6.54E-18	74.1402	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#21958 - 	CGI_10010307	superfamily	241628	18	300	1.24E-15	75.2026	cl00130	PseudoU_synth superfamily	 - 	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#21960 - 	CGI_10010309	superfamily	192370	37	116	6.44E-17	73.2257	cl12371	WD-3 superfamily	C	 - 	"WD-repeat region; This entry is of a region of approximately 100 residues containing three WD repeats and six cysteine residues possibly as three cystine-bridges. These regions are contained within the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. The WD repeats are required for interaction with other subunits of the FA complex."
Q#21961 - 	CGI_10010310	superfamily	241628	99	317	1.21E-47	160.966	cl00130	PseudoU_synth superfamily	 - 	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#21963 - 	CGI_10010312	superfamily	192370	3	146	2.31E-40	141.406	cl12371	WD-3 superfamily	N	 - 	"WD-repeat region; This entry is of a region of approximately 100 residues containing three WD repeats and six cysteine residues possibly as three cystine-bridges. These regions are contained within the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. The WD repeats are required for interaction with other subunits of the FA complex."
Q#21963 - 	CGI_10010312	superfamily	204746	154	222	1.32E-31	111.744	cl18258	FANCL_C superfamily	 - 	 - 	"FANCL C-terminal domain; This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2."
Q#21964 - 	CGI_10010313	superfamily	243166	42	231	2.33E-16	73.867	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#21965 - 	CGI_10010314	superfamily	243166	56	248	6.29E-19	81.5709	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#21966 - 	CGI_10010315	superfamily	243166	57	243	2.22E-18	80.0301	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#21967 - 	CGI_10010316	superfamily	246675	9	308	1.31E-135	390.037	cl14615	PI-PLCc_GDPD_SF superfamily	 - 	 - 	"Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases."
Q#21968 - 	CGI_10010317	superfamily	243092	14	308	7.50E-50	169.053	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#21970 - 	CGI_10004502	superfamily	241574	340	509	2.88E-69	224.002	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#21971 - 	CGI_10006767	superfamily	241736	88	251	8.00E-78	235.739	cl00263	TFold superfamily	 - 	 - 	"Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1),  6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and share a fold-related binding site with a glutamate or glutamine residue anchoring the substrate and a lot of conserved interactions. They also share a similar oligomerization mode: several T-folds join together to form a beta(2n)alpha(n) barrel, then two barrels join together in a head-to-head fashion to made up the native enzymes. The functional enzyme is a tetramer for UO, a hexamer for PTPS, an octamer for DHNA/DHNTPE and a decamer for GTPCH-1. The substrate is located in a deep and narrow pocket at the interface between monomers. In PTPS, the active site is located at the interface of three monomers, two from one trimer and one from the other trimer. In GTPCH-1, it is also located at the interface of three subunits, two from one pentamer and one from the other pentamer. There are four equivalent active sites in UO, six in PTPS, eight in DHNA/DHNTPE and ten in GTPCH-1.   Each globular multimeric enzyme encloses a tunnel which is lined with charged residues for DHNA and UO, and with basic residues in PTPS. The N and C-terminal ends are located on one side of the T-fold while the residues involved in the catalytic activity are located at the opposite side. In PTPS, UO and DHNA/DHNTPE, the N and C-terminal extremities of the enzyme are located on the exterior side of the functional multimeric enzyme. In GTPCH-1, the extra C-terminal helix places the extremity inside the tunnel."
Q#21972 - 	CGI_10006768	superfamily	247057	362	424	1.01E-34	126.673	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#21972 - 	CGI_10006768	superfamily	204178	425	535	9.86E-05	41.3642	cl07759	PHAT superfamily	 - 	 - 	"PHAT; The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding."
Q#21974 - 	CGI_10006770	superfamily	215754	23	107	4.80E-26	99.6352	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21974 - 	CGI_10006770	superfamily	215754	211	306	6.30E-21	84.9976	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21974 - 	CGI_10006770	superfamily	215754	121	204	2.94E-14	66.8932	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#21975 - 	CGI_10006771	superfamily	241773	40	148	1.95E-42	138.42	cl00312	Ribosomal_S12_like superfamily	 - 	 - 	"Ribosomal protein S12-like family; composed of  prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code."
Q#21976 - 	CGI_10006772	superfamily	247723	74	156	8.10E-40	141.978	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#21976 - 	CGI_10006772	superfamily	243087	688	758	5.35E-22	91.2527	cl02562	PWI superfamily	 - 	 - 	PWI domain; PWI domain.  
Q#21985 - 	CGI_10001104	superfamily	241619	25	94	3.63E-06	42.4569	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#21985 - 	CGI_10001104	superfamily	241568	132	184	0.00902469	32.5472	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#21989 - 	CGI_10025458	superfamily	216981	57	209	7.41E-11	59.4686	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#21995 - 	CGI_10025464	superfamily	246902	23	89	2.50E-24	92.2968	cl15239	PLDc_SF superfamily	N	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#21999 - 	CGI_10025468	superfamily	245816	4	163	1.44E-44	147.03	cl11964	CYTH-like_Pase superfamily	 - 	 - 	"CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; CYTH-like superfamily enzymes hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB), and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions."
Q#22000 - 	CGI_10025469	superfamily	242274	1	130	7.14E-05	40.0882	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#22001 - 	CGI_10025470	superfamily	193607	573	704	1.50E-63	208.965	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#22001 - 	CGI_10025470	superfamily	247792	526	567	9.64E-05	40.892	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22001 - 	CGI_10025470	superfamily	241554	277	458	2.34E-47	165.136	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#22002 - 	CGI_10025471	superfamily	193607	7	138	4.84E-61	187.009	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#22003 - 	CGI_10025472	superfamily	241554	233	408	7.87E-42	148.958	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#22003 - 	CGI_10025472	superfamily	241554	468	606	6.62E-15	73.0735	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#22004 - 	CGI_10025473	superfamily	241600	4	139	1.88E-52	167.032	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#22005 - 	CGI_10025474	superfamily	241694	6	279	2.83E-96	297.568	cl00216	L-asparaginase_like superfamily	 - 	 - 	"Bacterial L-asparaginases and related enzymes; Asparaginases (amidohydrolases, E.C. 3.5.1.1) are dimeric or tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localized to the periplasm (type II L-asparaginase), and a second (asparaginase- glutaminase) present in the cytosol (type I L-asparaginase) that hydrolyzes both asparagine and glutamine with similar specificities and has a lower affinity for its substrate. Bacterial L-asparaginases (type II) are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL). A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. This wider family also includes a subunit of an archaeal Glu-tRNA amidotransferase."
Q#22005 - 	CGI_10025474	superfamily	243072	356	512	6.60E-28	108.24	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22006 - 	CGI_10025475	superfamily	241694	29	372	1.50E-100	311.05	cl00216	L-asparaginase_like superfamily	 - 	 - 	"Bacterial L-asparaginases and related enzymes; Asparaginases (amidohydrolases, E.C. 3.5.1.1) are dimeric or tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localized to the periplasm (type II L-asparaginase), and a second (asparaginase- glutaminase) present in the cytosol (type I L-asparaginase) that hydrolyzes both asparagine and glutamine with similar specificities and has a lower affinity for its substrate. Bacterial L-asparaginases (type II) are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL). A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. This wider family also includes a subunit of an archaeal Glu-tRNA amidotransferase."
Q#22006 - 	CGI_10025475	superfamily	243072	449	605	9.73E-28	108.625	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22007 - 	CGI_10025477	superfamily	241694	94	282	4.77E-59	194.034	cl00216	L-asparaginase_like superfamily	N	 - 	"Bacterial L-asparaginases and related enzymes; Asparaginases (amidohydrolases, E.C. 3.5.1.1) are dimeric or tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localized to the periplasm (type II L-asparaginase), and a second (asparaginase- glutaminase) present in the cytosol (type I L-asparaginase) that hydrolyzes both asparagine and glutamine with similar specificities and has a lower affinity for its substrate. Bacterial L-asparaginases (type II) are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL). A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. This wider family also includes a subunit of an archaeal Glu-tRNA amidotransferase."
Q#22007 - 	CGI_10025477	superfamily	241694	36	79	0.00118758	38.6772	cl00216	L-asparaginase_like superfamily	C	 - 	"Bacterial L-asparaginases and related enzymes; Asparaginases (amidohydrolases, E.C. 3.5.1.1) are dimeric or tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localized to the periplasm (type II L-asparaginase), and a second (asparaginase- glutaminase) present in the cytosol (type I L-asparaginase) that hydrolyzes both asparagine and glutamine with similar specificities and has a lower affinity for its substrate. Bacterial L-asparaginases (type II) are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL). A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. This wider family also includes a subunit of an archaeal Glu-tRNA amidotransferase."
Q#22008 - 	CGI_10025478	superfamily	243072	247	371	3.19E-27	104.773	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22008 - 	CGI_10025478	superfamily	243072	346	403	1.52E-07	49.3042	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22008 - 	CGI_10025478	superfamily	241694	41	181	9.04E-50	173.234	cl00216	L-asparaginase_like superfamily	N	 - 	"Bacterial L-asparaginases and related enzymes; Asparaginases (amidohydrolases, E.C. 3.5.1.1) are dimeric or tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localized to the periplasm (type II L-asparaginase), and a second (asparaginase- glutaminase) present in the cytosol (type I L-asparaginase) that hydrolyzes both asparagine and glutamine with similar specificities and has a lower affinity for its substrate. Bacterial L-asparaginases (type II) are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL). A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. This wider family also includes a subunit of an archaeal Glu-tRNA amidotransferase."
Q#22009 - 	CGI_10025479	superfamily	217046	180	348	6.68E-46	156.199	cl03599	Reticulon superfamily	 - 	 - 	"Reticulon; Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of the three reticulon isoforms and their homologues."
Q#22010 - 	CGI_10025480	superfamily	241782	159	523	2.57E-154	448.933	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#22011 - 	CGI_10025481	superfamily	241782	54	377	1.12E-136	402.218	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#22014 - 	CGI_10025484	superfamily	241862	428	585	1.79E-21	93.96	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#22016 - 	CGI_10025486	superfamily	241622	6	84	3.37E-19	76.0662	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#22017 - 	CGI_10025487	superfamily	217247	373	488	9.76E-07	50.4694	cl18397	Glyco_hydro_2_C superfamily	C	 - 	"Glycosyl hydrolases family 2, TIM barrel domain; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities."
Q#22017 - 	CGI_10025487	superfamily	217248	67	131	0.00521736	37.2503	cl18398	Glyco_hydro_2_N superfamily	NC	 - 	"Glycosyl hydrolases family 2, sugar binding domain; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold."
Q#22018 - 	CGI_10025488	superfamily	217247	371	485	1.15E-06	49.3138	cl18397	Glyco_hydro_2_C superfamily	C	 - 	"Glycosyl hydrolases family 2, TIM barrel domain; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities."
Q#22018 - 	CGI_10025488	superfamily	217248	79	143	0.0097869	35.7095	cl18398	Glyco_hydro_2_N superfamily	NC	 - 	"Glycosyl hydrolases family 2, sugar binding domain; This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold."
Q#22021 - 	CGI_10025491	superfamily	243098	14	63	0.000117468	39.8888	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#22025 - 	CGI_10025495	superfamily	248097	115	229	9.09E-10	53.8453	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22026 - 	CGI_10025496	superfamily	201217	13	61	2.03E-07	47.1352	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22026 - 	CGI_10025496	superfamily	201217	65	121	3.51E-05	40.5868	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22027 - 	CGI_10025497	superfamily	248312	20	173	4.46E-05	40.7997	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#22029 - 	CGI_10025499	superfamily	247736	174	219	9.83E-07	44.6278	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#22031 - 	CGI_10025501	superfamily	191430	14	66	0.00746089	32.833	cl05523	Gly_acyl_tr_N superfamily	C	 - 	Aralkyl acyl-CoA:amino acid N-acyltransferase; This family consists of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins EC:2.3.1.13.
Q#22032 - 	CGI_10025502	superfamily	247736	163	232	7.69E-10	53.4874	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#22035 - 	CGI_10025505	superfamily	247736	88	152	5.09E-11	55.4134	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#22036 - 	CGI_10025506	superfamily	247736	128	195	1.38E-13	63.1174	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#22039 - 	CGI_10025509	superfamily	241580	137	214	6.37E-47	156.945	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#22039 - 	CGI_10025509	superfamily	220199	334	391	5.13E-05	40.9148	cl09612	HNF_C superfamily	 - 	 - 	"HNF3 C-terminal domain; This presumed domain is found in the C-terminal region of Hepatocyte Nuclear Factor 3 alpha and beta chains. Its specific function is uncertain. The N-terminal region of this presumed domain contains an EH1 (engrailed homology 1) motif, that is characterized by the FxIxxIL sequence."
Q#22045 - 	CGI_10025515	superfamily	145533	23	120	1.07E-40	142.888	cl03592	Ski_Sno superfamily	 - 	 - 	"SKI/SNO/DAC family; This family contains a presumed domain that is about 100 amino acids long. All members of this family contain a conserved CLPQ motif. The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation. Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli. Dachshund also contains this domain. It is involved in various aspects of development."
Q#22045 - 	CGI_10025515	superfamily	198898	131	222	5.68E-40	140.966	cl07406	c-SKI_SMAD_bind superfamily	 - 	 - 	c-SKI Smad4 binding domain; c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins. This domain binds to Smad4
Q#22046 - 	CGI_10007338	superfamily	241874	8	485	2.60E-176	508.983	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#22047 - 	CGI_10007339	superfamily	247724	147	178	1.51E-05	42.162	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22048 - 	CGI_10007340	superfamily	247724	44	236	6.37E-46	154.099	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22050 - 	CGI_10007342	superfamily	247792	16	58	1.55E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22051 - 	CGI_10007343	superfamily	247792	16	55	3.47E-08	51.6776	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22052 - 	CGI_10010533	superfamily	243066	46	133	4.33E-27	104.557	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22052 - 	CGI_10010533	superfamily	219619	382	451	2.97E-11	59.5287	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#22054 - 	CGI_10010536	superfamily	241750	6	121	1.31E-16	72.221	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#22057 - 	CGI_10010540	superfamily	245531	81	152	8.22E-06	41.1954	cl11158	BEN superfamily	 - 	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#22060 - 	CGI_10017629	superfamily	246908	548	696	1.97E-12	64.913	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#22060 - 	CGI_10017629	superfamily	145817	454	526	0.00288539	38.6149	cl03748	STAT_bind superfamily	NC	 - 	"STAT protein, DNA binding domain; STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. This family represents the DNA binding domain of STAT, which has an ig-like fold. STAT proteins also include an SH2 domain pfam00017."
Q#22061 - 	CGI_10017630	superfamily	246908	19	101	6.79E-14	67.9946	cl15255	SH2 superfamily	C	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#22062 - 	CGI_10017631	superfamily	247856	1007	1065	4.72E-07	49.4685	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	247856	552	610	1.67E-06	47.5425	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	247856	428	483	0.000101497	42.1497	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	247856	1718	1778	0.000454124	40.2237	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	247856	897	957	0.000528594	40.2237	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	247856	318	376	0.000732798	39.8385	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	117542	1486	1595	2.50E-07	50.9703	cl07545	DUF1880 superfamily	 - 	 - 	Domain of unknown function (DUF1880); This domain is found predominantly in DJ binding protein. It has no known function.
Q#22062 - 	CGI_10017631	superfamily	241707	151	218	5.27E-05	45.6377	cl00230	CIS_IPPS superfamily	N	 - 	"Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity."
Q#22062 - 	CGI_10017631	superfamily	247856	662	722	0.00193988	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	247856	1596	1657	0.00242447	38.2977	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22062 - 	CGI_10017631	superfamily	247856	1113	1173	0.00969477	36.3717	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22063 - 	CGI_10017632	superfamily	247744	74	212	7.38E-19	87.2922	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#22063 - 	CGI_10017632	superfamily	247744	1471	1632	5.35E-17	81.8994	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#22063 - 	CGI_10017632	superfamily	247744	1136	1216	1.64E-10	61.4838	cl17190	NK superfamily	NC	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#22063 - 	CGI_10017632	superfamily	247744	1028	1073	1.72E-07	52.239	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#22063 - 	CGI_10017632	superfamily	247807	431	465	6.39E-06	46.5193	cl17253	AAA_17 superfamily	C	 - 	AAA domain; AAA domain.  
Q#22063 - 	CGI_10017632	superfamily	221381	961	1017	2.17E-05	47.0008	cl13455	DUF3508 superfamily	N	 - 	Domain of unknown function (DUF3508); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 280 amino acids in length. This domain has two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704.
Q#22064 - 	CGI_10017633	superfamily	247848	52	139	0.00478903	37.45	cl17294	PhosphMutase superfamily	N	 - 	"2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Members of this family are found in various bacterial 2,3-bisphosphoglycerate-independent phosphoglycerate mutase enzymes, which catalyze the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in the reaction: [2-phospho-D-glycerate + 2,3-diphosphoglycerate = 3-phospho-D-glycerate + 2,3-diphosphoglycerate]."
Q#22065 - 	CGI_10017634	superfamily	247805	142	230	6.37E-05	41.7014	cl17251	DEXDc superfamily	NC	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#22066 - 	CGI_10017635	superfamily	242203	21	297	5.81E-71	225.256	cl00935	Brix superfamily	 - 	 - 	Brix domain; Brix domain.  
Q#22068 - 	CGI_10017637	superfamily	248022	11	368	7.69E-47	167.455	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#22069 - 	CGI_10017638	superfamily	241607	157	185	7.51E-05	39.9458	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#22069 - 	CGI_10017638	superfamily	241607	23	48	0.00351083	34.9382	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#22070 - 	CGI_10017639	superfamily	241607	72	91	2.97E-06	39.9458	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#22071 - 	CGI_10017640	superfamily	241832	3	97	1.08E-29	111.594	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#22072 - 	CGI_10017641	superfamily	219275	317	640	6.96E-99	315.829	cl06188	ORC3_N superfamily	 - 	 - 	Origin recognition complex (ORC) subunit 3 N-terminus; This family represents the N-terminus (approximately 300 residues) of subunit 3 of the eukaryotic origin recognition complex (ORC). Origin recognition complex (ORC) is composed of six subunits that are essential for cell viability. They collectively bind to the autonomously replicating sequence (ARS) in a sequence-specific manner and lead to the chromatin loading of other replication factors that are essential for initiation of DNA replication.
Q#22073 - 	CGI_10017642	superfamily	218079	21	155	3.15E-22	88.4936	cl04507	CHD5 superfamily	 - 	 - 	CHD5-like protein; Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. In Saccharomyces cerevisiae this protein localises to the ER and is thought to play a homeostatic role.
Q#22074 - 	CGI_10017643	superfamily	222150	847	872	0.000160532	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22074 - 	CGI_10017643	superfamily	222150	875	900	0.00284073	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22075 - 	CGI_10017644	superfamily	241596	90	126	3.71E-05	39.8899	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#22078 - 	CGI_10017647	superfamily	241596	99	142	6.54E-10	52.2163	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#22079 - 	CGI_10017648	superfamily	241596	17	58	2.81E-13	61.0759	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#22080 - 	CGI_10017650	superfamily	241596	2	43	3.33E-15	65.3131	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#22083 - 	CGI_10017653	superfamily	246664	2	78	3.30E-36	126.535	cl14561	An_peroxidase_like superfamily	N	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#22084 - 	CGI_10017654	superfamily	243072	118	250	3.33E-30	112.477	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22084 - 	CGI_10017654	superfamily	243072	189	318	1.46E-28	107.855	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22088 - 	CGI_10017658	superfamily	245201	21	216	2.93E-39	143.146	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22089 - 	CGI_10017659	superfamily	241659	275	357	4.05E-19	82.5954	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#22090 - 	CGI_10017660	superfamily	241754	14	350	2.28E-161	486.214	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#22090 - 	CGI_10017660	superfamily	242185	1145	1179	5.87E-05	42.9054	cl00910	Multi_Drug_Res superfamily	N	 - 	"Small Multidrug Resistance protein; This family is the Small Multidrug Resistance (SMR) family. Several members have been shown to export a range of toxins, including ethidium bromide and quaternary ammonium compounds, through coupling with proton influx."
Q#22091 - 	CGI_10017661	superfamily	246598	6	189	1.40E-63	197.132	cl13996	MPN superfamily	 - 	 - 	"Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors.  These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface.  Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function."
Q#22092 - 	CGI_10017662	superfamily	245206	3	271	4.61E-139	397.202	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#22093 - 	CGI_10017663	superfamily	221913	164	375	2.58E-65	209.319	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#22093 - 	CGI_10017663	superfamily	222258	116	153	3.52E-05	42.9404	cl18656	AAA_30 superfamily	NC	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#22094 - 	CGI_10017664	superfamily	216112	102	153	1.93E-08	55.3803	cl02964	RNB superfamily	N	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#22096 - 	CGI_10017666	superfamily	221913	485	696	1.72E-60	203.156	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#22096 - 	CGI_10017666	superfamily	222005	254	314	2.41E-05	43.1096	cl18632	AAA_19 superfamily	C	 - 	Part of AAA domain; Part of AAA domain.  
Q#22096 - 	CGI_10017666	superfamily	222258	397	474	3.32E-05	44.096	cl18656	AAA_30 superfamily	C	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#22097 - 	CGI_10017667	superfamily	216112	919	1021	8.89E-15	75.4107	cl02964	RNB superfamily	C	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#22098 - 	CGI_10017668	superfamily	241782	23	390	1.07E-48	169.829	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#22099 - 	CGI_10007421	superfamily	241564	23	88	8.21E-30	108.507	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#22099 - 	CGI_10007421	superfamily	247792	236	272	0.000242751	37.8104	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22100 - 	CGI_10007422	superfamily	246669	231	364	1.57E-77	238.562	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22100 - 	CGI_10007422	superfamily	246669	98	222	2.93E-60	193.25	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22101 - 	CGI_10007423	superfamily	243092	399	694	5.26E-65	220.669	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22101 - 	CGI_10007423	superfamily	243092	36	220	1.70E-40	151.719	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22101 - 	CGI_10007423	superfamily	217837	793	899	1.36E-19	86.1073	cl04367	Utp12 superfamily	 - 	 - 	Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.
Q#22102 - 	CGI_10007424	superfamily	241563	63	100	2.02E-05	42.4664	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22103 - 	CGI_10007425	superfamily	241563	92	135	1.60E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22103 - 	CGI_10007425	superfamily	128778	133	249	0.00573388	35.3183	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#22104 - 	CGI_10007426	superfamily	241563	57	100	2.24E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22108 - 	CGI_10015109	superfamily	243161	11	96	3.12E-16	71.6565	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#22109 - 	CGI_10015110	superfamily	247856	223	281	2.84E-06	44.0757	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22109 - 	CGI_10015110	superfamily	246925	16	161	2.15E-17	80.0921	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#22110 - 	CGI_10015111	superfamily	243066	198	289	5.82E-43	149.626	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22110 - 	CGI_10015111	superfamily	219619	501	562	7.51E-13	64.9215	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#22111 - 	CGI_10015112	superfamily	247723	101	183	1.71E-50	165.882	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22111 - 	CGI_10015112	superfamily	221466	1	92	3.22E-11	59.2023	cl13630	U1snRNP70_N superfamily	 - 	 - 	"U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with pfam00076. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition."
Q#22115 - 	CGI_10015116	superfamily	243034	749	848	2.89E-10	59.316	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22115 - 	CGI_10015116	superfamily	243034	1259	1359	1.84E-07	50.8416	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22115 - 	CGI_10015116	superfamily	243034	518	617	1.24E-05	45.0636	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22115 - 	CGI_10015116	superfamily	243034	993	1080	3.87E-05	43.5228	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22115 - 	CGI_10015116	superfamily	243034	331	413	0.00265705	37.7448	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22115 - 	CGI_10015116	superfamily	243034	1336	1403	0.00877533	36.204	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22117 - 	CGI_10015118	superfamily	243176	8	533	0	1033.02	cl02777	chaperonin_like superfamily	 - 	 - 	"chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and  in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains."
Q#22119 - 	CGI_10015120	superfamily	144129	243	270	0.00969671	33.9095	cl02863	Tubulin-binding superfamily	 - 	 - 	"Tau and MAP protein, tubulin-binding repeat; This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif."
Q#22120 - 	CGI_10015121	superfamily	144129	324	353	0.000101044	40.0727	cl02863	Tubulin-binding superfamily	 - 	 - 	"Tau and MAP protein, tubulin-binding repeat; This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif."
Q#22120 - 	CGI_10015121	superfamily	144129	385	414	0.00225066	35.8355	cl02863	Tubulin-binding superfamily	 - 	 - 	"Tau and MAP protein, tubulin-binding repeat; This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif."
Q#22120 - 	CGI_10015121	superfamily	144129	356	384	0.00287428	35.8355	cl02863	Tubulin-binding superfamily	 - 	 - 	"Tau and MAP protein, tubulin-binding repeat; This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif."
Q#22122 - 	CGI_10015123	superfamily	242372	33	199	1.67E-28	107.457	cl01221	DTW superfamily	 - 	 - 	DTW domain; This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after.
Q#22123 - 	CGI_10015124	superfamily	247723	145	218	1.01E-33	125.957	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22123 - 	CGI_10015124	superfamily	241546	454	520	0.00148402	38.4109	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22125 - 	CGI_10015126	superfamily	220115	398	542	3.94E-42	147.889	cl07655	N-glycanase_C superfamily	 - 	 - 	"Peptide-N-glycosidase F, C terminal; Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins."
Q#22125 - 	CGI_10015126	superfamily	220114	254	376	9.24E-24	97.4725	cl07654	N-glycanase_N superfamily	 - 	 - 	"Peptide-N-glycosidase F, N terminal; Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins."
Q#22125 - 	CGI_10015126	superfamily	244870	103	183	9.70E-14	68.6047	cl08238	PA superfamily	N	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#22128 - 	CGI_10015129	superfamily	220545	266	315	2.17E-24	95.0002	cl15332	DUF2296 superfamily	 - 	 - 	"Predicted integral membrane metal-binding protein (DUF2296); This domain, found in various hypothetical bacterial and eukaryotic metal-binding proteins, has no known function."
Q#22128 - 	CGI_10015129	superfamily	221116	46	117	0.00689106	35.3634	cl12981	DUF3021 superfamily	N	 - 	Protein of unknown function (DUF3021); This is a bacterial family of uncharacterized proteins.
Q#22129 - 	CGI_10015130	superfamily	247999	277	328	4.93E-05	40.273	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#22129 - 	CGI_10015130	superfamily	245225	30	83	0.00131634	38.9819	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#22131 - 	CGI_10015132	superfamily	241563	62	101	0.00220982	33.6068	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22137 - 	CGI_10017116	superfamily	241645	12	76	1.54E-05	37.9274	cl00155	UBQ superfamily	N	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#22139 - 	CGI_10017118	superfamily	222150	306	329	0.00527523	35.0601	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22143 - 	CGI_10017122	superfamily	246616	1	319	1.12E-31	121.645	cl14105	MetH superfamily	 - 	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#22144 - 	CGI_10017123	superfamily	246918	353	389	1.05E-05	42.9591	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22145 - 	CGI_10017124	superfamily	246616	3	261	3.72E-21	90.0589	cl14105	MetH superfamily	 - 	 - 	"Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]"
Q#22146 - 	CGI_10017125	superfamily	246669	1923	2039	3.16E-05	45.1355	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22146 - 	CGI_10017125	superfamily	246669	1480	1631	2.74E-53	186.477	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22148 - 	CGI_10017127	superfamily	242913	121	167	2.42E-22	89.2171	cl02162	Fip1 superfamily	 - 	 - 	Fip1 motif; This short motif is about 40 amino acids in length. In the Fip1 protein that is a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase. This region of Fip1 is needed for the interaction with the Th1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor.
Q#22152 - 	CGI_10017131	superfamily	248097	89	214	1.03E-22	89.6318	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22154 - 	CGI_10017133	superfamily	128469	350	446	5.64E-25	100.222	cl17971	VPS9 superfamily	 - 	 - 	Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
Q#22155 - 	CGI_10014336	superfamily	245213	821	853	1.59E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22155 - 	CGI_10014336	superfamily	245213	1287	1321	2.40E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22155 - 	CGI_10014336	superfamily	245213	1203	1231	0.00228272	38.0014	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22155 - 	CGI_10014336	superfamily	243124	84	237	1.02E-18	85.9416	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#22155 - 	CGI_10014336	superfamily	243065	364	544	1.59E-08	55.1405	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#22155 - 	CGI_10014336	superfamily	241578	1369	1412	9.34E-06	47.7648	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22155 - 	CGI_10014336	superfamily	243060	1468	1555	1.37E-05	45.4476	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#22155 - 	CGI_10014336	superfamily	241578	862	902	1.47E-05	46.9944	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22155 - 	CGI_10014336	superfamily	245213	1116	1155	0.000155635	41.5656	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22155 - 	CGI_10014336	superfamily	241578	1323	1371	0.000342606	42.7572	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22155 - 	CGI_10014336	superfamily	241578	942	986	0.000822324	41.6016	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22155 - 	CGI_10014336	superfamily	221695	927	950	0.000910639	39.3606	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#22155 - 	CGI_10014336	superfamily	245213	1074	1107	0.00475642	37.2264	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22156 - 	CGI_10014337	superfamily	238159	26	456	0	575.89	cl15670	VATPase_H superfamily	 - 	 - 	"VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses  ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example."
Q#22159 - 	CGI_10014340	superfamily	241629	108	245	1.37E-45	156.52	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#22160 - 	CGI_10014341	superfamily	245213	257	286	0.000186571	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22160 - 	CGI_10014341	superfamily	241629	41	139	4.38E-32	118.212	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#22161 - 	CGI_10014342	superfamily	247912	44	405	9.84E-45	159.589	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#22164 - 	CGI_10014345	superfamily	241584	645	733	0.000492401	39.4019	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22164 - 	CGI_10014345	superfamily	241571	736	823	0.000191267	40.8587	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#22167 - 	CGI_10014348	superfamily	247725	19	147	4.89E-50	169.479	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22167 - 	CGI_10014348	superfamily	245201	187	436	4.21E-65	214.306	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22168 - 	CGI_10000558	superfamily	246936	415	435	0.00964864	34.7816	cl15354	CBS_pair superfamily	C	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#22170 - 	CGI_10000886	superfamily	247755	252	489	1.58E-147	425.415	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22170 - 	CGI_10000886	superfamily	216049	1	207	7.96E-44	157.062	cl18356	ABC_membrane superfamily	N	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#22173 - 	CGI_10019912	superfamily	216939	70	127	1.88E-07	44.5761	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#22173 - 	CGI_10019912	superfamily	216939	5	55	0.000520262	35.3313	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#22175 - 	CGI_10019914	superfamily	247743	161	279	4.05E-11	59.8523	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#22177 - 	CGI_10019916	superfamily	241845	95	259	4.28E-40	140.934	cl00407	tRNA_m1G_MT superfamily	 - 	 - 	"tRNA (Guanine-1)-methyltransferase; This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyzes the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA."
Q#22179 - 	CGI_10019918	superfamily	222324	148	214	1.25E-15	69.343	cl16352	zf-3CxxC superfamily	 - 	 - 	Zinc-binding domain; This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue.
Q#22179 - 	CGI_10019918	superfamily	205872	109	138	2.54E-11	55.9637	cl16353	zf-CCHC_2 superfamily	 - 	 - 	Zinc knuckle; This is a zinc-binding domain of the form CxxCxxxGHxxxxC from a variety of different species.
Q#22180 - 	CGI_10019919	superfamily	247069	187	358	1.36E-34	127.887	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#22180 - 	CGI_10019919	superfamily	247643	124	169	3.35E-11	59.1003	cl16919	CRAL_TRIO_N superfamily	 - 	 - 	"CRAL/TRIO, N-terminal domain; This all-alpha domain is found to the N-terminus of pfam00650."
Q#22180 - 	CGI_10019919	superfamily	218219	2	31	8.51E-06	44.6179	cl04693	PRELI superfamily	N	 - 	"PRELI-like family; This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins."
Q#22182 - 	CGI_10019921	superfamily	246669	444	593	1.07E-84	276.051	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22182 - 	CGI_10019921	superfamily	246669	1861	1993	2.53E-70	234.48	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22182 - 	CGI_10019921	superfamily	246669	1622	1745	1.76E-64	217.032	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22182 - 	CGI_10019921	superfamily	246669	983	1119	1.37E-63	215.1	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22182 - 	CGI_10019921	superfamily	246669	279	389	1.54E-56	193.947	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22182 - 	CGI_10019921	superfamily	149289	366	436	9.82E-30	115.461	cl06959	FerI superfamily	 - 	 - 	FerI (NUC094) domain; This domain is present in proteins of the Ferlin family. It is often located between two C2 domains.
Q#22182 - 	CGI_10019921	superfamily	116739	864	941	3.00E-29	114.517	cl06958	FerB superfamily	 - 	 - 	FerB (NUC096) domain; This is central domain B in proteins of the Ferlin family.
Q#22182 - 	CGI_10019921	superfamily	246669	14	117	1.29E-28	114.273	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22183 - 	CGI_10019922	superfamily	233514	387	658	1.27E-127	381.122	cl11769	EYA-cons_domain superfamily	 - 	 - 	eyes absent protein conserved domain; This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences.
Q#22185 - 	CGI_10019924	superfamily	243090	550	679	8.62E-63	210.031	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#22185 - 	CGI_10019924	superfamily	243077	23	74	1.37E-13	67.5705	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#22185 - 	CGI_10019924	superfamily	243090	723	850	5.95E-50	173.732	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#22185 - 	CGI_10019924	superfamily	243090	371	486	7.25E-39	141.802	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#22187 - 	CGI_10019926	superfamily	197729	128	146	0.00871968	31.8937	cl11732	LRRcap superfamily	 - 	 - 	occurring C-terminal to leucine-rich repeats; A motif occurring C-terminal to leucine-rich repeats in "sds22-like" and "typical" LRR-containing proteins.
Q#22188 - 	CGI_10019927	superfamily	243199	5	87	1.68E-09	54.9898	cl02808	RT_like superfamily	N	 - 	"RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs."
Q#22189 - 	CGI_10019928	superfamily	243109	20	203	1.49E-90	267.546	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#22189 - 	CGI_10019928	superfamily	243073	193	227	6.87E-07	44.5098	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#22190 - 	CGI_10019929	superfamily	247725	34	169	3.43E-30	114.399	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22191 - 	CGI_10019930	superfamily	247725	6	125	4.82E-21	84.3982	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22192 - 	CGI_10019931	superfamily	241637	1	70	7.77E-12	60.3998	cl00146	TFIIS_I superfamily	 - 	 - 	N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Q#22192 - 	CGI_10019931	superfamily	243122	129	246	2.15E-35	126.601	cl02637	TFIIS_M superfamily	 - 	 - 	"Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity."
Q#22192 - 	CGI_10019931	superfamily	207668	306	344	1.46E-17	75.3058	cl02609	TFIIS_C superfamily	 - 	 - 	Transcription factor S-II (TFIIS); Transcription factor S-II (TFIIS).  
Q#22193 - 	CGI_10019932	superfamily	217725	302	583	4.12E-25	105.658	cl18425	FGE-sulfatase superfamily	 - 	 - 	"Formylglycine-generating sulfatase enzyme; This domain is found in eukaryotic proteins required for post-translational sulphatase modification (SUMF1). These proteins are associated with the rare disorder multiple sulphatase deficiency (MSD). The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase. Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases. FGE is localised to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesised sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilised by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidized cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases."
Q#22193 - 	CGI_10019932	superfamily	247727	644	800	1.31E-14	73.404	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#22194 - 	CGI_10019933	superfamily	247907	926	1077	2.42E-33	127.92	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#22194 - 	CGI_10019933	superfamily	247907	1139	1298	2.55E-30	119.06	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#22194 - 	CGI_10019933	superfamily	247907	677	828	3.43E-29	115.978	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#22194 - 	CGI_10019933	superfamily	246676	341	561	4.58E-22	96.2598	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#22194 - 	CGI_10019933	superfamily	246671	25	176	3.91E-09	56.2772	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#22194 - 	CGI_10019933	superfamily	245213	1104	1132	8.20E-06	44.935	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22194 - 	CGI_10019933	superfamily	245213	874	916	0.0013592	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22194 - 	CGI_10019933	superfamily	246710	199	373	6.68E-17	80.5496	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#22195 - 	CGI_10019934	superfamily	245201	554	824	2.68E-166	498.485	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22195 - 	CGI_10019934	superfamily	247725	391	497	2.01E-45	160.845	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22195 - 	CGI_10019934	superfamily	146323	1139	1271	6.28E-52	180.32	cl04185	Focal_AT superfamily	 - 	 - 	"Focal adhesion targeting region; Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not."
Q#22195 - 	CGI_10019934	superfamily	215882	275	395	4.98E-13	67.691	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#22197 - 	CGI_10019936	superfamily	241551	54	153	2.73E-30	107.385	cl00016	Cyt_c_Oxidase_Vb superfamily	 - 	 - 	"Cytochrome c oxidase subunit Vb.  Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome.  Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region.  Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A.  The abnormally extended conformation is stable only in the CcO assembly."
Q#22199 - 	CGI_10019938	superfamily	220723	172	298	7.53E-23	91.5986	cl11043	ATG11 superfamily	 - 	 - 	"Autophagy-related protein 11; The function of this family is conflicting. In the fission yeast, Schizosaccharomyces pombe, this protein has been shown to interact with the telomere cap complex. However, in budding yeast, Saccharomyces cerevisiae, this protein is called ATG11 and is shown to be involved in autophagy."
Q#22201 - 	CGI_10019940	superfamily	112433	40	180	3.25E-83	258.184	cl04181	GCM superfamily	 - 	 - 	GCM motif protein; GCM motif protein.  
Q#22209 - 	CGI_10009003	superfamily	241563	8	53	0.00106703	37.3167	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22209 - 	CGI_10009003	superfamily	241563	62	103	0.00463115	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22210 - 	CGI_10009004	superfamily	241563	62	98	0.00162332	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22210 - 	CGI_10009004	superfamily	241563	8	53	0.00606967	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22212 - 	CGI_10009007	superfamily	110440	176	203	0.000470377	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#22214 - 	CGI_10009009	superfamily	222150	100	125	0.00142549	34.2897	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22214 - 	CGI_10009009	superfamily	222150	45	67	0.00249516	33.9045	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22214 - 	CGI_10009009	superfamily	222150	128	153	0.00462655	33.1342	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22215 - 	CGI_10006420	superfamily	241874	10	225	7.06E-106	317.886	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#22216 - 	CGI_10006421	superfamily	241874	7	306	2.40E-95	297.47	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#22217 - 	CGI_10006422	superfamily	241832	196	277	1.75E-36	127.25	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#22218 - 	CGI_10006423	superfamily	243072	97	179	6.47E-24	95.5282	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22220 - 	CGI_10006425	superfamily	241575	477	541	2.00E-09	54.9711	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#22220 - 	CGI_10006425	superfamily	241647	321	350	0.000844798	37.9655	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#22221 - 	CGI_10006426	superfamily	221494	48	334	5.05E-49	177.983	cl13664	DUF3608 superfamily	 - 	 - 	"Protein of unknown function (DUF3608); This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with pfam00610."
Q#22221 - 	CGI_10006426	superfamily	243038	1070	1152	1.54E-14	71.5381	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#22222 - 	CGI_10006427	superfamily	241809	179	288	7.33E-18	79.8431	cl00353	Ribosomal_L16_L10e superfamily	 - 	 - 	"Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus."
Q#22222 - 	CGI_10006427	superfamily	241809	392	501	7.33E-18	79.8431	cl00353	Ribosomal_L16_L10e superfamily	 - 	 - 	"Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus."
Q#22225 - 	CGI_10001381	superfamily	246680	40	105	8.20E-08	47.1964	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22225 - 	CGI_10001381	superfamily	246680	127	210	5.39E-07	45.0586	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22228 - 	CGI_10001462	superfamily	241574	112	201	1.27E-19	86.8709	cl00053	PTPc superfamily	NC	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#22228 - 	CGI_10001462	superfamily	241574	276	455	2.32E-14	71.0777	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#22231 - 	CGI_10001010	superfamily	242878	59	348	2.01E-99	297.663	cl02095	CDC50 superfamily	 - 	 - 	"LEM3 (ligand-effect modulator 3) family / CDC50 family; Members of this family have been predicted to contain transmembrane helices. The family member LEM3 is a ligand-effect modulator, mutation of which increases glucocorticoid receptor activity in response to dexamethasone and also confers increased activity on other intracellular receptors including the progesterone, oestrogen and mineralocorticoid receptors. LEM3 is thought to affect a downstream step in the glucocorticoid receptor pathway. Factors that modulate ligand responsiveness are likely to contribute to the context-specific actions of the glucocorticoid receptor in mammalian cells. The products of genes YNR048w, YNL323w and YCR094w (CDC50) show redundancy of function and are involved in regulation of transcription via CDC39. CDC39 (also known as NOT1) is normally a negative regulator of transcription either by affecting the general RNA polymerase II machinery or by altering chromatin structure. One function of CDC39 is to block activation of the mating response pathway in the absence of pheromone, and mutation causes arrest in G1 by activation of the pathway. It may be that the cold-sensitive arrest in G1 noticed in CDC50 mutants may be due to inactivation of CDC39. The effects of LEM3 on glucocorticoid receptor activity may also be due to effects on transcription via CDC39."
Q#22233 - 	CGI_10002196	superfamily	246683	79	388	2.29E-108	326.77	cl14648	Aldose_epim superfamily	 - 	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#22234 - 	CGI_10005487	superfamily	203136	17	138	9.23E-30	107.815	cl04867	LRAT superfamily	 - 	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#22235 - 	CGI_10005488	superfamily	203136	18	138	3.30E-31	110.897	cl04867	LRAT superfamily	 - 	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#22236 - 	CGI_10005490	superfamily	203136	22	146	7.88E-32	112.823	cl04867	LRAT superfamily	 - 	 - 	"Lecithin retinol acyltransferase; The full-length members of this family are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester."
Q#22237 - 	CGI_10005491	superfamily	245596	86	383	1.57E-112	336.099	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#22239 - 	CGI_10005493	superfamily	241644	59	197	6.44E-64	196.654	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#22240 - 	CGI_10005494	superfamily	220393	169	408	2.01E-57	192.59	cl10751	Tmem26 superfamily	 - 	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#22243 - 	CGI_10002360	superfamily	241575	280	335	0.00534282	36.13	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#22244 - 	CGI_10002361	superfamily	245029	15	140	2.51E-20	81.1547	cl09190	MAPEG superfamily	 - 	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#22246 - 	CGI_10002363	superfamily	220646	29	285	1.26E-54	179.505	cl10925	DUF2464 superfamily	 - 	 - 	"Protein of unknown function (DUF2464); This is a family of proteins conserved from worms to humans. Members have been annotated as FAM125A proteins, but their function is unknown."
Q#22247 - 	CGI_10013291	superfamily	243033	51	147	3.16E-07	46.1573	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#22248 - 	CGI_10013292	superfamily	243033	1	107	1.31E-08	48.0833	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#22249 - 	CGI_10013293	superfamily	243033	126	244	5.72E-23	91.2257	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#22250 - 	CGI_10013294	superfamily	192535	28	216	8.61E-07	48.361	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#22251 - 	CGI_10013295	superfamily	248067	635	751	4.91E-41	147.74	cl17513	ABC1 superfamily	 - 	 - 	"ABC1 family; This family includes ABC1 from yeast and AarF from E. coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex and E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins."
Q#22252 - 	CGI_10013296	superfamily	247799	121	186	2.62E-19	82.5243	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#22252 - 	CGI_10013296	superfamily	247799	480	543	1.09E-11	61.0367	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#22253 - 	CGI_10013297	superfamily	248054	11	77	2.61E-14	69.8084	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#22253 - 	CGI_10013297	superfamily	241563	535	560	0.00151999	37.844	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22253 - 	CGI_10013297	superfamily	245835	559	669	0.00155538	40.0595	cl12013	BAR superfamily	NC	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#22255 - 	CGI_10013299	superfamily	243109	325	461	1.41E-16	77.7021	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#22255 - 	CGI_10013299	superfamily	243109	697	812	4.05E-09	55.3605	cl02614	SPRY superfamily	 - 	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#22259 - 	CGI_10013303	superfamily	217062	174	414	1.06E-39	143.949	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#22261 - 	CGI_10013306	superfamily	203495	356	406	1.78E-05	42.6102	cl10663	Cep57_MT_bd superfamily	N	 - 	"Centrosome microtubule-binding domain of Cep57; This C-terminal region of Cep57 binds, nucleates and bundles microtubules. The N-terminal part, family Cep57_CLD, pfam14073, is the centrosome localisation domain Cep57."
Q#22265 - 	CGI_10013310	superfamily	247637	55	404	3.26E-158	453.218	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#22267 - 	CGI_10021955	superfamily	245847	62	203	3.01E-34	130.165	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#22267 - 	CGI_10021955	superfamily	247907	210	366	4.59E-27	109.815	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#22267 - 	CGI_10021955	superfamily	247907	825	970	1.78E-21	93.6368	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#22267 - 	CGI_10021955	superfamily	247907	421	542	9.72E-16	76.688	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#22267 - 	CGI_10021955	superfamily	247907	1045	1185	4.08E-15	74.762	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#22267 - 	CGI_10021955	superfamily	245213	570	604	4.64E-05	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22268 - 	CGI_10021956	superfamily	222150	355	378	5.22E-05	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22268 - 	CGI_10021956	superfamily	222150	232	256	0.00108577	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22269 - 	CGI_10021957	superfamily	241739	203	527	2.87E-171	489.77	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#22269 - 	CGI_10021957	superfamily	245205	92	191	2.33E-45	155.799	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#22270 - 	CGI_10021958	superfamily	206130	100	191	0.000343476	39.1091	cl16501	DUF4218 superfamily	C	 - 	Domain of unknown function (DUF4218); Domain of unknown function (DUF4218).  
Q#22271 - 	CGI_10021959	superfamily	247941	42	176	2.69E-08	50.4121	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#22272 - 	CGI_10021960	superfamily	247724	21	185	1.11E-118	337.655	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22274 - 	CGI_10021962	superfamily	243058	399	510	2.23E-07	50.0055	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#22274 - 	CGI_10021962	superfamily	243058	130	246	2.44E-07	49.6203	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#22274 - 	CGI_10021962	superfamily	243689	36	103	2.86E-10	57.639	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#22275 - 	CGI_10021963	superfamily	192997	289	443	1.96E-29	115.757	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#22276 - 	CGI_10021964	superfamily	243072	511	638	4.35E-31	120.181	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22276 - 	CGI_10021964	superfamily	243072	580	700	6.64E-25	102.462	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22276 - 	CGI_10021964	superfamily	243072	340	468	8.54E-25	102.077	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22276 - 	CGI_10021964	superfamily	243072	268	396	3.86E-24	100.151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22276 - 	CGI_10021964	superfamily	243072	164	290	2.03E-22	95.143	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22278 - 	CGI_10021966	superfamily	247986	428	506	0.000169123	43.1306	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#22279 - 	CGI_10021967	superfamily	247986	444	585	4.65E-10	59.309	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#22279 - 	CGI_10021967	superfamily	247986	262	342	3.43E-08	53.531	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#22279 - 	CGI_10021967	superfamily	245225	6	186	1.02E-10	63.0873	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#22279 - 	CGI_10021967	superfamily	241888	347	456	0.000265945	41.7853	cl00473	BI-1-like superfamily	C	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#22280 - 	CGI_10021968	superfamily	247692	2	639	0	1053.68	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#22281 - 	CGI_10021969	superfamily	218423	143	501	7.12E-168	493.307	cl09358	NAGLU superfamily	 - 	 - 	"Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain; Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterized by neurological dysfunction but relatively mild somatic manifestations. The structure shows that the enzyme is composed of three domains. This central domain has a tim barrel fold."
Q#22281 - 	CGI_10021969	superfamily	221877	506	801	4.90E-75	247.236	cl15206	NAGLU_C superfamily	 - 	 - 	"Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain; Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterized by neurological dysfunction but relatively mild somatic manifestations. The structure shows that the enzyme is composed of three domains. This C-terminal domain has an all alpha helical fold."
Q#22281 - 	CGI_10021969	superfamily	193444	43	129	5.09E-21	89.2288	cl15205	NAGLU_N superfamily	 - 	 - 	"Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterized by neurological dysfunction but relatively mild somatic manifestations. The structure shows that the enzyme is composed of three domains. This N-terminal domain has an alpha-beta fold."
Q#22282 - 	CGI_10021970	superfamily	247769	187	304	0.000198835	40.7857	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#22283 - 	CGI_10021971	superfamily	247856	33	75	9.73E-07	42.9201	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22283 - 	CGI_10021971	superfamily	247856	103	163	1.11E-06	42.9201	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22284 - 	CGI_10021972	superfamily	221138	10	303	1.33E-64	228.592	cl18592	Med23 superfamily	C	 - 	"Mediator complex subunit 23; Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice."
Q#22285 - 	CGI_10021973	superfamily	221138	2	991	0	1085.66	cl18592	Med23 superfamily	N	 - 	"Mediator complex subunit 23; Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice."
Q#22287 - 	CGI_10021975	superfamily	217473	106	276	1.42E-14	70.8569	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#22288 - 	CGI_10021976	superfamily	246918	249	300	0.000167775	39.1071	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22288 - 	CGI_10021976	superfamily	246918	14	70	0.000376313	37.9515	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22288 - 	CGI_10021976	superfamily	246918	190	217	0.0076423	33.9182	cl15278	TSP_1 superfamily	C	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22289 - 	CGI_10021977	superfamily	245201	3	258	2.47E-157	460.478	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22289 - 	CGI_10021977	superfamily	201217	577	625	5.20E-10	56.38	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22289 - 	CGI_10021977	superfamily	201217	410	458	2.24E-09	54.454	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22289 - 	CGI_10021977	superfamily	205718	561	590	0.000280812	39.3958	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22289 - 	CGI_10021977	superfamily	201217	628	672	0.000340644	39.4312	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22290 - 	CGI_10021978	superfamily	245604	6	78	1.11E-19	82.8375	cl11404	Biotinyl_lipoyl_domains superfamily	 - 	 - 	"Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue."
Q#22290 - 	CGI_10021978	superfamily	215782	218	430	1.30E-87	268.264	cl18344	2-oxoacid_dh superfamily	 - 	 - 	2-oxoacid dehydrogenases acyltransferase (catalytic domain); These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain.
Q#22290 - 	CGI_10021978	superfamily	202412	115	151	3.42E-13	63.9805	cl03729	E3_binding superfamily	 - 	 - 	e3 binding domain; This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit.
Q#22291 - 	CGI_10021979	superfamily	246597	27	324	4.41E-86	269.556	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#22292 - 	CGI_10021980	superfamily	241766	1	258	5.05E-107	324.675	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#22292 - 	CGI_10021980	superfamily	241766	307	546	5.78E-95	293.474	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#22294 - 	CGI_10021983	superfamily	217956	227	374	7.93E-38	134.845	cl04443	PDCD2_C superfamily	N	 - 	"Programmed cell death protein 2, C-terminal putative domain; Programmed cell death protein 2, C-terminal putative domain.  "
Q#22295 - 	CGI_10021984	superfamily	218936	32	176	8.35E-55	173.93	cl05619	PITH superfamily	 - 	 - 	"PITH domain; This family was formerly known as DUF1000. The full-length, Txnl1, protein which is a probable component of the 26S proteasome, uses its C-terminal, PITH, domain to associate specifically with the 26S proteasome. PITH derives from proteasome-interacting thioredoxin domain."
Q#22296 - 	CGI_10021985	superfamily	220226	9	279	4.09E-107	314.551	cl09658	XendoU superfamily	 - 	 - 	Endoribonuclease XendoU; This is a family of endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.
Q#22297 - 	CGI_10021986	superfamily	241872	4	73	1.17E-16	73.2694	cl00453	CDP-OH_P_transf superfamily	C	 - 	CDP-alcohol phosphatidyltransferase; All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.
Q#22298 - 	CGI_10021987	superfamily	241886	1	226	1.84E-61	197.782	cl00470	Aldo_ket_red superfamily	C	 - 	"Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others."
Q#22300 - 	CGI_10021989	superfamily	241884	2	138	2.12E-84	249.844	cl00467	Ntn_hydrolase superfamily	N	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#22302 - 	CGI_10021991	superfamily	247916	152	222	2.82E-13	65.8671	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#22303 - 	CGI_10021992	superfamily	248312	25	182	5.66E-05	40.4232	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#22304 - 	CGI_10019751	superfamily	220087	63	137	9.02E-12	58.8132	cl18544	zf-DNA_Pol superfamily	C	 - 	"DNA Polymerase alpha zinc finger; The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain."
Q#22305 - 	CGI_10019752	superfamily	245230	3	409	0	906.651	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#22308 - 	CGI_10019756	superfamily	241594	1910	2378	5.96E-104	339.926	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#22308 - 	CGI_10019756	superfamily	243072	364	476	3.54E-21	92.8318	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22308 - 	CGI_10019756	superfamily	115363	1286	1347	7.24E-31	118.628	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#22308 - 	CGI_10019756	superfamily	203750	1117	1250	1.94E-16	79.2761	cl18248	Sad1_UNC superfamily	 - 	 - 	"Sad1 / UNC-like C-terminal; The C. elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development. The S. pombe Sad1 protein localises at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2. The SUN domain of Sun2 has been demonstrated to be in the periplasm."
Q#22309 - 	CGI_10019757	superfamily	247755	392	603	5.85E-69	222.799	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22309 - 	CGI_10019757	superfamily	241940	14	293	3.86E-57	195.526	cl00549	ABC_membrane_2 superfamily	 - 	 - 	ABC transporter transmembrane region 2; This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with pfam00664. Mutations in this domain in human ABCD3 (PMP70) are believed responsible for Zellweger Syndrome-2; mutations in human ABCD1 (ALD) are responsible for recessive X-linked adrenoleukodystrophy. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids.
Q#22311 - 	CGI_10019759	superfamily	243072	124	189	5.42E-17	75.1126	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22312 - 	CGI_10019760	superfamily	242205	34	148	5.98E-39	130.887	cl00937	Ribosomal_L21e superfamily	N	 - 	Ribosomal protein L21e; Ribosomal protein L21e.  
Q#22315 - 	CGI_10019763	superfamily	241874	36	429	1.45E-88	280.56	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#22317 - 	CGI_10019765	superfamily	241984	148	398	2.97E-56	186.693	cl00615	Membrane-FADS-like superfamily	 - 	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#22317 - 	CGI_10019765	superfamily	242849	11	84	4.06E-23	92.2668	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#22320 - 	CGI_10019769	superfamily	247723	596	689	5.79E-33	123.482	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22320 - 	CGI_10019769	superfamily	247723	243	318	1.99E-28	110.038	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22320 - 	CGI_10019769	superfamily	247723	446	526	7.95E-27	105.371	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22320 - 	CGI_10019769	superfamily	247723	16	89	1.94E-26	104.236	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22320 - 	CGI_10019769	superfamily	247723	148	217	0.000593476	38.7289	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22326 - 	CGI_10019775	superfamily	245226	29	116	0.00149432	37.3356	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#22328 - 	CGI_10019777	superfamily	216939	60	124	3.17E-06	41.4945	cl03492	PC4 superfamily	 - 	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#22331 - 	CGI_10019780	superfamily	241568	455	493	0.000124918	40.9092	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#22331 - 	CGI_10019780	superfamily	241568	391	435	0.00109908	38.2128	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#22331 - 	CGI_10019780	superfamily	214531	731	774	4.01E-07	47.9817	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#22331 - 	CGI_10019780	superfamily	214531	774	814	1.21E-05	43.7445	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#22331 - 	CGI_10019780	superfamily	214531	238	278	1.91E-05	42.9741	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#22332 - 	CGI_10019781	superfamily	214531	13	56	3.28E-08	46.0557	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#22332 - 	CGI_10019781	superfamily	214531	58	99	1.47E-07	44.1297	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#22333 - 	CGI_10010471	superfamily	242203	1	252	2.94E-62	200.989	cl00935	Brix superfamily	 - 	 - 	Brix domain; Brix domain.  
Q#22336 - 	CGI_10010474	superfamily	245202	8	53	2.61E-23	84.6091	cl09927	S1_like superfamily	C	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#22340 - 	CGI_10010478	superfamily	245856	2	184	9.84E-71	217.958	cl12060	AP2Ec superfamily	N	 - 	"AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-hexulose 3-phosphate to D-fructose 6-phosphate, via cleaving the phosphoesterbond with the sugar."
Q#22341 - 	CGI_10001323	superfamily	241578	55	200	1.65E-31	120.474	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22341 - 	CGI_10001323	superfamily	241578	458	609	8.17E-23	95.8214	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22341 - 	CGI_10001323	superfamily	245213	417	450	5.54E-12	61.4986	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22341 - 	CGI_10001323	superfamily	241578	235	392	2.23E-24	100.38	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22342 - 	CGI_10001324	superfamily	247947	51	85	0.0001726	34.6677	cl17393	HTH_Hin_like superfamily	 - 	 - 	"Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a DNA-binding domain (HTH_Hin) and a catalytic domain."
Q#22343 - 	CGI_10001516	superfamily	207654	228	273	8.37E-15	67.0826	cl02574	Annexin superfamily	C	 - 	Annexin; This family of annexins also includes giardin that has been shown to function as an annexin.
Q#22345 - 	CGI_10016952	superfamily	243119	289	333	0.00498261	34.3317	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#22347 - 	CGI_10016954	superfamily	245201	2	136	4.65E-31	120.804	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22348 - 	CGI_10016955	superfamily	245201	43	240	9.83E-46	161.636	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22349 - 	CGI_10016956	superfamily	241748	213	521	7.10E-177	502.936	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#22350 - 	CGI_10016957	superfamily	246748	52	383	1.55E-126	374.586	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#22351 - 	CGI_10016958	superfamily	246748	1	56	2.63E-25	96.0863	cl14876	Zinc_peptidase_like superfamily	N	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#22352 - 	CGI_10016959	superfamily	241743	22	140	3.92E-35	121.647	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#22353 - 	CGI_10016960	superfamily	219898	1	54	7.96E-09	51.0712	cl18533	DUF1751 superfamily	N	 - 	"Eukaryotic integral membrane protein (DUF1751); This domain is found in eukaryotic integral membrane proteins. YOL107W, a Saccharomyces cerervisiae protein, has been shown to localise COP II vesicles."
Q#22355 - 	CGI_10016962	superfamily	241832	3	90	3.87E-49	158.286	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#22355 - 	CGI_10016962	superfamily	243175	104	227	1.33E-45	150.549	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#22357 - 	CGI_10016964	superfamily	241584	209	299	2.09E-18	81.7739	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22357 - 	CGI_10016964	superfamily	241584	304	388	2.09E-08	52.4987	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22357 - 	CGI_10016964	superfamily	241584	105	204	1.66E-07	49.8023	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22357 - 	CGI_10016964	superfamily	241584	403	494	2.56E-06	46.3355	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22358 - 	CGI_10016965	superfamily	241584	247	331	3.17E-10	57.5063	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22358 - 	CGI_10016965	superfamily	241584	172	242	1.26E-08	52.8839	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22358 - 	CGI_10016965	superfamily	241584	73	166	1.38E-07	49.8023	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22358 - 	CGI_10016965	superfamily	241584	346	437	3.68E-06	45.5651	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22360 - 	CGI_10016967	superfamily	241607	503	538	1.50E-15	72.3369	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#22364 - 	CGI_10016971	superfamily	243092	19	320	3.95E-57	191.394	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22365 - 	CGI_10016972	superfamily	245201	202	406	3.85E-42	150.465	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22365 - 	CGI_10016972	superfamily	216276	7	86	4.02E-18	79.5143	cl15639	Activin_recp superfamily	 - 	 - 	"Activin types I and II receptor domain; This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box."
Q#22365 - 	CGI_10016972	superfamily	243113	168	194	2.67E-09	53.2682	cl02621	TGF_beta_GS superfamily	 - 	 - 	Transforming growth factor beta type I GS-motif; This motif is found in the transforming growth factor beta (TGF-beta) type I which regulates cell growth and differentiation. The name of the GS motif comes from its highly conserved GSGSGLP signature in the cytoplasmic juxtamembrane region immediately preceding the protein's kinase domain. Point mutations in the GS motif modify the signaling ability of the type I receptor.
Q#22370 - 	CGI_10009208	superfamily	241734	37	449	0	539.003	cl00261	PLPDE_III superfamily	 - 	 - 	"Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity."
Q#22373 - 	CGI_10009211	superfamily	245456	126	395	0	570.657	cl10970	AP_MHD_Cterm superfamily	 - 	 - 	"C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15."
Q#22373 - 	CGI_10009211	superfamily	242876	4	111	6.54E-06	44.2673	cl02092	Clat_adaptor_s superfamily	N	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#22374 - 	CGI_10009212	superfamily	241754	392	695	2.64E-44	165.101	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#22374 - 	CGI_10009212	superfamily	203134	363	394	0.00167551	38.0465	cl04866	CHORD superfamily	N	 - 	"CHORD; CHORD represents a Zn binding domain. Silencing of the C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development."
Q#22375 - 	CGI_10009214	superfamily	241883	130	191	1.03E-06	45.518	cl00466	ATP-synt_C superfamily	 - 	 - 	ATP synthase subunit C; ATP synthase subunit C.  
Q#22375 - 	CGI_10009214	superfamily	241883	264	325	1.03E-06	45.518	cl00466	ATP-synt_C superfamily	 - 	 - 	ATP synthase subunit C; ATP synthase subunit C.  
Q#22375 - 	CGI_10009214	superfamily	241883	43	92	0.00415562	34.7324	cl00466	ATP-synt_C superfamily	C	 - 	ATP synthase subunit C; ATP synthase subunit C.  
Q#22376 - 	CGI_10009215	superfamily	243082	1403	1773	4.27E-125	399.324	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#22376 - 	CGI_10009215	superfamily	241643	5	41	2.21E-07	50.1503	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#22377 - 	CGI_10009216	superfamily	245201	26	318	0	550.997	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22380 - 	CGI_10003919	superfamily	243034	29	93	0.00248949	36.5892	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22381 - 	CGI_10003920	superfamily	241587	3	57	1.10E-10	51.521	cl00069	GGL superfamily	 - 	 - 	"G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors"
Q#22382 - 	CGI_10003921	superfamily	241583	208	408	4.35E-56	193.994	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#22382 - 	CGI_10003921	superfamily	216572	76	177	2.80E-12	65.3738	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#22382 - 	CGI_10003921	superfamily	246918	978	1030	3.66E-07	48.7371	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22382 - 	CGI_10003921	superfamily	246918	517	554	0.000340432	39.8775	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22383 - 	CGI_10003922	superfamily	248312	127	284	1.92E-09	54.6669	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#22384 - 	CGI_10003923	superfamily	207922	2	69	8.02E-19	73.4345	cl03352	Ribosomal_L38e superfamily	 - 	 - 	Ribosomal L38e protein family; Ribosomal L38e protein family.  
Q#22385 - 	CGI_10002695	superfamily	241764	109	187	1.35E-26	101.585	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#22385 - 	CGI_10002695	superfamily	247743	269	330	3.06E-10	57.5411	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#22385 - 	CGI_10002695	superfamily	247743	322	357	2.66E-05	42.2017	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#22386 - 	CGI_10002696	superfamily	243066	22	123	1.76E-20	85.7469	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22386 - 	CGI_10002696	superfamily	198867	133	240	6.60E-12	61.5884	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#22387 - 	CGI_10002697	superfamily	243092	2	277	5.01E-20	86.2348	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22388 - 	CGI_10002698	superfamily	241550	82	366	2.62E-95	289.869	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#22389 - 	CGI_10002699	superfamily	246925	15	166	1.25E-09	57.3654	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#22390 - 	CGI_10002700	superfamily	220534	1	222	3.46E-78	237.699	cl10820	RLL superfamily	 - 	 - 	Putative carnitine deficiency-associated protein; This family of proteins conserved from nematodes to humans is of approximately 250 amino acids. It is purported to be carnitine deficiency-associated protein but this could not be confirmed. It carries a characteristic RLL sequence-motif. The function is unknown.
Q#22391 - 	CGI_10002701	superfamily	246669	45	109	2.16E-21	87.5968	cl14603	C2 superfamily	N	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22391 - 	CGI_10002701	superfamily	246708	1	19	2.00E-05	42.1178	cl14781	PI-PLC-Y superfamily	N	 - 	"Phosphatidylinositol-specific phospholipase C, Y domain; This associates with pfam00388 to form a single structural unit."
Q#22392 - 	CGI_10016747	superfamily	247683	242	298	8.32E-21	86.971	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#22392 - 	CGI_10016747	superfamily	245601	366	593	7.92E-14	69.2732	cl11399	HP superfamily	 - 	 - 	"Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed."
Q#22392 - 	CGI_10016747	superfamily	241643	22	59	1.18E-05	43.2167	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#22393 - 	CGI_10016748	superfamily	209411	250	369	1.14E-10	60.0397	cl12008	FANCE_c-term superfamily	N	 - 	"Fanconi anemia complementation group E protein, C-terminal domain; Fanconi Anemia (FA) is an autosomal recessive disorder associated with increased susceptibility to various cancers, bone marrow failure, cardiac, renal, and limb malformations, and other characteristics. Cells are highly sensitive to DNA damaging agents. A multi-subunit protein complex, the FA core complex, is responsible for ubiquitination of the protein FANCD2 in response to DNA damage. This monoubiquitination results in a downstream effect on homology-directed DNA repair. FANCE is part of the FA core complex and its C-terminal domain, which is modeled here, has been shown to directly interact with FANCD2. The domain contains a five-fold repeat of a structural unit similar to ARM and HEAT repeats. FANCE appears conserved in metazoa and in plants."
Q#22395 - 	CGI_10016750	superfamily	241624	118	303	2.19E-14	70.0778	cl00120	PP2Cc superfamily	N	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#22396 - 	CGI_10016751	superfamily	245087	9	272	3.69E-33	125.434	cl09515	PCNA superfamily	 - 	 - 	"Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea.  These polymerase processivity factors play a role in DNA replication and repair.  PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.   PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY]."
Q#22397 - 	CGI_10016752	superfamily	246597	9	186	2.51E-125	353.437	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#22399 - 	CGI_10016754	superfamily	243091	66	191	9.27E-27	100.101	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#22400 - 	CGI_10016755	superfamily	247805	509	662	5.38E-05	43.48	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#22400 - 	CGI_10016755	superfamily	222427	1055	1330	3.33E-119	376.14	cl18674	Helicase_C_4 superfamily	 - 	 - 	"Helicase_C-like; Strawberry notch proteins carry DExD/H-box groups and Helicase_C domains. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes."
Q#22401 - 	CGI_10016756	superfamily	247057	122	183	1.04E-21	88.5051	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#22401 - 	CGI_10016756	superfamily	248012	224	325	1.92E-17	77.618	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#22401 - 	CGI_10016756	superfamily	247057	53	121	9.93E-17	74.646	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#22402 - 	CGI_10016757	superfamily	243058	332	436	1.84E-06	46.1535	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#22405 - 	CGI_10016760	superfamily	247755	1148	1368	1.03E-121	379.53	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22405 - 	CGI_10016760	superfamily	247755	525	726	5.27E-105	332.512	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22405 - 	CGI_10016760	superfamily	216049	824	1101	4.52E-15	76.1706	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#22407 - 	CGI_10016762	superfamily	247755	1130	1350	2.58E-122	381.071	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22407 - 	CGI_10016762	superfamily	247755	507	708	1.22E-105	334.438	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22407 - 	CGI_10016762	superfamily	216049	212	463	9.32E-17	81.1782	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#22407 - 	CGI_10016762	superfamily	216049	806	1083	2.72E-15	76.5558	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#22408 - 	CGI_10016763	superfamily	243058	25	137	0.000200212	39.9904	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#22408 - 	CGI_10016763	superfamily	247804	536	569	0.00361142	36.0059	cl17250	SANT superfamily	C	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#22409 - 	CGI_10016764	superfamily	245210	30	408	8.04E-115	371.891	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#22409 - 	CGI_10016764	superfamily	247637	1139	1248	0.000119572	44.8674	cl16912	MDR superfamily	NC	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#22410 - 	CGI_10016765	superfamily	243092	107	371	3.32E-34	128.607	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22411 - 	CGI_10016766	superfamily	203903	70	115	2.24E-13	65.2613	cl07067	cwf21 superfamily	 - 	 - 	cwf21 domain; The cwf21 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe. The function of the cwf21 domain is to bind directly to the spliceosomal protein Prp8. Mutations in the cwf21 domain prevent Prp8 from binding. The structure of this domain has recently been solved which shows this domain to be composed of two alpha helices.
Q#22413 - 	CGI_10016768	superfamily	246679	4	129	8.47E-79	237.623	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#22413 - 	CGI_10016768	superfamily	246679	139	251	3.99E-09	52.8054	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#22414 - 	CGI_10016769	superfamily	150420	13	123	7.98E-12	62.0602	cl18042	Jnk-SapK_ap_N superfamily	C	 - 	JNK_SAPK-associated protein-1; This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end.
Q#22414 - 	CGI_10016769	superfamily	221118	326	388	9.40E-06	42.7096	cl12985	RILP superfamily	 - 	 - 	Rab interacting lysosomal protein; RILP contains a domain which contains two coiled-coil regions and is found mainly in the cytosol. RILP is recruited onto late endosomal and lysosomal membranes by Rab7 and acts as a downstream effector of Rab7. This recruitment process is important for phagosome maturation and fusion with late endosomes and lysosomes.
Q#22415 - 	CGI_10016770	superfamily	216301	1	155	7.79E-50	160.122	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#22416 - 	CGI_10016771	superfamily	247861	185	283	2.64E-06	45.5804	cl17307	SpoU_methylase superfamily	C	 - 	SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
Q#22417 - 	CGI_10016772	superfamily	243066	2	78	1.64E-20	86.4529	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22417 - 	CGI_10016772	superfamily	219619	343	393	1.15E-11	60.6843	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#22422 - 	CGI_10016777	superfamily	152008	330	375	0.00730259	34.6649	cl13085	DUF3234 superfamily	C	 - 	Protein of unknown function (DUF3234); This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed.
Q#22424 - 	CGI_10016779	superfamily	247792	367	411	1.10E-12	63.6188	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22425 - 	CGI_10016780	superfamily	214020	5	97	1.37E-13	64.7762	cl17165	SKA2 superfamily	 - 	 - 	"Spindle and kinetochore-associated protein 2; SKA2, also called FAM33A, is a component of the SKA complex, which is formed by the association of three subunits (SKA1, SKA2, annd SKA3). The SKA complex is essential for accurate cell division. It functions with the Ndc80 network to establish stable kinetochore-microtubule interactions, which are crucial for the highly orchestrated chromosome movements during mitosis. The biological unit is a W-shaped homodimer of the three-subunit complex. SKA2 has also been identified as a glucocorticoid receptor-interacting protein and may be involved in regulating cancer cell proliferation."
Q#22425 - 	CGI_10016780	superfamily	151803	176	247	3.49E-06	43.6869	cl12898	DUF3161 superfamily	 - 	 - 	Protein of unknown function (DUF3161); This eukaryotic family of proteins has no known function.
Q#22426 - 	CGI_10016781	superfamily	243074	6	51	5.90E-08	49.0421	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#22428 - 	CGI_10016783	superfamily	221180	57	130	2.17E-18	76.9843	cl13206	Vma12 superfamily	C	 - 	"Endoplasmic reticulum-based factor for assembly of V-ATPase; The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterized member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum."
Q#22429 - 	CGI_10016784	superfamily	220379	22	137	6.01E-23	95.5747	cl10734	DRY_EERY superfamily	 - 	 - 	"Alternative splicing regulator; This entry represents the conserved N-terminal region of SWAP (suppressor-of-white-apricot protein) proteins. This region contains two highly conserved motifs, viz: DRY and EERY, which appear to be the sites for alternative splicing of exons 2 and 3 of the SWAP mRNA. These proteins are thus thought to be involved in auto-regulation of pre-mRNA splicing. Most family members are associated with two Surp domains pfam01805 and an Arginine- serine-rich binding region towards the C-terminus."
Q#22429 - 	CGI_10016784	superfamily	243154	181	231	2.79E-15	71.8497	cl02715	Surp superfamily	 - 	 - 	Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
Q#22429 - 	CGI_10016784	superfamily	243154	418	450	0.000168382	40.2633	cl02715	Surp superfamily	C	 - 	Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
Q#22430 - 	CGI_10016785	superfamily	241623	158	439	6.50E-179	507.924	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#22430 - 	CGI_10016785	superfamily	202180	505	535	1.25E-11	59.7848	cl03505	FATC superfamily	 - 	 - 	"FATC domain; The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability."
Q#22438 - 	CGI_10023210	superfamily	150820	18	304	5.42E-63	206.994	cl10894	DuoxA superfamily	 - 	 - 	"Dual oxidase maturation factor; DuoxA (Dual oxidase maturation factor) is the essential protein necessary for the final release of DUOX2 (an NADPH:O2 oxidoreductase flavoprotein) from the endoplasmic reticulum. Dual oxidases (DUOX1 and DUOX2) constitute the catalytic core of the hydrogen peroxide generator, which generates H2O2 at the apical membrane of thyroid follicular cells, essential for iodination of thyroglobulin by thyroid peroxidases. DuoxA carries five membrane-integral regions including a reverse signal-anchor with external N-terminus (type III) and two N-glycosylation sites. It is conserved from nematodes to humans."
Q#22439 - 	CGI_10023211	superfamily	150820	18	303	7.18E-68	219.32	cl10894	DuoxA superfamily	 - 	 - 	"Dual oxidase maturation factor; DuoxA (Dual oxidase maturation factor) is the essential protein necessary for the final release of DUOX2 (an NADPH:O2 oxidoreductase flavoprotein) from the endoplasmic reticulum. Dual oxidases (DUOX1 and DUOX2) constitute the catalytic core of the hydrogen peroxide generator, which generates H2O2 at the apical membrane of thyroid follicular cells, essential for iodination of thyroglobulin by thyroid peroxidases. DuoxA carries five membrane-integral regions including a reverse signal-anchor with external N-terminus (type III) and two N-glycosylation sites. It is conserved from nematodes to humans."
Q#22440 - 	CGI_10023212	superfamily	243066	3	107	4.65E-11	59.9385	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22440 - 	CGI_10023212	superfamily	217312	256	380	7.43E-07	49.5213	cl03827	NPH3 superfamily	N	 - 	"NPH3 family; Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase. Mutations in NPH3 disrupt early signaling occurring downstream of the NPH1 photoreceptor. The NPH3 gene encodes a NPH1-interacting protein. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay."
Q#22441 - 	CGI_10023213	superfamily	247723	548	613	3.40E-20	85.8016	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22441 - 	CGI_10023213	superfamily	241762	7	47	3.28E-14	68.6346	cl00297	R3H superfamily	N	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#22442 - 	CGI_10023214	superfamily	248097	37	167	8.47E-22	85.7798	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22443 - 	CGI_10023215	superfamily	248097	21	151	7.33E-22	85.7798	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22444 - 	CGI_10023216	superfamily	248097	4	134	1.70E-18	76.1498	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22445 - 	CGI_10023217	superfamily	248097	4	135	7.89E-19	76.9202	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22447 - 	CGI_10023219	superfamily	217293	1	196	4.17E-46	158.565	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#22447 - 	CGI_10023219	superfamily	202474	203	286	6.11E-16	74.9977	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#22448 - 	CGI_10023220	superfamily	217293	1	196	4.32E-39	139.305	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#22448 - 	CGI_10023220	superfamily	202474	203	286	5.15E-14	69.2197	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#22452 - 	CGI_10023224	superfamily	247683	72	125	0.00013035	37.8523	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#22452 - 	CGI_10023224	superfamily	205121	171	195	0.00124956	34.7872	cl18263	zf-met superfamily	 - 	 - 	"Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding."
Q#22453 - 	CGI_10023225	superfamily	217545	46	352	7.02E-107	319.265	cl04056	Peptidase_C54 superfamily	 - 	 - 	Peptidase family C54; Peptidase family C54.  
Q#22458 - 	CGI_10023230	superfamily	215754	69	151	4.23E-18	76.9084	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#22458 - 	CGI_10023230	superfamily	215754	178	252	1.98E-14	66.508	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#22458 - 	CGI_10023230	superfamily	215754	1	64	5.63E-11	57.2632	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#22459 - 	CGI_10023231	superfamily	241578	30	196	4.00E-39	141.211	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22459 - 	CGI_10023231	superfamily	241578	258	405	2.05E-29	114.311	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22459 - 	CGI_10023231	superfamily	241578	446	601	2.09E-05	43.7559	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22461 - 	CGI_10023233	superfamily	241570	139	250	1.86E-22	93.1593	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#22462 - 	CGI_10023234	superfamily	242183	26	69	0.00972993	32.2178	cl00907	Glutaminase superfamily	N	 - 	Glutaminase; This family of enzymes deaminates glutamine to glutamate EC:3.5.1.2.
Q#22464 - 	CGI_10023236	superfamily	217203	31	565	0	583.482	cl03678	CDC45 superfamily	 - 	 - 	"CDC45-like protein; CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others."
Q#22465 - 	CGI_10023237	superfamily	248458	191	357	0.000667393	41.1453	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22465 - 	CGI_10023237	superfamily	227469	392	632	6.02E-70	233.295	cl12196	UFD1 superfamily	C	 - 	"Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]"
Q#22465 - 	CGI_10023237	superfamily	199528	12	130	2.48E-10	61.8764	cl15392	PRK10429 superfamily	C	 - 	melibiose:sodium symporter; Provisional
Q#22466 - 	CGI_10023238	superfamily	241581	45	142	3.48E-12	62.789	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#22466 - 	CGI_10023238	superfamily	245201	169	440	4.00E-79	250.926	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22467 - 	CGI_10023239	superfamily	241567	147	379	3.80E-71	232.491	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#22467 - 	CGI_10023239	superfamily	246680	11	97	6.18E-08	50.6632	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22467 - 	CGI_10023239	superfamily	246680	394	478	1.00E-07	49.8928	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22467 - 	CGI_10023239	superfamily	241567	529	660	4.32E-47	166.645	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#22468 - 	CGI_10023240	superfamily	241567	14	129	3.61E-23	91.1227	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#22469 - 	CGI_10023241	superfamily	242978	943	1352	1.59E-45	175.476	cl02310	Glyco_hydro_81 superfamily	N	 - 	"Glycosyl hydrolase family 81; Family of eukaryotic beta-1,3-glucanases. Within the Aspergillus fumigatus protein two perfectly conserved Glu residues (E550 or E554) have been proposed as putative nucleophiles of the active site of the Engl1 endoglucanase, while the proton donor would be D475. The endo-beta-1,3-glucanase activity is essential for efficient spore release."
Q#22471 - 	CGI_10023243	superfamily	245596	100	358	2.87E-20	88.3003	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#22472 - 	CGI_10023244	superfamily	204041	29	178	3.10E-30	110.364	cl07367	GLTP superfamily	 - 	 - 	Glycolipid transfer protein (GLTP); GLTP is a cytosolic protein that catalyzes the intermembrane transfer of glycolipids.
Q#22473 - 	CGI_10023245	superfamily	204041	30	172	1.42E-26	100.349	cl07367	GLTP superfamily	 - 	 - 	Glycolipid transfer protein (GLTP); GLTP is a cytosolic protein that catalyzes the intermembrane transfer of glycolipids.
Q#22474 - 	CGI_10023246	superfamily	241600	137	346	2.83E-81	249.08	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#22475 - 	CGI_10023247	superfamily	243264	12	399	5.80E-165	471.775	cl02993	P2X_receptor superfamily	 - 	 - 	ATP P2X receptor; ATP P2X receptor.  
Q#22476 - 	CGI_10023248	superfamily	243066	7	90	1.09E-16	75.2821	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22476 - 	CGI_10023248	superfamily	219619	339	402	1.95E-10	56.8323	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#22478 - 	CGI_10023250	superfamily	241578	119	199	3.58E-07	48.331	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22479 - 	CGI_10023251	superfamily	247727	56	148	3.88E-06	42.8023	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#22480 - 	CGI_10023252	superfamily	247725	215	317	1.30E-28	111.224	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22482 - 	CGI_10023254	superfamily	241571	316	426	4.02E-26	103.646	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#22482 - 	CGI_10023254	superfamily	243051	504	618	6.59E-17	78.5737	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#22482 - 	CGI_10023254	superfamily	241568	434	494	0.000331012	38.9832	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#22482 - 	CGI_10023254	superfamily	246918	271	310	7.85E-10	55.6707	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22482 - 	CGI_10023254	superfamily	246918	113	156	0.000302985	39.1071	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22482 - 	CGI_10023254	superfamily	243093	160	252	0.00374932	36.2941	cl02568	WSC superfamily	 - 	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#22483 - 	CGI_10023255	superfamily	247069	94	260	3.19E-32	119.797	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#22483 - 	CGI_10023255	superfamily	247643	35	75	6.95E-07	46.0405	cl16919	CRAL_TRIO_N superfamily	 - 	 - 	"CRAL/TRIO, N-terminal domain; This all-alpha domain is found to the N-terminus of pfam00650."
Q#22484 - 	CGI_10023256	superfamily	247069	75	243	1.25E-29	112.479	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#22484 - 	CGI_10023256	superfamily	247643	16	57	1.31E-10	56.7891	cl16919	CRAL_TRIO_N superfamily	 - 	 - 	"CRAL/TRIO, N-terminal domain; This all-alpha domain is found to the N-terminus of pfam00650."
Q#22485 - 	CGI_10023257	superfamily	243066	23	113	3.38E-24	95.3124	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22485 - 	CGI_10023257	superfamily	219619	284	360	5.37E-10	55.6767	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#22486 - 	CGI_10023258	superfamily	246597	131	215	6.37E-15	68.4086	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#22486 - 	CGI_10023258	superfamily	246597	10	67	3.27E-12	60.7047	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#22491 - 	CGI_10023263	superfamily	247938	56	127	2.45E-36	121.936	cl17384	TAF12 superfamily	 - 	 - 	"TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex; The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure.  TAF12 domain interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes."
Q#22492 - 	CGI_10023264	superfamily	205480	212	297	7.29E-12	62.2933	cl16219	DUF4078 superfamily	 - 	 - 	"Domain of unknown function (DUF4078); This family is found from fungi to humans, but its exact function is not known."
Q#22492 - 	CGI_10023264	superfamily	221501	518	612	0.000549782	39.0006	cl13679	RCR superfamily	N	 - 	"Chitin synthesis regulation, resistance to Congo red; RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5."
Q#22493 - 	CGI_10023265	superfamily	202715	15	113	1.38E-47	150.036	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#22495 - 	CGI_10003607	superfamily	241839	26	178	1.95E-39	145.02	cl00396	PHO4 superfamily	C	 - 	Phosphate transporter family; This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter. This family also contains the leukaemia virus receptor.
Q#22495 - 	CGI_10003607	superfamily	241839	427	570	2.56E-36	136.16	cl00396	PHO4 superfamily	N	 - 	Phosphate transporter family; This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter. This family also contains the leukaemia virus receptor.
Q#22496 - 	CGI_10003608	superfamily	218674	414	590	5.63E-13	67.9406	cl05292	Miff superfamily	 - 	 - 	Mitochondrial and peroxisomal fission factor Mff; This protein has a role in mitochondrial and peroxisomal fission.
Q#22500 - 	CGI_10003612	superfamily	243034	484	588	2.74E-05	43.1376	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22500 - 	CGI_10003612	superfamily	243034	23	141	0.000230964	40.056	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22501 - 	CGI_10003613	superfamily	243034	15	114	4.64E-12	62.7828	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22501 - 	CGI_10003613	superfamily	243034	365	429	7.19E-05	41.2116	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22502 - 	CGI_10003339	superfamily	248458	322	604	6.19E-11	63.1017	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22502 - 	CGI_10003339	superfamily	248458	84	212	6.27E-07	50.7753	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22503 - 	CGI_10003593	superfamily	241573	60	346	3.29E-81	255.334	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#22503 - 	CGI_10003593	superfamily	241653	369	429	0.00323096	36.5075	cl00165	Calpain_III superfamily	C	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#22504 - 	CGI_10003594	superfamily	241573	82	370	4.41E-81	261.112	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#22504 - 	CGI_10003594	superfamily	241653	386	495	9.63E-09	53.8636	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#22506 - 	CGI_10007980	superfamily	241580	68	148	8.45E-35	126.9	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#22509 - 	CGI_10007983	superfamily	242274	56	134	7.19E-08	48.8247	cl01053	SGNH_hydrolase superfamily	NC	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#22510 - 	CGI_10007984	superfamily	205872	225	250	0.00158673	35.1629	cl16353	zf-CCHC_2 superfamily	 - 	 - 	Zinc knuckle; This is a zinc-binding domain of the form CxxCxxxGHxxxxC from a variety of different species.
Q#22512 - 	CGI_10007986	superfamily	242826	30	119	1.11E-39	131.267	cl01993	Ribosomal_S26e superfamily	 - 	 - 	Ribosomal protein S26e; Ribosomal protein S26e.  
Q#22516 - 	CGI_10018818	superfamily	246918	453	505	6.30E-14	67.6119	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22516 - 	CGI_10018818	superfamily	246918	396	448	2.98E-12	62.6043	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22516 - 	CGI_10018818	superfamily	246918	550	602	8.19E-12	61.4487	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22516 - 	CGI_10018818	superfamily	152683	57	157	1.09E-09	56.5273	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#22520 - 	CGI_10018822	superfamily	243035	40	168	4.11E-14	65.3337	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22523 - 	CGI_10018825	superfamily	118685	215	388	2.19E-27	105.655	cl10854	DUF2365 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2365); This is a family of conserved proteins found from nematodes to humans. The function is unknown.
Q#22524 - 	CGI_10018826	superfamily	242203	134	302	7.82E-61	194.875	cl00935	Brix superfamily	 - 	 - 	Brix domain; Brix domain.  
Q#22525 - 	CGI_10018827	superfamily	218954	2	185	1.37E-77	238.759	cl05646	Isy1 superfamily	C	 - 	Isy1-like splicing family; Isy1 protein is important in the optimisation of splicing.
Q#22525 - 	CGI_10018827	superfamily	218954	241	269	2.21E-05	43.4631	cl05646	Isy1 superfamily	N	 - 	Isy1-like splicing family; Isy1 protein is important in the optimisation of splicing.
Q#22526 - 	CGI_10018828	superfamily	205524	16	118	2.68E-20	84.7852	cl17723	Hydrolase_6 superfamily	 - 	 - 	Haloacid dehalogenase-like hydrolase; This family is part of the HAD superfamily.
Q#22527 - 	CGI_10018829	superfamily	241568	369	427	2.70E-08	50.9244	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#22529 - 	CGI_10018831	superfamily	243035	80	114	0.00248968	35.3582	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22530 - 	CGI_10018832	superfamily	248264	85	202	7.98E-08	50.3134	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#22531 - 	CGI_10018833	superfamily	242173	47	186	3.08E-16	71.5142	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#22532 - 	CGI_10018834	superfamily	242173	281	421	1.10E-24	98.093	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#22541 - 	CGI_10005080	superfamily	248312	33	183	9.44E-10	54.2904	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#22542 - 	CGI_10005081	superfamily	247692	10	52	0.00610398	32.5841	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#22544 - 	CGI_10009755	superfamily	245814	213	276	1.50E-07	47.8059	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22544 - 	CGI_10009755	superfamily	245814	3	34	0.00017239	38.6405	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22544 - 	CGI_10009755	superfamily	241584	38	136	0.00294579	35.1647	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#22545 - 	CGI_10009756	superfamily	243157	24	104	8.38E-47	158.445	cl02720	PB1 superfamily	 - 	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#22546 - 	CGI_10009757	superfamily	248458	33	419	1.25E-39	150.542	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22547 - 	CGI_10009758	superfamily	243098	1059	1102	4.99E-12	63.3859	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#22547 - 	CGI_10009758	superfamily	243098	1285	1331	7.49E-12	63.0007	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#22547 - 	CGI_10009758	superfamily	243098	547	599	7.63E-12	63.0007	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#22547 - 	CGI_10009758	superfamily	243098	772	817	1.84E-11	61.8451	cl02573	TUDOR superfamily	 - 	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#22547 - 	CGI_10009758	superfamily	247792	45	78	0.00100413	38.966	cl17238	RING superfamily	N	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22547 - 	CGI_10009758	superfamily	241563	193	230	7.27E-07	48.2444	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22547 - 	CGI_10009758	superfamily	128778	274	360	0.00111396	39.5555	cl17972	BBC superfamily	N	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#22547 - 	CGI_10009758	superfamily	243098	1491	1522	0.00893674	36.0368	cl02573	TUDOR superfamily	C	 - 	"Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal."
Q#22548 - 	CGI_10009759	superfamily	241564	106	172	3.69E-25	96.5659	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#22548 - 	CGI_10009759	superfamily	241564	25	93	9.36E-20	81.5431	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#22548 - 	CGI_10009759	superfamily	247792	300	338	0.000641928	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22549 - 	CGI_10009760	superfamily	241563	13	51	1.34E-05	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22550 - 	CGI_10009761	superfamily	148298	10	59	0.00747764	31.661	cl05897	Prokineticin superfamily	N	 - 	"Prokineticin; This family consists of several prokineticin proteins and related BM8 sequences. The suprachiasmatic nucleus (SCN) controls the circadian rhythm of physiological and behavioural processes in mammals. It has been shown that prokineticin 2 (PK2), a cysteine-rich secreted protein, functions as an output molecule from the SCN circadian clock. PK2 messenger RNA is rhythmically expressed in the SCN, and the phase of PK2 rhythm is responsive to light entrainment. Molecular and genetic studies have revealed that PK2 is a gene that is controlled by a circadian clock."
Q#22551 - 	CGI_10009762	superfamily	247792	175	220	1.78E-12	59.3156	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22552 - 	CGI_10009763	superfamily	241567	226	436	1.02E-60	199.749	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#22552 - 	CGI_10009763	superfamily	246680	9	86	1.77E-07	48.4688	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22553 - 	CGI_10009764	superfamily	243066	33	139	1.66E-17	78.0429	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22553 - 	CGI_10009764	superfamily	198867	153	248	8.03E-16	72.9615	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#22556 - 	CGI_10009767	superfamily	111397	432	509	1.38E-08	52.7286	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#22561 - 	CGI_10012203	superfamily	241599	214	272	6.34E-23	89.9952	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22563 - 	CGI_10012205	superfamily	243077	16	72	2.00E-14	65.2593	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#22564 - 	CGI_10012206	superfamily	247918	105	260	0.00190818	38.3266	cl17364	PMT_2 superfamily	 - 	 - 	Dolichyl-phosphate-mannose-protein mannosyltransferase; This family contains members that are not captured by pfam02366.
Q#22566 - 	CGI_10012208	superfamily	241599	142	199	4.23E-14	64.1868	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22566 - 	CGI_10012208	superfamily	119045	199	229	1.02E-11	57.3243	cl11160	Engrail_1_C_sig superfamily	 - 	 - 	Engrailed homeobox C-terminal signature domain; Engrailed homeobox proteins are characterized by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for this subfamily of proteins.
Q#22567 - 	CGI_10012209	superfamily	241599	127	185	9.44E-21	82.2912	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22567 - 	CGI_10012209	superfamily	119045	184	212	4.63E-11	55.0131	cl11160	Engrail_1_C_sig superfamily	 - 	 - 	Engrailed homeobox C-terminal signature domain; Engrailed homeobox proteins are characterized by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for this subfamily of proteins.
Q#22569 - 	CGI_10012211	superfamily	243035	18	110	1.80E-12	58.7853	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22570 - 	CGI_10012212	superfamily	247068	1143	1238	1.23E-10	60.4049	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22570 - 	CGI_10012212	superfamily	247068	1251	1337	1.32E-06	48.4638	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22570 - 	CGI_10012212	superfamily	247068	532	621	2.66E-06	47.3082	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22570 - 	CGI_10012212	superfamily	247068	733	825	5.78E-06	46.1526	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22570 - 	CGI_10012212	superfamily	247068	630	725	2.15E-05	44.6118	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22570 - 	CGI_10012212	superfamily	247068	954	1012	2.64E-05	44.2266	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22570 - 	CGI_10012212	superfamily	247068	1041	1135	0.00012682	42.3006	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22570 - 	CGI_10012212	superfamily	247068	429	524	0.000159861	41.9154	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22571 - 	CGI_10012213	superfamily	247736	85	163	3.38E-05	39.9446	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#22572 - 	CGI_10012214	superfamily	220695	35	163	8.87E-05	42.1807	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#22573 - 	CGI_10012215	superfamily	247736	128	206	1.94E-05	41.1002	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#22574 - 	CGI_10012216	superfamily	247736	87	164	1.86E-06	43.4114	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#22577 - 	CGI_10012219	superfamily	245835	446	644	3.25E-88	275.681	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#22577 - 	CGI_10012219	superfamily	243088	303	426	5.99E-62	203.317	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#22577 - 	CGI_10012219	superfamily	247683	61	115	8.64E-16	72.7447	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#22582 - 	CGI_10009571	superfamily	247725	85	187	6.18E-18	82.1342	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22583 - 	CGI_10009572	superfamily	247755	425	663	4.16E-105	332.547	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22583 - 	CGI_10009572	superfamily	247755	1202	1241	4.04E-11	62.9076	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22584 - 	CGI_10009573	superfamily	247755	1	132	1.59E-68	213.906	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22585 - 	CGI_10009574	superfamily	241832	37	105	2.81E-25	94.1528	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#22585 - 	CGI_10009574	superfamily	243175	115	184	1.32E-07	46.4618	cl02776	GST_C_family superfamily	C	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#22585 - 	CGI_10009574	superfamily	247755	1	30	3.28E-06	44.418	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22586 - 	CGI_10009575	superfamily	241594	4009	4364	8.66E-143	453.175	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#22586 - 	CGI_10009575	superfamily	241643	1346	1381	0.000177401	42.4463	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#22586 - 	CGI_10009575	superfamily	218859	431	833	2.27E-74	256.141	cl15653	DUF913 superfamily	 - 	 - 	Domain of Unknown Function (DUF913); Members of this family are found in various ubiquitin protein ligases.
Q#22586 - 	CGI_10009575	superfamily	222719	3015	3125	5.48E-36	135.932	cl16839	DUF4414 superfamily	 - 	 - 	Domain of unknown function (DUF4414); This family is frequently found on DNA binding proteins of the URE-B1 type and on ligases.
Q#22586 - 	CGI_10009575	superfamily	207713	1649	1710	6.62E-13	68.1149	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#22586 - 	CGI_10009575	superfamily	244870	2693	2743	1.36E-09	59.2964	cl08238	PA superfamily	C	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#22587 - 	CGI_10009576	superfamily	241628	64	327	8.94E-60	198.99	cl00130	PseudoU_synth superfamily	N	 - 	"Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA)."
Q#22588 - 	CGI_10009577	superfamily	217473	281	439	6.52E-24	102.058	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#22591 - 	CGI_10003833	superfamily	243051	11	97	2.50E-18	75.0796	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#22593 - 	CGI_10003835	superfamily	243051	67	154	6.06E-17	73.1809	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#22595 - 	CGI_10003837	superfamily	245201	18	211	1.79E-51	172.806	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22597 - 	CGI_10008458	superfamily	245226	6	45	5.91E-07	45.3687	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#22602 - 	CGI_10008463	superfamily	245226	432	505	9.21E-06	44.5989	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#22612 - 	CGI_10004578	superfamily	243051	463	617	5.84E-24	98.9893	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#22612 - 	CGI_10004578	superfamily	241571	337	409	4.35E-08	51.6443	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#22612 - 	CGI_10004578	superfamily	241583	115	287	4.66E-39	142.325	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#22612 - 	CGI_10004578	superfamily	241609	623	661	1.30E-06	46.9998	cl00100	KR superfamily	C	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#22616 - 	CGI_10004583	superfamily	192997	336	484	1.06E-12	67.2215	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#22617 - 	CGI_10007004	superfamily	241546	603	763	1.36E-38	140.768	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22617 - 	CGI_10007004	superfamily	241546	785	914	1.56E-37	137.686	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22617 - 	CGI_10007004	superfamily	241546	280	398	7.74E-35	129.982	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22617 - 	CGI_10007004	superfamily	241546	411	498	2.66E-30	116.886	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22617 - 	CGI_10007004	superfamily	241546	159	263	3.82E-23	96.47	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22617 - 	CGI_10007004	superfamily	241546	560	583	0.000140152	41.3864	cl00011	PLAT superfamily	N	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22618 - 	CGI_10007005	superfamily	245599	217	440	9.51E-93	281.946	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#22618 - 	CGI_10007005	superfamily	207662	100	192	6.82E-63	200.471	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#22620 - 	CGI_10007007	superfamily	247866	7	233	6.66E-20	85.582	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#22623 - 	CGI_10025039	superfamily	243065	31	191	0.00247569	35.8805	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#22627 - 	CGI_10025043	superfamily	247744	89	124	0.00233722	37.6332	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#22628 - 	CGI_10025044	superfamily	216981	59	153	2.55E-13	62.9354	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#22630 - 	CGI_10025046	superfamily	248097	3	117	8.73E-18	74.2238	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22631 - 	CGI_10025047	superfamily	110440	396	416	0.000256929	38.5429	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#22632 - 	CGI_10025048	superfamily	110440	294	321	0.00309907	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#22635 - 	CGI_10025051	superfamily	141815	6	323	5.07E-128	371.312	cl04275	Mtc superfamily	 - 	 - 	Tricarboxylate carrier; Tricarboxylate carrier.  
Q#22636 - 	CGI_10025052	superfamily	241599	165	223	1.83E-21	84.9876	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22637 - 	CGI_10025053	superfamily	241599	198	256	3.21E-21	84.9876	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22638 - 	CGI_10025054	superfamily	241599	182	240	2.26E-21	85.3728	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22642 - 	CGI_10025058	superfamily	247911	40	391	5.65E-132	385.153	cl17357	Fumble superfamily	 - 	 - 	"Fumble; Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organisation, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with high similarity to the pantothenate kinases of A. nidulans and mouse. A role of fumble in membrane synthesis has been proposed."
Q#22643 - 	CGI_10025059	superfamily	245201	131	219	4.46E-08	50.3129	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22644 - 	CGI_10025060	superfamily	241624	413	588	1.09E-60	204.483	cl00120	PP2Cc superfamily	N	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#22644 - 	CGI_10025060	superfamily	241624	14	105	1.72E-21	93.9788	cl00120	PP2Cc superfamily	C	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#22648 - 	CGI_10025064	superfamily	248054	97	147	2.07E-09	54.4004	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#22649 - 	CGI_10025065	superfamily	243074	169	211	9.08E-13	63.6797	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#22649 - 	CGI_10025065	superfamily	243092	453	563	1.08E-08	55.4188	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22652 - 	CGI_10025068	superfamily	243034	748	858	1.68E-13	69.7163	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	1150	1261	2.09E-11	63.5532	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	628	738	7.67E-11	62.0124	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	1031	1138	1.71E-10	60.8568	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	167	223	3.78E-10	60.0864	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	868	974	6.08E-10	59.316	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	511	614	8.68E-10	58.9308	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	951	1058	5.54E-09	56.6196	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	428	538	6.46E-07	50.0712	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	243034	354	458	0.00055894	41.2116	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22652 - 	CGI_10025068	superfamily	248422	1553	1864	1.38E-52	189.454	cl17868	CHAT superfamily	 - 	 - 	CHAT domain; These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins.
Q#22653 - 	CGI_10025069	superfamily	243034	40	110	2.23E-05	43.5228	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22653 - 	CGI_10025069	superfamily	248012	601	706	1.78E-11	62.2909	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#22654 - 	CGI_10025070	superfamily	243034	158	264	0.000622728	38.5152	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22654 - 	CGI_10025070	superfamily	248012	427	532	7.65E-12	62.6761	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#22656 - 	CGI_10025072	superfamily	247986	37	132	1.04E-11	62.3906	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#22656 - 	CGI_10025072	superfamily	197504	243	358	1.82E-07	48.8249	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#22657 - 	CGI_10025073	superfamily	247724	568	770	7.77E-75	244.367	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22657 - 	CGI_10025073	superfamily	243072	409	447	2.59E-07	49.6894	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22660 - 	CGI_10025076	superfamily	246671	379	507	2.52E-29	112.516	cl14606	Reeler_cohesin_like superfamily	 - 	 - 	"Domains similar to the eukaryotic reeler domain and bacterial cohesins; This diverse family summarizes a set of distantly related domains, as revealed by structural similarity."
Q#22661 - 	CGI_10025077	superfamily	242173	257	394	1.84E-19	86.537	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#22661 - 	CGI_10025077	superfamily	242173	412	558	3.17E-16	77.2922	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#22661 - 	CGI_10025077	superfamily	242173	728	873	6.25E-15	73.4402	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#22661 - 	CGI_10025077	superfamily	242173	637	714	7.52E-06	45.7059	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	N	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#22662 - 	CGI_10025078	superfamily	247723	124	199	2.79E-48	168.377	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22662 - 	CGI_10025078	superfamily	247723	221	298	2.81E-42	151.266	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22663 - 	CGI_10025079	superfamily	245206	4	225	6.06E-96	301.936	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#22663 - 	CGI_10025079	superfamily	245226	291	460	1.28E-40	147.725	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#22664 - 	CGI_10025080	superfamily	241760	44	92	2.74E-23	93.5655	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#22665 - 	CGI_10025081	superfamily	244870	21	137	7.96E-44	142.513	cl08238	PA superfamily	 - 	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#22666 - 	CGI_10000247	superfamily	243072	80	195	5.82E-33	120.566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22666 - 	CGI_10000247	superfamily	243072	141	262	1.80E-29	110.551	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22666 - 	CGI_10000247	superfamily	243072	14	130	1.08E-17	78.1942	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22666 - 	CGI_10000247	superfamily	243072	236	300	3.18E-05	41.9855	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22668 - 	CGI_10006912	superfamily	247724	34	111	1.77E-10	54.8487	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22672 - 	CGI_10006916	superfamily	243092	138	469	7.19E-42	151.334	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22673 - 	CGI_10006917	superfamily	243035	134	254	2.31E-17	75.3489	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22673 - 	CGI_10006917	superfamily	243035	42	94	1.65E-09	53.7578	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22674 - 	CGI_10006918	superfamily	243035	53	173	5.22E-18	76.1193	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22675 - 	CGI_10006919	superfamily	243035	53	173	1.29E-18	77.6601	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22676 - 	CGI_10006920	superfamily	243035	52	172	1.50E-17	74.5785	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22677 - 	CGI_10006921	superfamily	243035	53	173	3.23E-19	79.2009	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22678 - 	CGI_10006922	superfamily	243035	52	172	2.11E-17	74.1933	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22679 - 	CGI_10008112	superfamily	248097	228	356	3.09E-14	68.0606	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22680 - 	CGI_10008113	superfamily	248097	235	363	2.03E-16	74.2238	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22681 - 	CGI_10008114	superfamily	248097	151	279	4.29E-15	71.9126	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22681 - 	CGI_10008114	superfamily	248097	395	523	2.54E-14	69.6014	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22682 - 	CGI_10008115	superfamily	248097	109	220	7.83E-14	64.979	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22684 - 	CGI_10008117	superfamily	243072	1180	1295	2.27E-21	92.4466	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22684 - 	CGI_10008117	superfamily	243037	715	871	7.37E-65	217.973	cl02440	DAGK_acc superfamily	 - 	 - 	Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
Q#22684 - 	CGI_10008117	superfamily	248019	566	686	2.16E-49	172.866	cl17465	DAGK_cat superfamily	 - 	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#22684 - 	CGI_10008117	superfamily	241566	445	503	6.85E-07	48.2195	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#22688 - 	CGI_10008121	superfamily	248097	9	122	4.51E-26	95.795	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22689 - 	CGI_10007757	superfamily	243258	2	193	1.19E-97	284.444	cl02977	Ribosomal_L15e superfamily	 - 	 - 	Ribosomal L15; Ribosomal L15.  
Q#22690 - 	CGI_10007758	superfamily	213107	12	51	0.00279755	35.3236	cl02594	DD_R_PKA superfamily	 - 	 - 	"Dimerization/Docking domain of the Regulatory subunit of cAMP-dependent protein kinase and similar domains; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis."
Q#22691 - 	CGI_10007759	superfamily	218811	4	490	9.03E-111	342.802	cl09392	API5 superfamily	 - 	 - 	"Apoptosis inhibitory protein 5 (API5); This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterized by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors."
Q#22692 - 	CGI_10007760	superfamily	216167	5	150	1.35E-51	174.312	cl02999	DNA_photolyase superfamily	 - 	 - 	DNA photolyase; This domain binds a light harvesting cofactor.
Q#22693 - 	CGI_10007761	superfamily	243096	41	213	3.06E-43	152.452	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#22693 - 	CGI_10007761	superfamily	247725	219	349	1.26E-19	84.9986	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22694 - 	CGI_10007762	superfamily	243050	102	156	5.32E-29	103.784	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#22694 - 	CGI_10007762	superfamily	243050	24	72	7.86E-23	87.6064	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#22696 - 	CGI_10007764	superfamily	243091	655	767	2.11E-12	66.2039	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#22698 - 	CGI_10007766	superfamily	245816	4	163	1.44E-44	147.03	cl11964	CYTH-like_Pase superfamily	 - 	 - 	"CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; CYTH-like superfamily enzymes hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB), and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions."
Q#22699 - 	CGI_10007767	superfamily	243015	17	135	1.18E-17	75.3762	cl02381	Tim17 superfamily	 - 	 - 	"Tim17/Tim22/Tim23/Pmp24 family; The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane. This family includes Tim17, Tim22 and Tim23. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27 in."
Q#22700 - 	CGI_10007768	superfamily	245819	483	645	1.36E-59	200.498	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#22700 - 	CGI_10007768	superfamily	219526	223	468	2.29E-70	231.354	cl06648	HNOBA superfamily	 - 	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#22700 - 	CGI_10007768	superfamily	203730	25	189	3.94E-63	210.203	cl18246	HNOB superfamily	 - 	 - 	"Heme NO binding; The HNOB (Heme NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#22701 - 	CGI_10007769	superfamily	248097	130	263	1.76E-16	74.9942	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22701 - 	CGI_10007769	superfamily	248097	271	404	1.59E-14	69.6014	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22701 - 	CGI_10007769	superfamily	218915	27	61	0.00222185	36.1219	cl15704	DUF972 superfamily	NC	 - 	Protein of unknown function (DUF972); This family consists of several hypothetical bacterial sequences. The function of this family is unknown.
Q#22703 - 	CGI_10021566	superfamily	245205	246	309	0.000228456	39.1046	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#22704 - 	CGI_10021567	superfamily	208843	84	254	1.51E-107	324.056	cl08275	RHD-n superfamily	 - 	 - 	"N-terminal sub-domain of the Rel homology domain (RHD); Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal sub-domain, which may be distantly related to the DNA-binding domain found in P53. The C-terminal sub-domain has an immunoglobulin-like fold and serves as a dimerization module that also binds DNA (see cd00102). The RHD is found in NF-kappa B, nuclear factor of activated T-cells (NFAT), the tonicity-responsive enhancer binding protein (TonEBP), and the arthropod proteins Dorsal and Relish (Rel)."
Q#22704 - 	CGI_10021567	superfamily	247038	259	361	9.71E-57	187.911	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#22705 - 	CGI_10021568	superfamily	245201	75	407	0	682.662	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22705 - 	CGI_10021568	superfamily	247725	1095	1228	6.81E-71	235.656	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22705 - 	CGI_10021568	superfamily	241566	1036	1085	3.07E-14	69.8283	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#22705 - 	CGI_10021568	superfamily	243036	1257	1525	1.86E-54	193.223	cl02434	CNH superfamily	 - 	 - 	"CNH domain; Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations."
Q#22705 - 	CGI_10021568	superfamily	241620	1591	1616	1.36E-05	44.5052	cl00113	CRIB superfamily	C	 - 	"PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules."
Q#22705 - 	CGI_10021568	superfamily	243054	484	652	0.0023925	40.1216	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#22706 - 	CGI_10021569	superfamily	243077	10	39	0.00389708	37.51	cl02542	DnaJ superfamily	C	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#22707 - 	CGI_10021570	superfamily	247903	2	99	9.03E-29	104.686	cl17349	Peptidase_M54 superfamily	N	 - 	"Peptidase family M54, also called archaemetzincins or archaelysins; Peptidase M54 (archaemetzincin or archaelysin) is a zinc-dependent aminopeptidase that contains the consensus zinc-binding sequence HEXXHXXGXXH/D and a conserved Met residue at the active site, and is thus classified as a metzincin. Archaemetzincins, first identified in archaea, are also found in bacteria and eukaryotes, including two human members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1 is mainly found in the liver and heart while AMZ2 is primarily expressed in testis and heart; both have been reported to degrade synthetic substrates and peptides. The Peptidase M54 family contains an extended metzincin concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that a second zinc ion is bound to four cysteines, thus resembling a zinc finger. Phylogenetic analysis of this family reveals a complex evolutionary process involving a series of lateral gene transfer, gene loss and genetic duplication events."
Q#22711 - 	CGI_10021574	superfamily	244547	602	676	2.08E-08	52.5841	cl06893	UME superfamily	 - 	 - 	"UME (NUC010) domain; This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1."
Q#22712 - 	CGI_10021575	superfamily	217473	96	326	1.95E-29	115.925	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#22713 - 	CGI_10021576	superfamily	241599	514	564	1.05E-08	52.2457	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22713 - 	CGI_10021576	superfamily	241599	425	476	1.11E-07	49.5493	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22715 - 	CGI_10021578	superfamily	217473	76	133	4.63E-07	48.9005	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#22717 - 	CGI_10021580	superfamily	246597	179	482	0	625.042	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#22717 - 	CGI_10021580	superfamily	243034	41	131	5.45E-21	87.8207	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22721 - 	CGI_10021584	superfamily	218087	55	91	0.000935533	36.2935	cl18440	SWIM superfamily	 - 	 - 	"SWIM zinc finger; This domain is found in bacterial, archaeal and eukaryotic proteins. It is predicted to be organised into two N-terminal beta-strands and a C-terminal alpha helix, thus possibly adopting a fold similar to that of the C2H2 zinc finger (pfam00096). SWIM is thought to be a versatile domain that can interact with DNA or proteins in different contexts."
Q#22723 - 	CGI_10021586	superfamily	247856	137	192	6.25E-18	74.8917	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22723 - 	CGI_10021586	superfamily	247856	62	124	2.86E-07	45.6165	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22727 - 	CGI_10021590	superfamily	220533	217	684	3.57E-115	362.042	cl12375	Dpy19 superfamily	N	 - 	"Q-cell neuroblast polarisation; Dyp-19, formerly known as DUF2211, is a transmembrane domain family that is required to orient the neuroblast cells, QR and QL accurately on the anterior-posterior axis: QL and QR are born in the same anterior-posterior position, but polarise and migrate left-right asymmetrically, QL migrating towards the posterior and QR migrating towards the anterior. It is also required, with unc-40, to express mab-5 correctly in the Q cell descendants. The Dpy-19 protein derives from the C. elegans DUMPY mutant."
Q#22730 - 	CGI_10013987	superfamily	246664	543	944	9.35E-160	477.837	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#22730 - 	CGI_10013987	superfamily	246664	4	311	3.80E-138	421.598	cl14561	An_peroxidase_like superfamily	N	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#22730 - 	CGI_10013987	superfamily	246664	438	480	1.25E-05	47.305	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#22732 - 	CGI_10013989	superfamily	198845	210	295	1.53E-19	81.5556	cl04394	BRICHOS superfamily	 - 	 - 	"BRICHOS domain; The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for it include (a) in targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialised intracellular protease processing system. This C-terminal domain is embedded in the endoplasmic reticulum lumen, and binds to the N-terminal, transmembrane, SP_C, pfam08999, provided that it is in non-helical conformation. Thus the Brichos domain of proSP-C is a chaperone that induces alpha-helix formation of an aggregation-prone TM region."
Q#22734 - 	CGI_10013991	superfamily	245847	1476	1625	4.59E-27	110.52	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#22734 - 	CGI_10013991	superfamily	245213	1845	1882	0.000372607	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22734 - 	CGI_10013991	superfamily	147730	2247	2437	5.25E-46	167.589	cl05347	TSP_C superfamily	 - 	 - 	Thrombospondin C-terminal region; This region is found at the C-terminus of thrombospondin and related proteins.
Q#22734 - 	CGI_10013991	superfamily	241611	2439	2590	6.79E-15	75.1176	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#22734 - 	CGI_10013991	superfamily	219525	1737	1780	2.37E-08	53.5769	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#22734 - 	CGI_10013991	superfamily	202235	1998	2032	5.33E-08	52.0023	cl15981	TSP_3 superfamily	 - 	 - 	Thrombospondin type 3 repeat; The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
Q#22734 - 	CGI_10013991	superfamily	205157	1926	1962	2.81E-07	50.2287	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#22734 - 	CGI_10013991	superfamily	244965	1051	1173	5.71E-07	50.0109	cl08459	PA14 superfamily	 - 	 - 	"PA14 domain; This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding."
Q#22734 - 	CGI_10013991	superfamily	202235	2191	2223	5.05E-06	46.2243	cl15981	TSP_3 superfamily	 - 	 - 	Thrombospondin type 3 repeat; The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
Q#22734 - 	CGI_10013991	superfamily	202235	2118	2151	1.34E-05	45.0687	cl15981	TSP_3 superfamily	 - 	 - 	Thrombospondin type 3 repeat; The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
Q#22734 - 	CGI_10013991	superfamily	246925	550	824	3.54E-05	46.965	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#22734 - 	CGI_10013991	superfamily	202235	2162	2189	6.42E-05	43.1427	cl15981	TSP_3 superfamily	 - 	 - 	Thrombospondin type 3 repeat; The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure.
Q#22734 - 	CGI_10013991	superfamily	247068	1366	1436	0.00128044	39.6403	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22738 - 	CGI_10013995	superfamily	245596	22	166	1.51E-65	202.042	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#22740 - 	CGI_10013997	superfamily	247097	18	51	0.00966308	29.2697	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#22741 - 	CGI_10013998	superfamily	247097	30	63	0.00168174	34.6625	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#22741 - 	CGI_10013998	superfamily	220611	98	146	0.0052066	34.4427	cl10864	Laps superfamily	NC	 - 	Learning-associated protein; This is a family of 121-amino acid secretory proteins. Laps functions in the regulation of neuronal cell adhesion and/or movement and synapse attachment. Laps binds to the ApC/EBP (Aplysia CCAAT/enhancer binding protein) promoter and activates the transcription of ApC/EBP mRNA.
Q#22742 - 	CGI_10013999	superfamily	247097	56	92	0.00594732	33.9638	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#22743 - 	CGI_10014000	superfamily	245319	5	48	4.70E-12	57.9961	cl10505	CBF superfamily	N	 - 	CBF/Mak21 family; CBF/Mak21 family.  
Q#22744 - 	CGI_10014001	superfamily	245319	95	148	6.15E-17	74.5597	cl10505	CBF superfamily	NC	 - 	CBF/Mak21 family; CBF/Mak21 family.  
Q#22745 - 	CGI_10013345	superfamily	243066	4	102	2.17E-20	84.2061	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22745 - 	CGI_10013345	superfamily	198867	112	220	1.31E-09	54.6548	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#22747 - 	CGI_10013347	superfamily	247787	19	295	0	529.108	cl17233	RecA-like_NTPases superfamily	 - 	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#22747 - 	CGI_10013347	superfamily	215848	304	406	1.46E-32	119.307	cl08258	ATP-synt_ab_C superfamily	 - 	 - 	"ATP synthase alpha/beta chain, C terminal domain; ATP synthase alpha/beta chain, C terminal domain.  "
Q#22748 - 	CGI_10013348	superfamily	243072	400	525	1.55E-32	123.263	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22748 - 	CGI_10013348	superfamily	243072	467	591	7.41E-32	121.337	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22748 - 	CGI_10013348	superfamily	243072	532	655	1.21E-23	97.8394	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22749 - 	CGI_10013349	superfamily	216101	88	601	1.41E-120	372.396	cl08288	Carn_acyltransf superfamily	 - 	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#22750 - 	CGI_10013350	superfamily	247804	506	551	0.000101813	40.6366	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#22758 - 	CGI_10005012	superfamily	115579	78	124	0.000586607	38.6003	cl06133	SSP160 superfamily	N	 - 	Special lobe-specific silk protein SSP160; This family consists of several special lobe-specific silk protein SSP160 sequences which appear to be specific to Chironomus (Midge) species.
Q#22760 - 	CGI_10000904	superfamily	247038	30	74	4.93E-11	56.5551	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#22761 - 	CGI_10004935	superfamily	243072	222	319	5.71E-22	88.9798	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22761 - 	CGI_10004935	superfamily	207800	13	142	7.48E-29	108.656	cl02972	Ephrin_RBD superfamily	 - 	 - 	"Receptor Binding Domain of Ephrins; Ephrins and their receptors EphR play an important role in cell communication in normal physiology, as well as in disease pathogenesis. Binding of the ephrin ligand to EphR requires cell-cell contact, since both molecules are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling, depending on Eph kinase activity) and ephrin-expressing cells (reverse signaling). Eph signaling controls cell morphology, adhesion, migration and invasion. Ephrins can be subdivided into 2 groups, A and B, depending on their respective receptors EphA or EphB. The nine human EphA receptors bind to five GPI-linked ephrin-A ligands and the five EphB receptors bind to three transmembrane ephrin-B ligands. Interactions are promiscuous within each class, and some Eph receptors can also bind to ephrins of the other class. All Ephrins contain a highly conserved extracellular receptor binding domain, which is characterized by this domain hierarchy."
Q#22762 - 	CGI_10004936	superfamily	246953	40	406	3.27E-179	507.566	cl15414	V-ATPase_C superfamily	 - 	 - 	V-ATPase subunit C; V-ATPase subunit C.  
Q#22763 - 	CGI_10004937	superfamily	246925	44	179	0.00125821	39.6462	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#22765 - 	CGI_10004939	superfamily	247068	316	391	3.69E-07	48.4638	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22765 - 	CGI_10004939	superfamily	247068	399	491	3.93E-06	45.3822	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22765 - 	CGI_10004939	superfamily	247068	33	127	0.000532502	38.8338	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22765 - 	CGI_10004939	superfamily	247068	197	286	0.000688666	38.4486	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22765 - 	CGI_10004939	superfamily	247068	125	181	0.00961028	34.9818	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22767 - 	CGI_10008416	superfamily	248312	22	221	3.08E-06	45.0369	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#22769 - 	CGI_10008418	superfamily	248312	20	210	1.41E-11	59.6745	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#22770 - 	CGI_10008419	superfamily	243073	377	411	4.69E-07	46.3093	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#22771 - 	CGI_10008420	superfamily	241737	27	194	1.07E-69	212.002	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#22772 - 	CGI_10008421	superfamily	241550	8	155	1.26E-95	282.919	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#22772 - 	CGI_10008421	superfamily	241550	204	313	6.55E-57	183.614	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#22773 - 	CGI_10008422	superfamily	248011	501	581	0.00304856	39.017	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#22773 - 	CGI_10008422	superfamily	241546	2277	2396	9.18E-44	158.593	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#22773 - 	CGI_10008422	superfamily	243061	299	394	1.62E-24	102.035	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#22774 - 	CGI_10000281	superfamily	147296	3	123	8.47E-35	121.168	cl04901	Cytochrom_B558a superfamily	C	 - 	Cytochrome Cytochrome b558 alpha-subunit; Cytochrome b-245 light chain (p22-phox) is one of the key electron transfer elements of the NADPH oxidase in phagocytes.
Q#22775 - 	CGI_10011351	superfamily	241563	25	58	5.68E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22776 - 	CGI_10011352	superfamily	241563	62	104	7.16E-07	46.7036	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22779 - 	CGI_10011355	superfamily	247098	385	510	4.45E-62	201.6	cl15841	COG0229 superfamily	 - 	 - 	"Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]"
Q#22779 - 	CGI_10011355	superfamily	222150	258	283	0.000460298	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22779 - 	CGI_10011355	superfamily	222150	202	227	0.00362949	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22779 - 	CGI_10011355	superfamily	222150	286	309	0.00760343	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22780 - 	CGI_10011356	superfamily	243035	2	59	1.12E-10	52.237	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22783 - 	CGI_10011359	superfamily	245716	1309	1329	0.00349481	37.2237	cl11592	zf-CCCH superfamily	N	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#22783 - 	CGI_10011359	superfamily	245716	1284	1304	0.00935467	35.6829	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#22784 - 	CGI_10011360	superfamily	241822	127	192	1.22E-12	60.3497	cl00373	Ribosomal_S18 superfamily	 - 	 - 	Ribosomal protein S18; Ribosomal protein S18.  
Q#22785 - 	CGI_10001566	superfamily	247683	25	88	1.58E-10	61.7276	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#22786 - 	CGI_10001567	superfamily	151110	1	230	2.68E-66	207.051	cl11201	UPF0552 superfamily	 - 	 - 	Uncharacterized protein family UPF0552; This family of proteins has no known function.
Q#22788 - 	CGI_10004756	superfamily	243555	19	204	4.81E-06	47.771	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#22789 - 	CGI_10004757	superfamily	245814	173	196	2.63E-05	40.0825	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22791 - 	CGI_10000895	superfamily	241750	69	176	4.07E-25	98.805	cl00281	metallo-dependent_hydrolases superfamily	C	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#22791 - 	CGI_10000895	superfamily	245874	2	49	0.00171724	35.0946	cl12111	TNFR superfamily	C	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#22793 - 	CGI_10002237	superfamily	241563	68	109	7.22E-07	46.7036	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22794 - 	CGI_10002238	superfamily	241563	68	109	5.07E-07	47.0888	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22795 - 	CGI_10002239	superfamily	241563	68	109	4.41E-07	47.0888	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22795 - 	CGI_10002239	superfamily	241563	28	59	0.00178565	36.6884	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22796 - 	CGI_10013494	superfamily	247724	426	587	1.08E-73	235.043	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22796 - 	CGI_10013494	superfamily	247856	23	79	4.38E-05	41.7645	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22798 - 	CGI_10013496	superfamily	245013	89	139	0.0067352	33.0025	cl09115	Ribosomal_L32p superfamily	C	 - 	Ribosomal L32p protein family; Ribosomal L32p protein family.  
Q#22799 - 	CGI_10013497	superfamily	241884	5	232	2.18E-153	428.664	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#22801 - 	CGI_10013499	superfamily	241867	8	329	1.24E-96	293.353	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#22803 - 	CGI_10013501	superfamily	241568	109	162	0.00117666	35.9016	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#22804 - 	CGI_10013502	superfamily	241600	341	558	9.93E-62	204.397	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#22804 - 	CGI_10013502	superfamily	243035	166	238	9.37E-05	41.0662	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22804 - 	CGI_10013502	superfamily	243035	114	162	0.00264732	36.829	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22805 - 	CGI_10013503	superfamily	241874	47	618	0	726.666	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#22810 - 	CGI_10011516	superfamily	241574	12	162	2.05E-49	167.763	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#22810 - 	CGI_10011516	superfamily	241574	247	366	2.26E-08	52.9733	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#22811 - 	CGI_10011517	superfamily	243034	48	127	1.79E-07	48.1452	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22814 - 	CGI_10011520	superfamily	218219	15	164	9.91E-41	137.836	cl04693	PRELI superfamily	 - 	 - 	"PRELI-like family; This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins."
Q#22815 - 	CGI_10011521	superfamily	241677	464	612	5.27E-100	303.614	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#22815 - 	CGI_10011521	superfamily	243092	57	219	4.53E-09	56.5744	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22817 - 	CGI_10011523	superfamily	245201	223	528	0	597.151	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22817 - 	CGI_10011523	superfamily	241622	779	867	1.27E-10	59.5756	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#22817 - 	CGI_10011523	superfamily	204097	30	190	5.24E-61	210.882	cl07500	DUF1908 superfamily	N	 - 	Domain of unknown function (DUF1908); This domain is found in a set of hypothetical/structural eukaryotic proteins.
Q#22818 - 	CGI_10011524	superfamily	247068	220	317	2.41E-24	97.7693	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22818 - 	CGI_10011524	superfamily	247068	326	406	5.40E-10	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22818 - 	CGI_10011524	superfamily	247068	104	210	4.54E-06	44.997	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22818 - 	CGI_10011524	superfamily	216897	454	532	2.21E-23	94.2852	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#22818 - 	CGI_10011524	superfamily	247068	25	49	0.000937609	37.7143	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22820 - 	CGI_10011526	superfamily	247068	175	275	7.49E-20	86.5985	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22820 - 	CGI_10011526	superfamily	247068	395	484	1.24E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22820 - 	CGI_10011526	superfamily	247068	74	167	1.38E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22820 - 	CGI_10011526	superfamily	247068	507	612	3.39E-13	66.9533	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22820 - 	CGI_10011526	superfamily	247068	286	380	1.74E-12	65.0273	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	517	615	3.67E-23	96.9989	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	428	509	3.65E-17	79.6649	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	741	837	1.72E-13	68.8793	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	1182	1263	1.45E-12	66.1829	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	1277	1353	2.07E-12	65.7977	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	324	399	6.31E-12	64.2569	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	899	967	1.30E-11	63.4865	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	626	732	6.12E-07	49.6194	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	269	313	3.15E-06	47.3082	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	815	888	0.000501615	40.4107	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22821 - 	CGI_10011528	superfamily	247068	59	131	0.00452775	37.3291	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22823 - 	CGI_10006408	superfamily	197732	819	852	5.01E-07	47.6323	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#22824 - 	CGI_10006409	superfamily	151853	319	401	1.18E-21	88.991	cl12943	Suppressor_APC superfamily	 - 	 - 	"Adenomatous polyposis coli tumour suppressor protein; The tumour suppressor protein, APC, has a nuclear export activity as well as many different intracellular functions. The structure consists of three alpha-helices forming two separate antiparallel coiled coils."
Q#22825 - 	CGI_10006410	superfamily	222150	35	60	0.000574582	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22825 - 	CGI_10006410	superfamily	222150	150	173	0.00186678	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#22826 - 	CGI_10006411	superfamily	112485	19	65	2.55E-07	43.016	cl04205	UPF0184 superfamily	N	 - 	Uncharacterized protein family (UPF0184); Uncharacterised protein family (UPF0184).  
Q#22827 - 	CGI_10006412	superfamily	247805	39	241	9.24E-72	226.597	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#22827 - 	CGI_10006412	superfamily	247905	256	389	1.39E-30	114.257	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#22828 - 	CGI_10006413	superfamily	247805	46	248	5.76E-84	260.11	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#22828 - 	CGI_10006413	superfamily	247905	263	389	2.32E-35	128.51	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#22830 - 	CGI_10006415	superfamily	241703	156	431	6.26E-94	288.003	cl00226	nuc_hydro superfamily	 - 	 - 	"nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity.  This group contains eukaryotic, bacterial and archeal proteins similar to the inosine-uridine preferring nucleoside hydrolase from Crithidia fasciculata,  the xanthosine-inosine-uridine-adenosine-preferring nucleoside hydrolase RihC from Salmonella enterica serovar Typhimurium, the purine-specific  inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax and, pyrimidine-specific uridine-cytidine preferring nucleoside hydrolases such as URH1 from Saccharomyces cerevisiae, RihA and RihB from Escherichia coli. Nucleoside hydrolases are of interest as a target for antiprotozoan drugs as, no nucleoside hydrolase activity or genes encoding these enzymes have been detected in humans and, parasitic protozoans lack de novo purine synthesis relying on nucleoside hydrolase to scavenge purine and/or pyrimidines from the environment."
Q#22830 - 	CGI_10006415	superfamily	241703	5	166	7.45E-57	191.318	cl00226	nuc_hydro superfamily	C	 - 	"nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity.  This group contains eukaryotic, bacterial and archeal proteins similar to the inosine-uridine preferring nucleoside hydrolase from Crithidia fasciculata,  the xanthosine-inosine-uridine-adenosine-preferring nucleoside hydrolase RihC from Salmonella enterica serovar Typhimurium, the purine-specific  inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax and, pyrimidine-specific uridine-cytidine preferring nucleoside hydrolases such as URH1 from Saccharomyces cerevisiae, RihA and RihB from Escherichia coli. Nucleoside hydrolases are of interest as a target for antiprotozoan drugs as, no nucleoside hydrolase activity or genes encoding these enzymes have been detected in humans and, parasitic protozoans lack de novo purine synthesis relying on nucleoside hydrolase to scavenge purine and/or pyrimidines from the environment."
Q#22831 - 	CGI_10006416	superfamily	247692	98	604	0	744.631	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#22833 - 	CGI_10006418	superfamily	247792	494	531	1.28E-08	51.6776	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22834 - 	CGI_10006419	superfamily	214781	244	357	2.58E-14	68.5228	cl02747	NRF superfamily	 - 	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#22836 - 	CGI_10007801	superfamily	245596	990	1208	8.21E-86	278.311	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#22836 - 	CGI_10007801	superfamily	243072	413	538	1.50E-40	147.53	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22836 - 	CGI_10007801	superfamily	243072	76	203	1.70E-36	135.974	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22836 - 	CGI_10007801	superfamily	243072	211	340	1.62E-31	121.337	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22837 - 	CGI_10007802	superfamily	245603	74	441	6.02E-167	480.382	cl11403	pepsin_retropepsin_like superfamily	 - 	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#22840 - 	CGI_10007805	superfamily	246680	42	115	1.71E-06	46.426	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22840 - 	CGI_10007805	superfamily	246680	387	446	2.95E-05	42.574	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22841 - 	CGI_10007806	superfamily	241832	72	153	1.16E-38	133.049	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#22842 - 	CGI_10007807	superfamily	247725	136	258	3.11E-74	237.205	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22842 - 	CGI_10007807	superfamily	243056	510	691	6.38E-51	176.396	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#22842 - 	CGI_10007807	superfamily	247725	293	431	7.17E-44	153.519	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22843 - 	CGI_10007808	superfamily	248097	124	255	0.000251268	38.4002	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22848 - 	CGI_10015835	superfamily	243066	30	128	8.86E-16	71.1828	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22849 - 	CGI_10015836	superfamily	245814	478	541	3.32E-06	45.5579	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22849 - 	CGI_10015836	superfamily	245814	338	391	0.000443859	39.0095	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22853 - 	CGI_10015840	superfamily	243139	218	272	8.99E-08	49.9912	cl02676	HSA superfamily	C	 - 	HSA; This domain is predicted to bind DNA and is often found associated with helicases.
Q#22855 - 	CGI_10015842	superfamily	248458	175	295	0.00504403	38.0637	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22855 - 	CGI_10015842	superfamily	245596	1	161	3.43E-70	228.346	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#22858 - 	CGI_10015845	superfamily	220080	709	845	6.50E-55	186.986	cl07526	DUF1900 superfamily	 - 	 - 	"Domain of unknown function (DUF1900); This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It has no known function."
Q#22858 - 	CGI_10015845	superfamily	220080	230	346	1.11E-37	138.45	cl07526	DUF1900 superfamily	 - 	 - 	"Domain of unknown function (DUF1900); This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It has no known function."
Q#22858 - 	CGI_10015845	superfamily	243092	506	710	1.41E-21	95.8648	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22858 - 	CGI_10015845	superfamily	243092	78	259	1.04E-14	74.2936	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#22858 - 	CGI_10015845	superfamily	149883	8	69	0.000776504	38.7593	cl07525	DUF1899 superfamily	 - 	 - 	Domain of unknown function (DUF1899); This set of domains is found in various eukaryotic proteins. Function is unknown.
Q#22859 - 	CGI_10015846	superfamily	243362	302	416	3.99E-44	153.735	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#22859 - 	CGI_10015846	superfamily	199908	236	296	2.00E-21	88.0814	cl16908	DnaJ_zf superfamily	 - 	 - 	"Zinc finger domain of DnaJ and HSP40; Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. Hsp40 proteins are characterized by the presence of an N-terminal J domain, which mediates the interaction with Hsp70. This central domain contains four repeats of a CxxCxGxG motif and binds to two Zinc ions. It has been implicated in substrate binding."
Q#22859 - 	CGI_10015846	superfamily	243077	78	132	5.85E-17	75.2745	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#22860 - 	CGI_10015847	superfamily	248194	35	210	0.00126358	39.9262	cl17640	PRMT5 superfamily	N	 - 	"PRMT5 arginine-N-methyltransferase; The human homologue of yeast Skb1 (Shk1 kinase-binding protein 1) is PRMT5, an arginine-N-methyltransferase. These proteins appear to be key mitotic regulators. They play a role in Jak signalling in higher eukaryotes."
Q#22862 - 	CGI_10015849	superfamily	247041	50	92	0.00218029	34.2485	cl15692	CE4_SF superfamily	NC	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#22864 - 	CGI_10015851	superfamily	241594	4931	5300	1.89E-105	346.089	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#22864 - 	CGI_10015851	superfamily	242903	3268	3417	1.32E-69	234.961	cl02148	APC10-like superfamily	 - 	 - 	"APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An  APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here."
Q#22864 - 	CGI_10015851	superfamily	151952	2887	2963	7.68E-42	152.205	cl13031	Cul7 superfamily	 - 	 - 	"Mouse development and cellular proliferation protein Cullin-7; The Cullin Ring Ligase family member, Cul7, is required for normal mouse development and cellular proliferation. Cul7 has a CPH domain which is a p53 interaction domain. The CPH domain interaction surface of P53 is present in the tetramerisation domain."
Q#22864 - 	CGI_10015851	superfamily	115363	2152	2210	4.70E-29	114.776	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#22864 - 	CGI_10015851	superfamily	242849	1440	1512	1.46E-23	99.2004	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#22864 - 	CGI_10015851	superfamily	201217	4724	4773	4.05E-15	74.0992	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	241760	3041	3085	5.10E-15	73.7724	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#22864 - 	CGI_10015851	superfamily	241760	3213	3257	5.10E-15	73.7724	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#22864 - 	CGI_10015851	superfamily	201217	689	740	1.24E-14	72.5584	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	3570	3619	2.13E-14	72.1732	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	242903	3096	3152	2.63E-14	74.3323	cl02148	APC10-like superfamily	C	 - 	"APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An  APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here."
Q#22864 - 	CGI_10015851	superfamily	201217	3622	3673	4.02E-14	71.0176	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	4618	4669	5.88E-14	70.6324	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	4566	4615	1.85E-13	69.0916	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	3728	3777	2.38E-13	69.0916	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	795	844	2.85E-13	68.7064	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	4777	4825	4.59E-12	65.2396	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	847	896	7.21E-12	64.4692	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	3780	3828	8.07E-11	61.7728	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	3515	3567	3.58E-09	56.7652	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	205718	673	702	1.27E-05	45.9442	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	637	686	1.48E-05	45.9796	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	3676	3725	3.32E-05	45.2092	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	201217	743	792	0.000282698	42.5128	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22864 - 	CGI_10015851	superfamily	205718	4708	4735	0.00253677	39.3958	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#22865 - 	CGI_10015852	superfamily	248097	132	255	1.06E-20	85.0094	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22866 - 	CGI_10015853	superfamily	248097	6	49	2.00E-08	46.1042	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22868 - 	CGI_10015855	superfamily	245814	11	94	5.13E-12	62.908	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22869 - 	CGI_10015856	superfamily	219571	291	789	0	661.822	cl06695	Cas1_AcylT superfamily	 - 	 - 	"10 TM Acyl Transferase domain found in Cas1p; Cas1p protein of Cryptococcus neoformans is required for the synthesis of O-acetylated glucuronoxylomannans, a consitutent of the capsule, and is critical for its virulence. The multi TM domain of the Cas1p was unified with the 10 TM Sugar Acyltransferase superfamily. This superfamily is comprised of members from the OatA, MdoC, OpgC, NolL and GumG families in addition to the Cas1p family. The Cas1p protein has a N terminal PC-Esterase domain with the opposing Acyl esterase activity."
Q#22869 - 	CGI_10015856	superfamily	242274	80	262	1.28E-07	52.4098	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#22870 - 	CGI_10015857	superfamily	241596	30	88	6.33E-05	37.1935	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#22871 - 	CGI_10005177	superfamily	243035	162	235	1.16E-07	49.1554	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22871 - 	CGI_10005177	superfamily	243035	265	381	3.03E-07	47.9998	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22871 - 	CGI_10005177	superfamily	243035	37	107	1.13E-05	43.3774	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22873 - 	CGI_10005180	superfamily	243519	12	136	5.52E-79	245.209	cl03757	phosphohexomutase superfamily	C	 - 	"The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model."
Q#22874 - 	CGI_10009715	superfamily	206084	81	105	1.30E-07	49.1364	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	523	547	1.33E-06	46.0548	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	695	719	1.44E-06	46.0548	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	390	413	4.84E-06	44.514	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	254	277	9.57E-06	43.7436	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	319	342	0.000221277	39.5064	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	186	207	0.000251343	39.5064	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	456	478	0.000685112	38.3508	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	622	645	0.00155421	37.1952	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	9	31	0.00199067	36.81	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22874 - 	CGI_10009715	superfamily	206084	581	603	0.00583525	35.2692	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#22875 - 	CGI_10009716	superfamily	245201	31	217	3.61E-64	209.4	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22875 - 	CGI_10009716	superfamily	241764	297	361	2.45E-21	88.3361	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#22875 - 	CGI_10009716	superfamily	241764	400	471	7.63E-08	49.956	cl00299	MIT superfamily	 - 	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#22875 - 	CGI_10009716	superfamily	245201	186	289	1.39E-05	46.4088	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22876 - 	CGI_10009717	superfamily	241613	93	127	3.84E-08	47.9718	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#22876 - 	CGI_10009717	superfamily	241613	54	88	1.20E-07	46.431	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#22877 - 	CGI_10009718	superfamily	243035	1045	1180	1.41E-15	76.5045	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22877 - 	CGI_10009718	superfamily	241571	2614	2719	2.35E-14	72.8302	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#22877 - 	CGI_10009718	superfamily	241571	915	1020	3.19E-14	72.445	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#22877 - 	CGI_10009718	superfamily	241613	1190	1224	5.13E-10	57.987	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#22877 - 	CGI_10009718	superfamily	243035	2744	2803	1.11E-07	52.6222	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#22877 - 	CGI_10009718	superfamily	241613	1514	1548	7.51E-06	46.0458	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#22877 - 	CGI_10009718	superfamily	245847	538	691	8.20E-17	80.8593	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#22877 - 	CGI_10009718	superfamily	241609	2271	2355	1.42E-06	48.9258	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#22877 - 	CGI_10009718	superfamily	241609	278	361	1.53E-06	48.9258	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#22877 - 	CGI_10009718	superfamily	241571	2459	2514	1.52E-05	45.8663	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#22877 - 	CGI_10009718	superfamily	192535	1711	1888	0.000256021	44.1238	cl18179	7TM_GPCR_Srsx superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#22877 - 	CGI_10009718	superfamily	241571	801	851	0.000661459	40.8587	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#22877 - 	CGI_10009718	superfamily	241619	708	773	0.00159432	39.4844	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#22877 - 	CGI_10009718	superfamily	217525	1651	1758	0.00411758	38.8845	cl04035	Serpentine_r_xa superfamily	C	 - 	"Caenorhabditis serpentine receptor-like protein, class xa; This family contains various Caenorhabditis proteins, some of which are annotated as being serpentine receptors, mainly of the xa class."
Q#22878 - 	CGI_10009719	superfamily	247724	62	255	1.07E-115	341.1	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#22878 - 	CGI_10009719	superfamily	243185	263	349	1.33E-36	130.32	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#22878 - 	CGI_10009719	superfamily	243184	354	447	3.98E-30	112.437	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#22879 - 	CGI_10009720	superfamily	241599	387	417	5.08E-05	41.0749	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#22880 - 	CGI_10009721	superfamily	245201	528	663	3.95E-24	102.7	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22880 - 	CGI_10009721	superfamily	245201	963	1129	8.41E-19	87.9714	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22881 - 	CGI_10009722	superfamily	221913	683	904	2.15E-57	196.607	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#22881 - 	CGI_10009722	superfamily	222005	504	550	1.37E-06	47.3468	cl18632	AAA_19 superfamily	C	 - 	Part of AAA domain; Part of AAA domain.  
Q#22882 - 	CGI_10009724	superfamily	247916	881	937	3.98E-07	48.9183	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#22883 - 	CGI_10009725	superfamily	243072	162	294	2.27E-27	104.388	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22884 - 	CGI_10000167	superfamily	241583	50	106	1.14E-11	57.1958	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#22886 - 	CGI_10000483	superfamily	243119	18	69	0.00062541	33.9465	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#22887 - 	CGI_10000542	superfamily	241563	56	92	0.00490572	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22889 - 	CGI_10003625	superfamily	241752	1823	2186	2.18E-72	248.724	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#22889 - 	CGI_10003625	superfamily	242589	1710	1806	2.92E-34	129.732	cl01581	WGR superfamily	 - 	 - 	"WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain."
Q#22889 - 	CGI_10003625	superfamily	243072	455	577	4.31E-23	98.2246	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	335	510	2.52E-20	90.1354	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	949	1095	3.33E-17	80.8906	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	248	393	1.03E-13	70.8754	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	839	966	2.29E-12	66.6382	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	559	690	7.05E-12	65.0974	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	1240	1403	6.46E-10	59.3194	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	1558	1627	4.46E-06	47.3782	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	734	877	6.78E-05	43.5263	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	243072	1191	1285	0.00315963	38.5187	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22889 - 	CGI_10003625	superfamily	242219	23	77	9.55E-10	58.4156	cl00955	Ribosomal_L34e superfamily	C	 - 	Ribosomal protein L34e; Ribosomal protein L34e.  
Q#22890 - 	CGI_10003626	superfamily	203149	12	90	1.40E-17	74.1713	cl09350	V-SNARE superfamily	 - 	 - 	Vesicle transport v-SNARE protein N-terminus; V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this. This domain is the N-terminal half of the V-Snare proteins.
Q#22890 - 	CGI_10003626	superfamily	152787	122	187	2.56E-07	45.6665	cl18053	V-SNARE_C superfamily	 - 	 - 	Snare region anchored in the vesicle membrane C-terminus; Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle pfam05008.
Q#22891 - 	CGI_10003627	superfamily	247786	9	98	9.76E-21	86.8785	cl17232	F420_oxidored superfamily	 - 	 - 	NADP oxidoreductase coenzyme F420-dependent; NADP oxidoreductase coenzyme F420-dependent.  
Q#22891 - 	CGI_10003627	superfamily	242267	272	373	3.42E-05	42.2772	cl01043	Ferric_reduct superfamily	N	 - 	"Ferric reductase like transmembrane component; This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease."
Q#22892 - 	CGI_10000759	superfamily	247058	1	168	3.61E-49	161.574	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#22897 - 	CGI_10001047	superfamily	241563	62	96	3.19E-05	41.8892	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22897 - 	CGI_10001047	superfamily	110440	483	509	0.0028551	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#22899 - 	CGI_10000701	superfamily	245856	572	804	1.53E-33	133.303	cl12060	AP2Ec superfamily	C	 - 	"AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-hexulose 3-phosphate to D-fructose 6-phosphate, via cleaving the phosphoesterbond with the sugar."
Q#22903 - 	CGI_10001705	superfamily	247794	1	145	4.38E-93	278.272	cl17240	FDH_GDH_like superfamily	N	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#22904 - 	CGI_10001557	superfamily	248097	18	137	2.36E-28	102.343	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#22905 - 	CGI_10010911	superfamily	241750	1430	1787	1.52E-172	532.797	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#22905 - 	CGI_10010911	superfamily	241555	182	358	7.01E-95	306.345	cl00020	GAT_1 superfamily	 - 	 - 	"Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E.  The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.  For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site.  Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain."
Q#22905 - 	CGI_10010911	superfamily	241720	1281	1407	8.02E-35	131.653	cl00245	MGS-like superfamily	 - 	 - 	"MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site."
Q#22905 - 	CGI_10010911	superfamily	247809	516	720	1.38E-76	255.689	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#22905 - 	CGI_10010911	superfamily	198801	4	142	5.04E-66	221.864	cl03056	CPSase_sm_chain superfamily	 - 	 - 	"Carbamoyl-phosphate synthase small chain, CPSase domain; The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See pfam00289. The small chain has a GATase domain in the carboxyl terminus. See pfam00117."
Q#22905 - 	CGI_10010911	superfamily	217204	1894	2036	4.77E-51	179.272	cl03681	OTCace_N superfamily	 - 	 - 	"Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain.  "
Q#22905 - 	CGI_10010911	superfamily	217231	808	930	5.87E-46	163.902	cl15983	CPSase_L_D3 superfamily	 - 	 - 	"Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain."
Q#22905 - 	CGI_10010911	superfamily	215776	2041	2191	1.96E-45	163.919	cl18343	OTCace superfamily	 - 	 - 	"Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain.  "
Q#22905 - 	CGI_10010911	superfamily	247809	1033	1213	4.45E-22	97.7576	cl17255	ATP-grasp_4 superfamily	 - 	 - 	ATP-grasp domain; This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Q#22905 - 	CGI_10010911	superfamily	201133	944	1038	7.24E-19	85.2265	cl02837	CPSase_L_chain superfamily	 - 	 - 	"Carbamoyl-phosphate synthase L chain, N-terminal domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117."
Q#22905 - 	CGI_10010911	superfamily	201133	411	510	2.83E-16	77.9077	cl02837	CPSase_L_chain superfamily	 - 	 - 	"Carbamoyl-phosphate synthase L chain, N-terminal domain; Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117."
Q#22906 - 	CGI_10010912	superfamily	248458	283	665	3.06E-09	58.0941	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22907 - 	CGI_10010913	superfamily	248458	86	181	9.45E-09	56.5533	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22907 - 	CGI_10010913	superfamily	248458	369	722	2.69E-08	55.0125	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22908 - 	CGI_10010914	superfamily	245201	289	567	0	566.871	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22908 - 	CGI_10010914	superfamily	243090	160	279	1.23E-50	174.47	cl02565	RGS superfamily	N	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#22908 - 	CGI_10010914	superfamily	243090	30	91	1.03E-35	133.253	cl02565	RGS superfamily	C	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#22908 - 	CGI_10010914	superfamily	247725	649	770	6.12E-35	129.736	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#22908 - 	CGI_10010914	superfamily	245597	548	614	6.24E-06	44.6588	cl11395	Pkinase_C superfamily	 - 	 - 	Protein kinase C terminal domain; Protein kinase C terminal domain.  
Q#22910 - 	CGI_10010916	superfamily	243056	924	1093	7.80E-42	154.002	cl02495	RabGAP-TBC superfamily	N	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#22910 - 	CGI_10010916	superfamily	243142	91	231	5.53E-28	111.179	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#22911 - 	CGI_10010917	superfamily	246954	36	467	2.18E-85	282.207	cl15415	Sec1 superfamily	C	 - 	Sec1 family; Sec1 family.  
Q#22911 - 	CGI_10010917	superfamily	246954	475	717	3.80E-38	148.543	cl15415	Sec1 superfamily	N	 - 	Sec1 family; Sec1 family.  
Q#22912 - 	CGI_10010918	superfamily	246669	193	300	6.82E-06	45.9059	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22912 - 	CGI_10010918	superfamily	246669	1033	1152	1.25E-30	119.265	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#22912 - 	CGI_10010918	superfamily	220800	919	1017	0.000437078	40.3663	cl11172	Membr_traf_MHD superfamily	 - 	 - 	"Munc13 (mammalian uncoordinated) homology domain; Munc13 proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster, mouse, rat and human, some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical."
Q#22913 - 	CGI_10010919	superfamily	247642	87	209	1.36E-44	148.533	cl16917	Complex1_30kDa superfamily	 - 	 - 	"Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Respiratory-chain NADH dehydrogenase, 30 Kd subunit.  "
Q#22914 - 	CGI_10010920	superfamily	241642	35	94	2.24E-05	40.5566	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#22914 - 	CGI_10010920	superfamily	241642	180	238	0.0089198	32.8845	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#22917 - 	CGI_10010923	superfamily	247856	22	79	6.32E-10	51.0093	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22920 - 	CGI_10010926	superfamily	245201	29	337	0	613.605	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22922 - 	CGI_10001740	superfamily	241563	96	121	0.00201011	36.3032	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22924 - 	CGI_10002037	superfamily	242004	114	348	1.10E-70	222.145	cl00650	Cu-oxidase_4 superfamily	 - 	 - 	Multi-copper polyphenol oxidoreductase laccase; Laccases are multi-copper oxidoreductases able to oxidise a wide variety of phenolic and non-phenolic compounds and are widely distributed among both prokaryotes and eukaryotes. There are two main active catalytic sites with conserved histidines that are capable of binding four copper atoms.
Q#22925 - 	CGI_10002038	superfamily	241567	408	617	3.65E-26	107.786	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#22925 - 	CGI_10002038	superfamily	245814	258	335	5.68E-10	57.553	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22925 - 	CGI_10002038	superfamily	245814	123	195	2.64E-07	49.0409	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#22925 - 	CGI_10002038	superfamily	246680	16	102	0.000116362	41.2442	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#22926 - 	CGI_10002039	superfamily	247986	126	222	7.30E-05	42.7454	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#22926 - 	CGI_10002039	superfamily	197504	328	460	1.02E-10	59.2253	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#22929 - 	CGI_10001790	superfamily	246748	355	597	5.33E-111	341.109	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#22929 - 	CGI_10001790	superfamily	244870	139	343	1.27E-75	245.662	cl08238	PA superfamily	 - 	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#22929 - 	CGI_10001790	superfamily	202944	625	748	6.09E-32	121.224	cl07854	TFR_dimer superfamily	 - 	 - 	Transferrin receptor-like dimerisation domain; This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
Q#22929 - 	CGI_10001790	superfamily	246748	61	115	3.25E-09	57.6025	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#22930 - 	CGI_10001791	superfamily	243072	41	174	1.22E-27	105.158	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22931 - 	CGI_10001792	superfamily	248012	2	62	4.50E-06	40.6389	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#22932 - 	CGI_10001793	superfamily	247953	11	159	4.01E-75	229.246	cl17399	3-HAO superfamily	 - 	 - 	3-hydroxyanthranilic acid dioxygenase; In eukaryotes 3-hydroxyanthranilic acid dioxygenase (EC:1.13.11.6) is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid.The prokaryotic homolog is involved in the 2-nitrobenzoate degradation pathway.
Q#22933 - 	CGI_10002105	superfamily	217473	146	369	1.43E-24	103.984	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#22934 - 	CGI_10010666	superfamily	222351	394	478	5.67E-19	83.3003	cl15817	Glyco_transf_7N superfamily	C	 - 	"N-terminal region of glycosyl transferase group 7; This is the N-terminal half of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalyzed reaction."
Q#22934 - 	CGI_10010666	superfamily	246031	249	330	2.50E-12	63.7128	cl12567	Beta-Casp superfamily	C	 - 	Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.
Q#22934 - 	CGI_10010666	superfamily	241867	25	180	2.55E-09	55.0393	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#22935 - 	CGI_10010667	superfamily	246681	358	569	4.04E-37	136.966	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#22936 - 	CGI_10010668	superfamily	247755	819	1066	1.32E-97	311.04	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#22936 - 	CGI_10010668	superfamily	248376	512	811	9.47E-46	167.585	cl17822	MutS_III superfamily	 - 	 - 	"MutS domain III; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in."
Q#22936 - 	CGI_10010668	superfamily	216613	214	323	8.09E-27	107.274	cl03286	MutS_I superfamily	 - 	 - 	"MutS domain I; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in."
Q#22936 - 	CGI_10010668	superfamily	218486	345	486	2.36E-09	56.6005	cl04975	MutS_II superfamily	 - 	 - 	"MutS domain II; This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam01624, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. This domain corresponds to domain II in Thermus aquaticus MutS as characterized in, and has similarity resembles RNAse-H-like domains (see pfam00075)."
Q#22937 - 	CGI_10010669	superfamily	247941	70	198	5.70E-07	46.9453	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#22940 - 	CGI_10010672	superfamily	217952	19	278	1.63E-73	235.266	cl04439	Gcd10p superfamily	 - 	 - 	Gcd10p family; eIF-3 is a multi-subunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit if eIF3. The Yeast protein Gcd10p has also been shown to be part of a complex with the methyltransferase Gcd14p that is involved in modifying tRNA.
Q#22942 - 	CGI_10010674	superfamily	247743	462	625	7.90E-27	107.617	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#22942 - 	CGI_10010674	superfamily	247743	208	347	2.76E-12	65.2451	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#22943 - 	CGI_10010675	superfamily	242274	29	75	0.00110179	34.1334	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#22944 - 	CGI_10010676	superfamily	242910	49	153	4.11E-51	179.791	cl02159	Peptidase_C13 superfamily	C	 - 	"Peptidase C13 family; Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterized as a 'haemoglobinase', but this term is probably incorrect. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed."
Q#22944 - 	CGI_10010676	superfamily	242910	150	195	4.56E-10	59.6083	cl02159	Peptidase_C13 superfamily	N	 - 	"Peptidase C13 family; Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterized as a 'haemoglobinase', but this term is probably incorrect. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed."
Q#22946 - 	CGI_10010678	superfamily	241565	146	221	0.00959049	34.6586	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#22948 - 	CGI_10010680	superfamily	248469	7	93	8.15E-05	39.2755	cl17915	HAD_like superfamily	C	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#22948 - 	CGI_10010680	superfamily	240421	86	141	0.000435797	38.1448	cl14774	PTZ00445 superfamily	N	 - 	p36-lilke protein; Provisional
Q#22949 - 	CGI_10010681	superfamily	241607	428	476	2.54E-17	76.9593	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#22949 - 	CGI_10010681	superfamily	248458	32	220	6.54E-08	53.4717	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22949 - 	CGI_10010681	superfamily	248458	312	397	0.000379282	41.9157	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#22950 - 	CGI_10010682	superfamily	241823	9	182	6.10E-78	237.857	cl00376	Ribosomal_L10_P0 superfamily	 - 	 - 	"Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2."
Q#22950 - 	CGI_10010682	superfamily	215914	231	313	8.54E-08	48.7728	cl18353	Ribosomal_60s superfamily	 - 	 - 	"60s Acidic ribosomal protein; This family includes archaebacterial L12, eukaryotic P0, P1 and P2."
Q#22954 - 	CGI_10010686	superfamily	217598	394	498	3.72E-49	171.113	cl04130	KCNQ_channel superfamily	N	 - 	KCNQ voltage-gated potassium channel; This family matches to the C-terminal tail of KCNQ type potassium channels.
Q#22954 - 	CGI_10010686	superfamily	219619	177	227	3.67E-15	71.4699	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#22955 - 	CGI_10020035	superfamily	247802	80	277	1.32E-119	352.6	cl17248	RIO superfamily	 - 	 - 	"RIO kinase family, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They function as non-ribosomal factors necessary for late 18S rRNA processing. RIO1 is also required for proper cell cycle progression and chromosome maintenance. The biological substrates for RIO kinases are still unknown."
Q#22955 - 	CGI_10020035	superfamily	220140	9	92	1.52E-35	127.277	cl07723	Rio2_N superfamily	 - 	 - 	"Rio2, N-terminal; Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains."
Q#22958 - 	CGI_10020038	superfamily	243066	10	100	1.88E-21	88.3789	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#22958 - 	CGI_10020038	superfamily	219619	336	400	3.81E-09	53.3655	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#22959 - 	CGI_10020039	superfamily	247068	721	822	6.47E-22	93.5321	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	247068	854	927	8.89E-11	60.7901	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	247068	1170	1256	2.55E-09	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	247068	1074	1161	6.84E-09	55.3974	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	247068	1281	1366	1.56E-08	54.2418	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	247068	615	706	3.98E-07	50.0046	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	247068	299	383	5.26E-07	49.6194	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	245213	1388	1425	2.03E-06	46.701	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22959 - 	CGI_10020039	superfamily	247068	509	603	0.000103554	42.6858	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22959 - 	CGI_10020039	superfamily	216265	1470	1618	6.21E-20	88.8988	cl03079	Cadherin_C superfamily	 - 	 - 	Cadherin cytoplasmic region; Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
Q#22959 - 	CGI_10020039	superfamily	247068	214	287	0.00114601	39.2551	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#22961 - 	CGI_10020041	superfamily	245010	106	203	0.00161731	37.3568	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#22961 - 	CGI_10020041	superfamily	241563	50	84	0.00649119	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#22962 - 	CGI_10020042	superfamily	246918	298	349	1.92E-14	69.1527	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22962 - 	CGI_10020042	superfamily	241583	161	241	3.78E-09	56.0927	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#22963 - 	CGI_10020043	superfamily	241583	277	375	2.65E-14	73.0415	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#22963 - 	CGI_10020043	superfamily	246918	486	536	4.42E-14	69.1527	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#22963 - 	CGI_10020043	superfamily	243051	774	903	0.00342769	38.1005	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#22965 - 	CGI_10020045	superfamily	216239	39	355	8.85E-117	353.534	cl18361	IRK superfamily	 - 	 - 	Inward rectifier potassium channel; Inward rectifier potassium channel.  
Q#22966 - 	CGI_10020046	superfamily	216239	50	369	2.17E-99	303.458	cl18361	IRK superfamily	 - 	 - 	Inward rectifier potassium channel; Inward rectifier potassium channel.  
Q#22967 - 	CGI_10020047	superfamily	243034	321	436	8.90E-05	41.2116	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#22967 - 	CGI_10020047	superfamily	215821	202	289	1.63E-22	92.6886	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#22968 - 	CGI_10020048	superfamily	241763	8	451	0	616.526	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#22969 - 	CGI_10020049	superfamily	220948	24	112	1.28E-37	124.456	cl12595	DUF2615 superfamily	 - 	 - 	"Protein of unknown function (DUF2615); This small. approximately 100 residue, family is conserved from worms to humans. It is cysteine-rich with a characteristic FDxCEC sequence motif. The function is not known."
Q#22970 - 	CGI_10020050	superfamily	241578	209	359	7.86E-29	115.467	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22970 - 	CGI_10020050	superfamily	241578	1022	1172	2.49E-26	108.148	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22970 - 	CGI_10020050	superfamily	241578	395	544	6.92E-15	74.6354	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22970 - 	CGI_10020050	superfamily	245213	712	748	8.95E-10	56.491	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	902	938	8.95E-10	56.491	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	864	900	1.70E-09	55.7206	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	941	976	1.81E-09	55.7206	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	751	786	2.68E-09	55.3354	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	788	824	3.91E-09	54.565	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	676	710	4.68E-09	54.565	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	128	163	1.83E-08	52.639	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	828	862	6.39E-08	51.0982	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	165	201	1.39E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	245213	978	1014	1.39E-06	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22970 - 	CGI_10020050	superfamily	248133	1308	1567	7.44E-60	209.379	cl17579	Fructosamin_kin superfamily	 - 	 - 	Fructosamine kinase; This family includes eukaryotic fructosamine-3-kinase enzymes. The family also includes bacterial members that have not been characterized but probably have a similar or identical function.
Q#22970 - 	CGI_10020050	superfamily	241578	1208	1289	1.74E-05	45.3602	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22971 - 	CGI_10020051	superfamily	241578	147	297	4.38E-29	110.074	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#22971 - 	CGI_10020051	superfamily	245213	103	139	4.69E-08	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#22972 - 	CGI_10020052	superfamily	242575	81	203	1.93E-05	42.2238	cl01548	YccV-like superfamily	 - 	 - 	Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.
Q#22974 - 	CGI_10020054	superfamily	243072	170	269	6.14E-07	48.5338	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#22979 - 	CGI_10020059	superfamily	247792	140	194	3.15E-05	40.892	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#22982 - 	CGI_10020062	superfamily	245201	173	486	6.01E-61	204.64	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#22983 - 	CGI_10020063	superfamily	247064	8	167	1.17E-47	164.773	cl15774	Hemerythrin-like superfamily	 - 	 - 	"Hemerythrin family; Hemerythrin (Hr) and related proteins are found in bacteria, archaea and eukaryotes. They are non-heme diiron oxygen transport proteins. In addition to oxygen transport, members are involved in cadmium fixation and host anti-bacterial defense. They have the same "four alpha helix bundle" motif and similar active site structures. Some members, like Hr, form oligomers, the octameric form being most prevalent, while others are monomeric."
Q#22983 - 	CGI_10020063	superfamily	243074	203	244	9.70E-14	66.7613	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#22983 - 	CGI_10020063	superfamily	199166	519	583	2.71E-07	50.4036	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#22983 - 	CGI_10020063	superfamily	199166	353	403	0.00119763	39.618	cl15308	AMN1 superfamily	NC	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#22986 - 	CGI_10020066	superfamily	219542	135	250	9.50E-42	148.159	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#22986 - 	CGI_10020066	superfamily	215896	309	430	4.98E-28	110.848	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#22986 - 	CGI_10020066	superfamily	219541	538	687	6.02E-27	107.169	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#22987 - 	CGI_10020067	superfamily	245208	18	650	0	566.958	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#22989 - 	CGI_10020069	superfamily	247856	65	126	5.84E-13	60.6393	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22989 - 	CGI_10020069	superfamily	247856	100	174	3.59E-09	49.8537	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#22989 - 	CGI_10020069	superfamily	244899	36	86	0.00257561	34.3878	cl08302	S-100 superfamily	N	 - 	"S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins."
Q#22992 - 	CGI_10020072	superfamily	217390	150	292	6.14E-22	89.5412	cl18407	TPT superfamily	 - 	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#22993 - 	CGI_10020073	superfamily	247723	9	85	1.05E-41	138.217	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#22993 - 	CGI_10020073	superfamily	199156	105	121	0.00495866	33.5708	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#22994 - 	CGI_10020074	superfamily	221741	314	409	2.36E-10	58.1111	cl15057	Cadherin-like superfamily	 - 	 - 	"Cadherin-like beta sandwich domain; This domain is found in several bacterial, metazoan and chlorophyte algal proteins. A profile-profile comparison recovered the cadherin domain and a comparison of the predicted structure of this domain with the crystal structure of the cadherin showed a congruent seven stranded secondary structure. The domain is widespread in bacteria and seen in the firmicutes, actinobacteria, certain proteobacteria, bacteroides and chlamydiae with an expansion in Clostridium. In contrast, it is limited in its distribution in eukaryotes suggesting that it was derived through lateral transfer from bacteria. In prokaryotes, this domain is widely fused to other domains such as FNIII (Fibronectin Type III), TIG, SLH (S-layer homology), discoidin, cell-wall-binding repeat domain and alpha-amylase-like glycohydrolases. These associations are suggestive of a carbohydrate-binding function for this cadherin-like domain. In animal proteins it is associated with an ATP-grasp domain."
Q#22994 - 	CGI_10020074	superfamily	242274	507	609	0.000259362	42.0094	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#23001 - 	CGI_10002852	superfamily	243267	7	284	4.94E-39	140.827	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#23009 - 	CGI_10020009	superfamily	241563	300	338	4.00E-07	46.8967	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#23009 - 	CGI_10020009	superfamily	188588	25	81	8.55E-05	40.6499	cl14866	exo_TIGR04073 superfamily	 - 	 - 	"putative exosortase-associated protein, TIGR04073 family; Members of this protein family are found in beta, gamma, and delta proteobacteria, and in the verrucomicrobia. Twenty-two of twenty-four species encountered contain the PEP-CTERM/exosortase system for modulating extracellular polysaccharide biosynthesis production, suggesting a role in protein sorting. The N-terminal signal sequence is divergent and not included in the model. PSI-BLAST and HMM searches suggest a distant sequence relationship between a region of this protein of about 100 amino acids and a corresponding region of the very large eukaryotic protein vps13, associated with vacuolar protein sorting in yeast."
Q#23011 - 	CGI_10020011	superfamily	241563	38	76	3.48E-06	44.5855	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#23011 - 	CGI_10020011	superfamily	110440	497	524	0.00449441	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#23012 - 	CGI_10020012	superfamily	222150	874	895	0.00820373	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23013 - 	CGI_10020013	superfamily	246597	77	280	9.63E-31	116.013	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#23014 - 	CGI_10020014	superfamily	217452	44	151	3.20E-28	106.347	cl12276	Tropomodulin superfamily	N	 - 	Tropomodulin; Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments. Limited proteolysis shows this protein is composed of two domains. The amino terminal domain contains the tropomyosin binding function.
Q#23015 - 	CGI_10020015	superfamily	193256	2393	2634	3.11E-70	241.005	cl18189	AAA_8 superfamily	 - 	 - 	"P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor."
Q#23015 - 	CGI_10020015	superfamily	193257	2997	3227	2.13E-53	190.967	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#23015 - 	CGI_10020015	superfamily	193251	2033	2304	5.04E-50	182.443	cl18188	AAA_7 superfamily	 - 	 - 	"P-loop containing dynein motor region D3; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site."
Q#23015 - 	CGI_10020015	superfamily	193253	2646	2975	7.73E-46	172.529	cl15084	MT superfamily	 - 	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#23015 - 	CGI_10020015	superfamily	247743	1724	1869	1.98E-07	52.6828	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23017 - 	CGI_10020017	superfamily	241600	18	235	1.40E-68	212.486	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23018 - 	CGI_10020018	superfamily	241600	9	180	6.65E-52	167.417	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23020 - 	CGI_10020020	superfamily	247085	900	1007	3.97E-28	111.443	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#23020 - 	CGI_10020020	superfamily	245596	792	878	1.61E-33	131.943	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23020 - 	CGI_10020020	superfamily	241815	603	737	2.01E-16	79.4103	cl00361	Transcrip_reg superfamily	C	 - 	"Transcriptional regulator; This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region."
Q#23023 - 	CGI_10020023	superfamily	247085	78	194	2.75E-29	106.821	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#23023 - 	CGI_10020023	superfamily	245596	1	37	3.57E-18	79.1705	cl11394	Glyco_tranf_GTA_type superfamily	NC	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23023 - 	CGI_10020023	superfamily	245596	23	65	1.51E-08	52.2066	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23025 - 	CGI_10020025	superfamily	247085	687	803	2.34E-28	111.443	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#23025 - 	CGI_10020025	superfamily	245596	606	645	1.55E-18	86.1041	cl11394	Glyco_tranf_GTA_type superfamily	NC	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23025 - 	CGI_10020025	superfamily	245596	647	674	1.19E-08	56.0586	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23028 - 	CGI_10020028	superfamily	243034	48	121	5.51E-08	46.6044	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23029 - 	CGI_10020029	superfamily	247746	55	122	0.00373586	36.0822	cl17192	ATP-synt_B superfamily	N	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#23030 - 	CGI_10020030	superfamily	243034	28	112	4.69E-09	49.3008	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23031 - 	CGI_10020031	superfamily	110440	489	513	0.00706678	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#23032 - 	CGI_10020032	superfamily	247068	46	139	6.55E-25	100.899	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23032 - 	CGI_10020032	superfamily	147567	575	838	1.45E-31	125.495	cl12309	DAG1 superfamily	 - 	 - 	"Dystroglycan (Dystrophin-associated glycoprotein 1); Dystroglycan is one of the dystrophin-associated glycoproteins, which is encoded by a 5.5 kb transcript in human. The protein product is cleaved into two non-covalently associated subunits, [alpha] (N-terminal) and [beta] (C-terminal). In skeletal muscle the dystroglycan complex works as a transmembrane linkage between the extracellular matrix and the cytoskeleton. [alpha]-dystroglycan is extracellular and binds to merosin ([alpha]-2 laminin) in the basement membrane, while [beta]-dystroglycan is a transmembrane protein and binds to dystrophin, which is a large rod-like cytoskeletal protein, absent in Duchenne muscular dystrophy patients. Dystrophin binds to intracellular actin cables. In this way, the dystroglycan complex, which links the extracellular matrix to the intracellular actin cables, is thought to provide structural integrity in muscle tissues. The dystroglycan complex is also known to serve as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. There is also evidence which suggests the function of dystroglycan as a part of the signal transduction pathway because it is shown that Grb2, a mediator of the Ras-related signal pathway, can interact with the cytoplasmic domain of dystroglycan. In general, aberrant expression of dystrophin-associated protein complex underlies the pathogenesis of Duchenne muscular dystrophy, Becker muscular dystrophy and severe childhood autosomal recessive muscular dystrophy. Interestingly, no genetic disease has been described for either [alpha]- or [beta]-dystroglycan. Dystroglycan is widely distributed in non-muscle tissues as well as in muscle tissues. During epithelial morphogenesis of kidney, the dystroglycan complex is shown to act as a receptor for the basement membrane. Dystroglycan expression in mouse brain and neural retina has also been reported. However, the physiological role of dystroglycan in non-muscle tissues has remained unclear."
Q#23032 - 	CGI_10020032	superfamily	206765	157	278	2.46E-28	111.267	cl16905	alpha_DG_C superfamily	 - 	 - 	"C-terminal domain of alpha dystroglycan; Dystroglycan is a glycoprotein widely distributed in skeletal muscle and other tissues; the pre-protein is cleaved into two subunits (alpha and beta) that form a complex which links the extracellular matrix to the cytoskeleton. This C-terminal domain of the alpha-subunit appears to contact neighboring cadherin-like repeats of alpha dystroglycan, and may also be involved in interactions with other components of the dystrophin-dystroglycan-complex (DGC). DGC has been shown to interact with extracellular matrix components such as laminin, perlecan and m-agrin, suggesting that the complex may play various different roles depending on the extracellular ligand."
Q#23036 - 	CGI_10012986	superfamily	219542	11	115	5.45E-37	133.136	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#23036 - 	CGI_10012986	superfamily	219541	397	569	2.09E-29	112.947	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#23036 - 	CGI_10012986	superfamily	215896	126	311	2.33E-16	76.5648	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#23037 - 	CGI_10012987	superfamily	219542	5	115	2.26E-35	129.669	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#23037 - 	CGI_10012987	superfamily	219541	403	577	8.72E-27	106.399	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#23037 - 	CGI_10012987	superfamily	215896	126	316	1.72E-16	76.95	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#23038 - 	CGI_10012988	superfamily	219542	11	115	2.48E-37	134.291	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#23038 - 	CGI_10012988	superfamily	219541	400	574	1.25E-27	108.325	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#23038 - 	CGI_10012988	superfamily	215896	126	312	2.25E-18	82.3428	cl18351	Cu-oxidase superfamily	 - 	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#23039 - 	CGI_10012989	superfamily	247805	33	184	3.90E-12	61.9696	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#23040 - 	CGI_10012991	superfamily	241546	3	117	9.40E-18	80.0756	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#23040 - 	CGI_10012991	superfamily	215847	225	632	2.87E-80	269.316	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#23041 - 	CGI_10012992	superfamily	215847	2	40	5.43E-06	43.2039	cl09510	Lipoxygenase superfamily	NC	 - 	Lipoxygenase; Lipoxygenase.  
Q#23042 - 	CGI_10012993	superfamily	247805	30	142	6.62E-12	58.888	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#23043 - 	CGI_10012994	superfamily	243072	52	121	1.03E-09	51.6154	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23044 - 	CGI_10012995	superfamily	243072	66	223	1.94E-10	58.9342	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23044 - 	CGI_10012995	superfamily	217473	327	557	2.40E-08	54.6785	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#23045 - 	CGI_10003400	superfamily	187403	2	360	1.26E-165	520.063	cl14649	BRO1_Alix_like superfamily	 - 	 - 	"Protein-interacting Bro1-like domain of mammalian Alix and related domains; This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, HD-PTP, and Brox) and Snf7 (in the case of yeast Bro1, and Rim20). The single domain protein human Brox, and the isolated Bro1-like domains of Alix, HD-PTP and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V) domain, which in the case of Alix, has been shown to be a dimerization domain and to contain a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in this superfamily. Alix, HD-PTP and Bro1 also have a proline-rich region (PRR); the Alix PRR binds multiple partners. Rhophilin-1, and -2, in addition to this Bro1-like domain, have an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This protein has a C-terminal, catalytically inactive tyrosine phosphatase domain."
Q#23045 - 	CGI_10003400	superfamily	187408	365	523	2.08E-48	180.179	cl14654	V_Alix_like superfamily	C	 - 	"Protein-interacting V-domain of mammalian Alix and related domains; This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain."
Q#23047 - 	CGI_10016207	superfamily	246669	19	49	1.42E-14	64.4267	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#23048 - 	CGI_10016208	superfamily	247723	386	439	5.96E-14	67.3273	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23049 - 	CGI_10016209	superfamily	241752	1806	1925	2.92E-44	159.022	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#23049 - 	CGI_10016209	superfamily	247723	192	263	1.16E-13	68.8332	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23049 - 	CGI_10016209	superfamily	241554	858	1029	1.87E-51	181.7	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#23049 - 	CGI_10016209	superfamily	241554	1077	1266	5.02E-22	95.4051	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#23049 - 	CGI_10016209	superfamily	247723	62	123	2.17E-09	56.5417	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23049 - 	CGI_10016209	superfamily	247723	275	343	2.70E-08	53.4601	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23049 - 	CGI_10016209	superfamily	241554	1344	1502	1.91E-07	51.9627	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#23049 - 	CGI_10016209	superfamily	207713	1660	1714	0.00100365	39.6101	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#23053 - 	CGI_10016213	superfamily	247724	141	273	1.39E-08	53.5656	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23054 - 	CGI_10016214	superfamily	247723	10	116	3.37E-29	105.533	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23055 - 	CGI_10016215	superfamily	245814	288	358	4.70E-08	50.5655	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#23055 - 	CGI_10016215	superfamily	214507	216	271	0.000905022	37.4096	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#23055 - 	CGI_10016215	superfamily	243030	32	64	0.00245547	36.1415	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#23057 - 	CGI_10016217	superfamily	248458	385	562	1.37E-18	86.2137	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23057 - 	CGI_10016217	superfamily	248458	27	207	3.97E-06	47.6937	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23057 - 	CGI_10016217	superfamily	248188	339	404	0.00245589	38.861	cl17634	Herpes_BBRF1 superfamily	NC	 - 	BRRF1-like protein; Family of herpesvirus proteins including Epstein-barr virus protein BBRF1.
Q#23059 - 	CGI_10016219	superfamily	241550	393	542	4.61E-82	258.266	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#23059 - 	CGI_10016219	superfamily	247725	30	118	2.55E-29	112.773	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23061 - 	CGI_10016221	superfamily	241878	33	81	7.51E-09	48.518	cl00460	CMD superfamily	 - 	 - 	"Carboxymuconolactone decarboxylase family; Carboxymuconolactone decarboxylase (CMD) EC:4.1.1.44 is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway. In these bifunctional proteins CMD represents the C-terminal domain, pfam00561 represents the N-terminal domain."
Q#23062 - 	CGI_10016222	superfamily	247684	166	482	5.31E-46	167.839	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#23062 - 	CGI_10016222	superfamily	247684	41	144	6.44E-07	50.7388	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#23065 - 	CGI_10016225	superfamily	241638	148	271	1.21E-07	48.5185	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#23065 - 	CGI_10016225	superfamily	241691	90	172	0.00432852	36.0911	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#23068 - 	CGI_10016228	superfamily	241638	123	245	3.34E-10	55.0669	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#23071 - 	CGI_10016231	superfamily	205988	80	197	5.01E-38	138.975	cl16417	Dzip-like_N superfamily	 - 	 - 	Iguana/Dzip1-like DAZ-interacting protein N-terminal; The DAZ gene-product - Deleted in Azoospermia - and a closely related sequence are required early in germ-cell development in order to maintain germ-cell populations. This family is the N-terminal region that is the only part of the protein in some fungi and lower metazoa.
Q#23072 - 	CGI_10016232	superfamily	243034	106	184	4.06E-13	65.094	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23072 - 	CGI_10016232	superfamily	243034	203	297	4.01E-09	53.538	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23072 - 	CGI_10016232	superfamily	243034	315	401	2.54E-06	45.0636	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23073 - 	CGI_10002224	superfamily	247824	34	332	4.91E-94	285.734	cl17270	APH_ChoK_like superfamily	 - 	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#23074 - 	CGI_10002225	superfamily	241754	6	337	0	577.417	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#23075 - 	CGI_10002226	superfamily	216739	461	495	0.000235864	39.7234	cl03383	PC_rep superfamily	 - 	 - 	Proteasome/cyclosome repeat; Proteasome/cyclosome repeat.  
Q#23075 - 	CGI_10002226	superfamily	216739	708	739	0.00428656	36.2566	cl03383	PC_rep superfamily	 - 	 - 	Proteasome/cyclosome repeat; Proteasome/cyclosome repeat.  
Q#23077 - 	CGI_10002389	superfamily	248097	144	266	1.26E-20	84.6242	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23078 - 	CGI_10002437	superfamily	247743	5	142	6.12E-19	80.6531	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23078 - 	CGI_10002437	superfamily	204202	212	271	2.60E-08	49.1761	cl07827	Vps4_C superfamily	 - 	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#23079 - 	CGI_10002438	superfamily	191619	1	149	6.27E-48	156.046	cl06071	DUF1241 superfamily	 - 	 - 	Protein of unknown function (DUF1241); This family consists of several programmed cell death 10 protein (PDCD10 or TFAR15) sequences. The function of this family is unknown.
Q#23080 - 	CGI_10002439	superfamily	241578	1927	2116	1.33E-76	254.761	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#23080 - 	CGI_10002439	superfamily	247743	97	253	1.36E-37	140.508	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23080 - 	CGI_10002439	superfamily	247743	990	1137	7.34E-24	100.833	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23080 - 	CGI_10002439	superfamily	247743	426	569	1.07E-20	91.588	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23080 - 	CGI_10002439	superfamily	247743	709	798	2.52E-07	51.5272	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23081 - 	CGI_10002440	superfamily	248458	246	418	1.02E-12	67.7241	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23082 - 	CGI_10002441	superfamily	248458	375	553	1.28E-08	55.7829	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23082 - 	CGI_10002441	superfamily	248458	67	173	0.00165568	39.6045	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23084 - 	CGI_10010019	superfamily	241583	49	194	8.23E-40	135.024	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23085 - 	CGI_10010020	superfamily	241804	206	490	2.00E-38	142.554	cl00348	COG0182 superfamily	 - 	 - 	"Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]"
Q#23086 - 	CGI_10010021	superfamily	247744	9	211	1.50E-92	272.573	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#23089 - 	CGI_10010024	superfamily	241571	40	136	1.09E-18	82.4602	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23089 - 	CGI_10010024	superfamily	241571	146	245	5.08E-16	74.7562	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23089 - 	CGI_10010024	superfamily	241609	253	321	1.50E-17	78.1165	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#23094 - 	CGI_10010029	superfamily	246954	33	626	1.64E-145	436.287	cl15415	Sec1 superfamily	 - 	 - 	Sec1 family; Sec1 family.  
Q#23095 - 	CGI_10010030	superfamily	241575	123	194	0.00209304	35.7111	cl00054	DSRM superfamily	 - 	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#23096 - 	CGI_10010031	superfamily	243263	45	335	6.41E-44	158.725	cl02990	ASC superfamily	C	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#23096 - 	CGI_10010031	superfamily	243263	340	358	6.25E-05	43.5506	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#23098 - 	CGI_10010033	superfamily	243035	5	109	5.67E-16	68.8005	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23099 - 	CGI_10010034	superfamily	248458	59	432	2.36E-34	132.052	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23100 - 	CGI_10010035	superfamily	243035	2	69	1.94E-08	46.613	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23102 - 	CGI_10004532	superfamily	243092	5	65	9.81E-10	53.4928	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23103 - 	CGI_10004533	superfamily	215754	186	267	2.19E-14	66.508	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#23103 - 	CGI_10004533	superfamily	215754	81	156	1.57E-09	53.4112	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#23103 - 	CGI_10004533	superfamily	215754	11	59	3.83E-06	43.396	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#23104 - 	CGI_10004534	superfamily	247724	8	202	1.68E-78	237.105	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23108 - 	CGI_10003069	superfamily	248275	70	94	6.37E-07	46.034	cl17721	zf-C2H2_jaz superfamily	 - 	 - 	"Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation."
Q#23110 - 	CGI_10003071	superfamily	248275	70	94	7.79E-07	45.2636	cl17721	zf-C2H2_jaz superfamily	 - 	 - 	"Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation."
Q#23111 - 	CGI_10003072	superfamily	242161	13	80	2.64E-33	112.493	cl00875	PTZ00255 superfamily	C	 - 	60S ribosomal protein L37a; Provisional
Q#23115 - 	CGI_10012160	superfamily	245213	41	77	5.29E-05	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23115 - 	CGI_10012160	superfamily	245213	266	295	0.000450334	38.3866	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23115 - 	CGI_10012160	superfamily	245213	298	332	0.00110847	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23115 - 	CGI_10012160	superfamily	245213	371	406	0.00402572	35.305	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23115 - 	CGI_10012160	superfamily	245213	340	368	0.00861947	34.5346	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23116 - 	CGI_10012161	superfamily	112833	35	162	1.99E-69	211.056	cl04372	DUF367 superfamily	 - 	 - 	Domain of unknown function (DUF367); Domain of unknown function (DUF367).  
Q#23116 - 	CGI_10012161	superfamily	217870	1	31	1.53E-10	54.0401	cl04386	RLI superfamily	 - 	 - 	"Possible Fer4-like domain in RNase L inhibitor, RLI; Possible metal-binding domain in endoribonuclease RNase L inhibitor. Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, pfam00037. Also often found adjacent to the DUF367 domain pfam04034 in uncharacterized proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons, and could possibly play a more general role in the regulation of RNA stability in mammalian cells. Inhibitory activity requires concentration-dependent association of RLI with RNase L."
Q#23120 - 	CGI_10005266	superfamily	245335	28	277	1.06E-125	365.801	cl10571	GT_MraY-like superfamily	 - 	 - 	"Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound polyprenol phosphate, which is the initiation step of protein N-glycosylation in eukaryotes and peptidoglycan biosynthesis in bacteria. One member, D-N-acetylhexosamine 1-phosphate transferase (GPT) is a eukaryotic enzyme, which is specific for UDP-GlcNAc as donor substrate and dolichol-phosphate as the membrane bound acceptor. The bacterial members MraY, WecA, and WbpL/WbcO utilize undecaprenol phosphate as the acceptor substrate, but use different UDP-sugar donor substrates. MraY-type transferases are highly specific for UDP-N-acetylmuramate-pentapeptide, whereas WecA proteins are selective for UDP-N-acetylglucosamine (UDP-GlcNAc). The WbcO/WbpL substrate specificity has not yet been determined, but the structure of their biosynthetic endproducts implies that UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or UDPN-acetyl-D-quinosamine (UDP-QuiNAc) are used. The eukaryotic reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for N-glycosylation. The prokaryotic reactions lead to the formation of polyprenol-linked oligosaccharides involved in bacterial cell wall and peptidoglycan assembly. Archaeal and eukaryotic enzymes may use the same substrates and are evolutionarily closer than the bacterial enzyme. Archaea possess the same N-glycosylation pathway as eukaryotes. A glycosyl transferase gene Mv1751 in M. voltae encodes for the enzyme that carries out the first step in the pathway, the attachment of GlcNAc to a dolichol lipid carrier in the membrane. A lethal mutation in the alg7 (GPT) gene in Saccharomyces cerevisiae was successfully complemented with Mv1751, the archaea gene."
Q#23121 - 	CGI_10005267	superfamily	241559	26	186	3.90E-12	66.9507	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#23121 - 	CGI_10005267	superfamily	109460	258	282	0.000348983	42.0254	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#23121 - 	CGI_10005267	superfamily	109460	339	362	0.000543267	41.255	cl02859	Calponin superfamily	 - 	 - 	Calponin family repeat; Calponin family repeat.  
Q#23122 - 	CGI_10005268	superfamily	202000	1	129	1.92E-17	80.5957	cl03375	XRCC1_N superfamily	 - 	 - 	XRCC1 N terminal domain; XRCC1 N terminal domain.  
Q#23123 - 	CGI_10005269	superfamily	247856	101	154	3.78E-08	46.7721	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23125 - 	CGI_10005272	superfamily	245598	53	90	3.22E-09	54.978	cl11396	Patatin_and_cPLA2 superfamily	N	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#23125 - 	CGI_10005272	superfamily	247856	187	257	0.000470259	37.9125	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23126 - 	CGI_10005273	superfamily	215847	188	629	4.01E-88	290.117	cl09510	Lipoxygenase superfamily	N	 - 	Lipoxygenase; Lipoxygenase.  
Q#23126 - 	CGI_10005273	superfamily	241546	3	87	6.88E-12	63.1269	cl00011	PLAT superfamily	N	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#23128 - 	CGI_10011003	superfamily	245227	1	341	0	601.507	cl10013	Glycosyltransferase_GTB_type superfamily	 - 	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#23129 - 	CGI_10011004	superfamily	241580	126	203	4.26E-45	152.323	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#23132 - 	CGI_10011007	superfamily	201217	333	381	9.99E-10	54.8392	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#23132 - 	CGI_10011007	superfamily	201217	151	200	1.07E-09	54.454	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#23132 - 	CGI_10011007	superfamily	201217	203	250	6.25E-08	49.4464	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#23132 - 	CGI_10011007	superfamily	201217	256	328	3.02E-06	44.824	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#23132 - 	CGI_10011007	superfamily	201217	432	482	0.00185697	36.3496	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#23133 - 	CGI_10011008	superfamily	214781	183	288	5.66E-14	69.2932	cl02747	NRF superfamily	 - 	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#23134 - 	CGI_10011009	superfamily	246723	19	640	0	652.832	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#23136 - 	CGI_10011011	superfamily	243064	38	96	6.86E-07	43.9434	cl02512	NTR_like superfamily	NC	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#23137 - 	CGI_10011012	superfamily	247905	190	296	5.09E-12	62.2552	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#23137 - 	CGI_10011012	superfamily	247805	43	130	0.00035616	39.5499	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#23140 - 	CGI_10011015	superfamily	243064	22	67	4.03E-10	52.361	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#23141 - 	CGI_10005713	superfamily	245202	81	169	2.07E-41	136.622	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#23141 - 	CGI_10005713	superfamily	243703	2	81	5.23E-39	130.38	cl04309	RNAP_Rpb7_N_like superfamily	 - 	 - 	"RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex."
Q#23143 - 	CGI_10005715	superfamily	245201	78	341	4.91E-163	472.888	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23144 - 	CGI_10005716	superfamily	248318	2212	2274	1.91E-05	45.4637	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#23144 - 	CGI_10005716	superfamily	218263	1340	1486	0.00112522	40.1795	cl04748	DUF547 superfamily	 - 	 - 	"Protein of unknown function, DUF547; Family of uncharacterized proteins from C. elegans and A. thaliana."
Q#23144 - 	CGI_10005716	superfamily	221338	1754	1852	0.00751899	39.9267	cl13402	PORR superfamily	C	 - 	"Plant organelle RNA recognition domain; This family, which was previously known as DUF860, has been shown to be a component of group II intron ribonucleoprotein particles in maize chloroplasts. The domain is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. All of the members are predicted to localise to mitochondria or chloroplasts. It seems likely that most PORR proteins function in organellar RNA metabolism."
Q#23145 - 	CGI_10005717	superfamily	195671	51	163	9.09E-34	118.708	cl08257	Ribosomal_L11 superfamily	 - 	 - 	"Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation."
Q#23146 - 	CGI_10005718	superfamily	248318	10	72	6.72E-06	44.6934	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#23147 - 	CGI_10005719	superfamily	195671	51	163	1.62E-33	117.937	cl08257	Ribosomal_L11 superfamily	 - 	 - 	"Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation."
Q#23148 - 	CGI_10005720	superfamily	112836	654	782	3.28E-79	255.239	cl04373	DUF382 superfamily	 - 	 - 	Domain of unknown function (DUF382); This domain is specific to the human splicing factor 3b subunit 2 and it's orthologues. Splicing factor 3b subunit 2 or SAP145 is a suppressor of U2 snRNA mutations. Pre-mRNA splicing is catalyzed by a large ribonucleoprotein complex called the spliceosome. Spliceosomes are multi-component enzymes that catalyze pre-mRNA splicing and form step-wise by the ordered interaction of UsnRNPs and non-snRNP proteins with short conserved regions of the pre-mRNA at the 5' and 3' splice sites and branch site.
Q#23148 - 	CGI_10005720	superfamily	207686	786	844	4.00E-20	86.2547	cl02643	PSP superfamily	 - 	 - 	PSP; Proline rich domain found in numerous spliceosome associated proteins.
Q#23148 - 	CGI_10005720	superfamily	207684	11	44	2.73E-08	51.6107	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#23149 - 	CGI_10005721	superfamily	215866	7	156	1.79E-40	141.309	cl18349	Arrestin_N superfamily	 - 	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#23149 - 	CGI_10005721	superfamily	243212	180	309	2.80E-26	102.037	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#23150 - 	CGI_10005722	superfamily	246954	134	450	3.76E-96	303.008	cl15415	Sec1 superfamily	N	 - 	Sec1 family; Sec1 family.  
Q#23150 - 	CGI_10005722	superfamily	246954	9	131	1.01E-44	164.722	cl15415	Sec1 superfamily	C	 - 	Sec1 family; Sec1 family.  
Q#23151 - 	CGI_10005723	superfamily	243175	106	241	5.70E-55	177.441	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#23151 - 	CGI_10005723	superfamily	241832	11	78	1.84E-20	83.0879	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#23152 - 	CGI_10005724	superfamily	248223	2	244	4.07E-22	94.761	cl17669	ampG superfamily	C	 - 	muropeptide transporter; Validated
Q#23156 - 	CGI_10011183	superfamily	242902	36	98	3.83E-11	59.9531	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#23157 - 	CGI_10011184	superfamily	242902	25	115	3.50E-14	69.1978	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#23159 - 	CGI_10011187	superfamily	248458	55	180	2.46E-11	65.0277	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23159 - 	CGI_10011187	superfamily	248458	235	398	1.23E-09	59.6349	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23159 - 	CGI_10011187	superfamily	195686	397	528	5.65E-34	129.051	cl08291	TCTP superfamily	 - 	 - 	Translationally controlled tumour protein; Translationally controlled tumour protein.  
Q#23159 - 	CGI_10011187	superfamily	247725	531	623	2.06E-12	65.1138	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23160 - 	CGI_10011188	superfamily	197361	365	456	2.68E-06	45.8031	cl15254	UBAN superfamily	 - 	 - 	"polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well."
Q#23165 - 	CGI_10002505	superfamily	241584	58	90	0.00961139	33.6239	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#23166 - 	CGI_10002506	superfamily	241584	102	164	0.00103474	35.8627	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#23167 - 	CGI_10005326	superfamily	243035	32	146	4.02E-26	96.5349	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23168 - 	CGI_10005327	superfamily	243035	138	235	4.29E-14	65.7189	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23168 - 	CGI_10005327	superfamily	243035	38	130	2.46E-05	41.4514	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23169 - 	CGI_10005328	superfamily	245206	12	271	1.38E-17	81.6456	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23171 - 	CGI_10005330	superfamily	245814	43	106	0.00231058	35.9279	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#23175 - 	CGI_10008161	superfamily	241607	96	128	9.45E-06	41.4866	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#23175 - 	CGI_10008161	superfamily	241607	55	87	0.0051986	33.7826	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#23176 - 	CGI_10008162	superfamily	216347	302	721	1.16E-121	374.18	cl08309	Cu_amine_oxid superfamily	 - 	 - 	"Copper amine oxidase, enzyme domain; Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme."
Q#23176 - 	CGI_10008162	superfamily	145726	50	138	0.00244241	36.9398	cl08353	Cu_amine_oxidN2 superfamily	 - 	 - 	"Copper amine oxidase, N2 domain; This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ)."
Q#23182 - 	CGI_10004315	superfamily	243134	30	149	3.30E-37	130.077	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#23182 - 	CGI_10004315	superfamily	243134	162	285	4.21E-29	108.506	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#23186 - 	CGI_10004319	superfamily	110440	293	318	0.00139182	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#23187 - 	CGI_10006058	superfamily	248097	65	184	3.16E-23	90.4022	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23188 - 	CGI_10006059	superfamily	246925	327	539	3.70E-08	55.0542	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#23188 - 	CGI_10006059	superfamily	246925	141	273	2.90E-07	51.9726	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#23188 - 	CGI_10006059	superfamily	214507	654	693	0.00555966	36.254	cl15307	LRRCT superfamily	C	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#23188 - 	CGI_10006059	superfamily	241640	750	813	0.00987397	37.4188	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#23190 - 	CGI_10006061	superfamily	247725	32	126	3.31E-15	72.2598	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23191 - 	CGI_10006063	superfamily	217293	27	238	8.33E-75	238.687	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#23191 - 	CGI_10006063	superfamily	202474	245	338	8.25E-26	105.428	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#23192 - 	CGI_10006064	superfamily	247639	45	398	1.80E-150	434.39	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#23193 - 	CGI_10006065	superfamily	247639	50	416	0	568.054	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#23194 - 	CGI_10006066	superfamily	245814	27	89	0.00640732	34.7723	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#23197 - 	CGI_10007625	superfamily	247743	174	310	1.33E-14	72.1787	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23198 - 	CGI_10007626	superfamily	241599	99	157	2.60E-24	95.7732	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#23198 - 	CGI_10007626	superfamily	146451	414	434	0.000694242	37.3387	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#23199 - 	CGI_10007627	superfamily	216554	25	188	6.01E-38	134.914	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#23200 - 	CGI_10007628	superfamily	241640	428	664	3.36E-77	248.73	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#23200 - 	CGI_10007628	superfamily	243040	104	227	1.46E-18	82.5546	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#23200 - 	CGI_10007628	superfamily	241613	240	274	7.26E-09	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23200 - 	CGI_10007628	superfamily	243040	24	100	5.27E-08	51.3535	cl02447	CRD_FZ superfamily	C	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#23200 - 	CGI_10007628	superfamily	243061	317	410	2.62E-06	45.9206	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23201 - 	CGI_10007629	superfamily	241583	186	373	3.60E-73	233.617	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23201 - 	CGI_10007629	superfamily	243051	416	567	4.43E-42	148.68	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23201 - 	CGI_10007629	superfamily	243051	47	125	1.82E-19	85.5073	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23202 - 	CGI_10007630	superfamily	241583	1	167	2.16E-65	210.505	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23202 - 	CGI_10007630	superfamily	243051	203	353	2.03E-40	143.287	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23202 - 	CGI_10007630	superfamily	243051	334	461	1.61E-24	98.9893	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23205 - 	CGI_10007633	superfamily	216062	22	91	2.04E-05	40.499	cl02928	TGFb_propeptide superfamily	C	 - 	TGF-beta propeptide; This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Q#23206 - 	CGI_10007634	superfamily	243062	11	113	3.96E-47	148.578	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#23208 - 	CGI_10016976	superfamily	216653	80	203	5.90E-15	68.3927	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#23209 - 	CGI_10016977	superfamily	216653	395	548	6.74E-23	94.5862	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#23209 - 	CGI_10016977	superfamily	207627	111	198	9.28E-21	87.3051	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#23209 - 	CGI_10016977	superfamily	207627	223	311	5.82E-17	76.5243	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#23210 - 	CGI_10016978	superfamily	216653	653	812	6.95E-20	87.2674	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#23210 - 	CGI_10016978	superfamily	216653	42	202	1.00E-14	72.2447	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#23210 - 	CGI_10016978	superfamily	207627	451	547	9.41E-14	68.4303	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#23210 - 	CGI_10016978	superfamily	207627	338	425	3.50E-11	60.7263	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#23211 - 	CGI_10016979	superfamily	245814	350	423	0.00704012	34.7885	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#23212 - 	CGI_10016980	superfamily	245622	105	161	1.06E-16	72.6422	cl11446	Rhomboid superfamily	C	 - 	"Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite."
Q#23214 - 	CGI_10016982	superfamily	220735	330	949	3.38E-166	505.647	cl15660	Ufd2P_core superfamily	 - 	 - 	"Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity."
Q#23214 - 	CGI_10016982	superfamily	248098	965	1036	1.60E-27	107.764	cl17544	U-box superfamily	 - 	 - 	U-box domain; This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
Q#23215 - 	CGI_10016983	superfamily	114359	7	308	9.62E-69	224.788	cl17943	DUF791 superfamily	 - 	 - 	Protein of unknown function (DUF791); This family consists of several eukaryotic proteins of unknown function.
Q#23216 - 	CGI_10016984	superfamily	216686	25	202	1.72E-41	143.232	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#23217 - 	CGI_10016985	superfamily	113585	127	241	1.85E-26	101.632	cl04775	DUF716 superfamily	 - 	 - 	"Family of unknown function (DUF716); This family is equally distributed in both metazoa and plants. Annotation associated with a member from Nicotiana tabacum suggest that it may be involved in response to viral attack in plants. However, no clear function has been assigned to this family."
Q#23218 - 	CGI_10016986	superfamily	247805	22	94	5.75E-10	51.8763	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#23219 - 	CGI_10016987	superfamily	247905	190	296	5.28E-12	62.2552	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#23219 - 	CGI_10016987	superfamily	247805	43	130	7.16E-05	41.8611	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#23220 - 	CGI_10016988	superfamily	218140	353	771	1.50E-76	258.682	cl04579	Anoctamin superfamily	 - 	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#23221 - 	CGI_10016989	superfamily	247905	6	109	4.70E-19	80.7448	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#23221 - 	CGI_10016989	superfamily	221155	183	302	3.65E-08	50.444	cl13152	RIG-I_C-RD superfamily	 - 	 - 	"C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity."
Q#23222 - 	CGI_10016990	superfamily	247805	109	260	7.98E-24	96.6375	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#23225 - 	CGI_10016993	superfamily	152119	182	234	0.00246823	36.1287	cl13182	DUF3278 superfamily	N	 - 	Protein of unknown function (DUF3278); This bacterial family of proteins has no known function.
Q#23228 - 	CGI_10016997	superfamily	241613	117	152	8.09E-05	38.3418	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23228 - 	CGI_10016997	superfamily	246918	54	106	2.50E-11	56.0559	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23230 - 	CGI_10016999	superfamily	241583	392	604	3.09E-25	105.398	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23231 - 	CGI_10017000	superfamily	217293	49	259	1.02E-37	137.379	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#23231 - 	CGI_10017000	superfamily	202474	266	357	7.45E-12	63.4417	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#23233 - 	CGI_10017002	superfamily	206050	28	124	1.19E-25	96.9595	cl16449	KIAA1430 superfamily	 - 	 - 	KIAA1430 homologue; This is a family of KIAA1430 homologues. The function is not known.
Q#23234 - 	CGI_10017003	superfamily	241599	103	159	2.01E-22	88.0692	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#23234 - 	CGI_10017003	superfamily	146451	266	284	0.000383259	37.3387	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#23235 - 	CGI_10017004	superfamily	246228	482	682	9.68E-55	187.104	cl13209	CPSF73-100_C superfamily	 - 	 - 	Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.
Q#23235 - 	CGI_10017004	superfamily	246031	251	372	4.23E-43	151.538	cl12567	Beta-Casp superfamily	 - 	 - 	Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.
Q#23235 - 	CGI_10017004	superfamily	241867	25	185	2.13E-11	62.358	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#23235 - 	CGI_10017004	superfamily	203663	385	427	5.07E-09	53.2623	cl06522	RMMBL superfamily	 - 	 - 	RNA-metabolising metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism.
Q#23236 - 	CGI_10017005	superfamily	247976	167	280	2.09E-49	162.74	cl17422	RF-1 superfamily	 - 	 - 	"RF-1 domain; This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis."
Q#23236 - 	CGI_10017005	superfamily	248299	34	138	8.44E-22	88.3607	cl17745	PCRF superfamily	 - 	 - 	PCRF domain; This domain is found in peptide chain release factors.
Q#23239 - 	CGI_10011798	superfamily	247856	7	30	0.00564633	30.9789	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23240 - 	CGI_10011799	superfamily	216212	350	832	8.75E-84	279.562	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#23240 - 	CGI_10011799	superfamily	241651	236	320	0.00020501	41.1566	cl00163	PTS_IIA_fru superfamily	N	 - 	"PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation."
Q#23241 - 	CGI_10011800	superfamily	219209	42	373	2.27E-29	116.301	cl06089	RNA_pol_I_A49 superfamily	 - 	 - 	"A49-like RNA polymerase I associated factor; Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homolog indicate that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA."
Q#23242 - 	CGI_10011801	superfamily	245596	74	369	0	517.913	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23242 - 	CGI_10011801	superfamily	247085	387	510	2.67E-22	92.5686	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#23243 - 	CGI_10011802	superfamily	241599	5	50	1.33E-07	47.2381	cl00084	homeodomain superfamily	N	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#23244 - 	CGI_10011803	superfamily	247856	161	224	1.80E-08	49.0833	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23244 - 	CGI_10011803	superfamily	215821	56	150	3.30E-37	127.357	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#23247 - 	CGI_10011806	superfamily	245201	248	514	1.60E-144	420.312	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23248 - 	CGI_10011807	superfamily	216686	106	297	3.37E-52	172.893	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#23252 - 	CGI_10012539	superfamily	243095	631	879	3.46E-57	195.637	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#23252 - 	CGI_10012539	superfamily	241900	264	483	9.22E-106	330.815	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#23253 - 	CGI_10012540	superfamily	245838	190	452	2.41E-45	158.762	cl12018	Peptidase_M48 superfamily	 - 	 - 	Peptidase family M48; Peptidase family M48.  
Q#23254 - 	CGI_10012541	superfamily	243043	168	187	7.11E-05	38.3766	cl02453	IlGF_like superfamily	N	 - 	"Insulin/insulin-like growth factor/relaxin family; insulin family of proteins. Members include a number of active peptides which are evolutionary related including insulin, relaxin, prorelaxin, insulin-like growth factors I and II, mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP; gene INSL4), insect prothoracicotropic hormone (bombyxin), locust insulin-related peptide (LIRP), molluscan insulin-related peptides 1 to 5 (MIP), and C. elegans insulin-like peptides. Typically, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the "A" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the "B" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds."
Q#23255 - 	CGI_10012542	superfamily	243043	52	146	1.20E-06	43.2346	cl02453	IlGF_like superfamily	 - 	 - 	"Insulin/insulin-like growth factor/relaxin family; insulin family of proteins. Members include a number of active peptides which are evolutionary related including insulin, relaxin, prorelaxin, insulin-like growth factors I and II, mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP; gene INSL4), insect prothoracicotropic hormone (bombyxin), locust insulin-related peptide (LIRP), molluscan insulin-related peptides 1 to 5 (MIP), and C. elegans insulin-like peptides. Typically, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the "A" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the "B" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds."
Q#23257 - 	CGI_10012544	superfamily	248458	348	732	5.28E-29	118.57	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23258 - 	CGI_10012545	superfamily	241571	6	130	3.12E-20	83.6158	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23258 - 	CGI_10012545	superfamily	241571	137	259	2.07E-12	62.0446	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23260 - 	CGI_10008246	superfamily	246921	322	374	1.65E-09	55.0741	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#23260 - 	CGI_10008246	superfamily	246921	254	305	5.32E-08	50.8369	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#23260 - 	CGI_10008246	superfamily	246921	31	78	0.00838168	35.4289	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#23261 - 	CGI_10008247	superfamily	245230	34	466	0	912.444	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#23266 - 	CGI_10007018	superfamily	216686	3	123	3.07E-19	80.8301	cl18377	Galactosyl_T superfamily	N	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#23269 - 	CGI_10007021	superfamily	241874	9	456	2.52E-125	387.992	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#23269 - 	CGI_10007021	superfamily	248289	679	715	0.00203628	37.1104	cl17735	VWC superfamily	C	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#23269 - 	CGI_10007021	superfamily	214565	597	662	0.00374413	36.3865	cl18312	VWC_out superfamily	 - 	 - 	von Willebrand factor (vWF) type C domain; von Willebrand factor (vWF) type C domain.  
Q#23269 - 	CGI_10007021	superfamily	248289	515	552	0.00526457	35.9548	cl17735	VWC superfamily	C	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#23271 - 	CGI_10006688	superfamily	242406	1	67	3.26E-10	53.3641	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#23275 - 	CGI_10003751	superfamily	146263	125	170	2.10E-07	46.9139	cl04138	SK_channel superfamily	C	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#23275 - 	CGI_10003751	superfamily	216423	169	199	4.00E-07	48.0015	cl18367	Glyco_hydro_35 superfamily	NC	 - 	Glycosyl hydrolases family 35; Glycosyl hydrolases family 35.  
Q#23276 - 	CGI_10003752	superfamily	198825	268	340	4.03E-37	129.841	cl03763	CaMBD superfamily	 - 	 - 	"Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other."
Q#23276 - 	CGI_10003752	superfamily	146263	11	95	2.45E-28	107.005	cl04138	SK_channel superfamily	N	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#23276 - 	CGI_10003752	superfamily	219619	175	250	2.34E-10	56.0619	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#23277 - 	CGI_10020447	superfamily	241559	19	134	2.61E-18	81.5883	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#23277 - 	CGI_10020447	superfamily	241559	163	268	9.88E-16	74.2695	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#23277 - 	CGI_10020447	superfamily	241559	285	391	5.15E-11	60.4023	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#23277 - 	CGI_10020447	superfamily	241559	408	511	1.53E-07	50.0019	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#23277 - 	CGI_10020447	superfamily	247829	531	560	2.36E-13	70.2946	cl17275	PRTase_typeII superfamily	N	 - 	"Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate phosphoribosyltransferase (NAPRTase), to be used in the synthesis of NAD. QAPRTase catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide, an important step in the de novo synthesis of NAD. NAPRTase catalyses a similar reaction leading to NAMN and pyrophosphate, using nicotinic acid an PPRP as substrates, used in the NAD salvage pathway."
Q#23278 - 	CGI_10020448	superfamily	247068	13	89	7.66E-16	73.1165	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23278 - 	CGI_10020448	superfamily	247068	130	217	3.11E-11	60.0197	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23279 - 	CGI_10020449	superfamily	243319	7	189	6.69E-110	314.981	cl03141	Ribosomal_S7e superfamily	 - 	 - 	Ribosomal protein S7e; Ribosomal protein S7e.  
Q#23280 - 	CGI_10020450	superfamily	241644	5	102	5.08E-29	104.977	cl00154	UBCc superfamily	C	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#23281 - 	CGI_10020451	superfamily	241756	164	237	1.61E-24	98.9345	cl00289	FIG superfamily	N	 - 	"FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule Inositol-1,4,5-triphosphate. Many of these enzymes are inhibited by Li+."
Q#23281 - 	CGI_10020451	superfamily	241756	45	162	7.14E-22	91.2305	cl00289	FIG superfamily	C	 - 	"FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule Inositol-1,4,5-triphosphate. Many of these enzymes are inhibited by Li+."
Q#23282 - 	CGI_10020452	superfamily	221744	19	285	3.84E-09	55.9051	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#23283 - 	CGI_10020453	superfamily	221744	45	309	7.30E-14	69.3871	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#23284 - 	CGI_10020454	superfamily	218122	306	608	2.17E-89	283.334	cl04558	Choline_transpo superfamily	 - 	 - 	Plasma-membrane choline transporter; This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals.
Q#23285 - 	CGI_10020455	superfamily	245201	946	1186	3.20E-34	133.431	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23287 - 	CGI_10020457	superfamily	219127	184	506	9.94E-70	227.963	cl05943	MIG-14_Wnt-bd superfamily	 - 	 - 	"Wnt-binding factor required for Wnt secretion; MIG-14 is a Wnt-binding factor. Newly synthesised EGL-20/Wnt binds to MIG-14 in the Golgi, targetting the Wnt to the cell membrane for secretion. AP-2-mediated endocytosis and retromer retrieval at the sorting endosome would recycle MIG-14 to the Golgi, where it can bind to EGL-20/Wnt for next cycle of secretion."
Q#23288 - 	CGI_10020458	superfamily	221744	54	303	9.42E-21	92.8842	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#23289 - 	CGI_10020459	superfamily	221744	92	301	7.23E-09	54.7495	cl18614	CABIT superfamily	 - 	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#23291 - 	CGI_10020461	superfamily	248097	14	125	4.56E-19	77.3054	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23292 - 	CGI_10020462	superfamily	202711	38	210	6.18E-92	269.607	cl04190	Mob1_phocein superfamily	 - 	 - 	"Mob1/phocein family; Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin."
Q#23293 - 	CGI_10020463	superfamily	215859	479	696	1.49E-70	230.566	cl18347	Peptidase_S9 superfamily	 - 	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#23294 - 	CGI_10020464	superfamily	248097	59	167	1.11E-12	60.7418	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23298 - 	CGI_10020468	superfamily	245225	38	494	5.08E-49	181.672	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#23298 - 	CGI_10020468	superfamily	245225	556	754	6.11E-28	117.344	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#23299 - 	CGI_10020469	superfamily	222150	456	481	5.54E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23299 - 	CGI_10020469	superfamily	222150	344	369	7.11E-05	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23299 - 	CGI_10020469	superfamily	222150	373	395	0.000233624	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23299 - 	CGI_10020469	superfamily	222150	401	425	0.000417124	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23299 - 	CGI_10020469	superfamily	222150	428	453	0.00146095	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23302 - 	CGI_10020472	superfamily	243061	667	764	2.19E-24	99.3386	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23302 - 	CGI_10020472	superfamily	243061	771	876	2.60E-22	93.5606	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23302 - 	CGI_10020472	superfamily	243061	96	203	1.69E-07	50.033	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23302 - 	CGI_10020472	superfamily	238012	233	262	0.00295393	36.9486	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#23303 - 	CGI_10020473	superfamily	241571	791	842	1.55E-06	47.7923	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23303 - 	CGI_10020473	superfamily	243061	544	636	5.36E-20	87.3974	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23303 - 	CGI_10020473	superfamily	243061	187	274	1.87E-08	53.4998	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23303 - 	CGI_10020473	superfamily	243061	367	446	3.25E-06	46.5662	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23303 - 	CGI_10020473	superfamily	243061	643	682	0.000243293	40.7882	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23303 - 	CGI_10020473	superfamily	238012	37	67	0.00267647	37.3338	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#23303 - 	CGI_10020473	superfamily	238012	119	152	0.00519408	36.1782	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#23304 - 	CGI_10020474	superfamily	241571	1727	1846	7.18E-11	62.0446	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23304 - 	CGI_10020474	superfamily	243061	1155	1257	7.27E-32	122.836	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23304 - 	CGI_10020474	superfamily	243061	406	514	4.68E-13	68.1374	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23304 - 	CGI_10020474	superfamily	243061	704	817	3.22E-10	59.663	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23304 - 	CGI_10020474	superfamily	243061	23	107	4.31E-09	56.1962	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23304 - 	CGI_10020474	superfamily	243061	1055	1148	2.87E-07	50.8034	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23304 - 	CGI_10020474	superfamily	243061	217	321	3.66E-05	44.255	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#23304 - 	CGI_10020474	superfamily	241574	2050	2087	0.000154204	44.1138	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#23304 - 	CGI_10020474	superfamily	243051	1343	1505	0.000545166	41.1821	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23304 - 	CGI_10020474	superfamily	205157	1599	1622	0.00143984	38.6727	cl18264	EGF_3 superfamily	N	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#23304 - 	CGI_10020474	superfamily	238012	833	867	0.00860652	36.5634	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#23305 - 	CGI_10020475	superfamily	243072	172	306	2.69E-32	118.64	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23306 - 	CGI_10020476	superfamily	247676	3	129	4.52E-59	183.61	cl17012	GINS_A superfamily	 - 	 - 	"Alpha-helical domain of GINS complex proteins; Sld5, Psf1, Psf2 and Psf3; The GINS complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In eukaryotes, GINS is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has been found in eukaryotes and archaea, but not in bacteria. The four subunits of the complex are homologous and consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3."
Q#23307 - 	CGI_10020477	superfamily	247757	22	433	0	601.806	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#23309 - 	CGI_10020479	superfamily	247692	58	655	0	942.743	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#23310 - 	CGI_10020480	superfamily	202484	1	44	2.52E-11	53.3868	cl03798	zf-Tim10_DDP superfamily	N	 - 	Tim10/DDP family zinc finger; Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein TIMM8A. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localised to the mitochondrial intermembrane space.
Q#23312 - 	CGI_10020482	superfamily	192729	7	60	1.57E-34	125.242	cl14978	IRF-2BP1_2 superfamily	 - 	 - 	Interferon regulatory factor 2-binding protein zinc finger; IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger represented in this family and C-terminal RING finger domains.
Q#23314 - 	CGI_10020484	superfamily	241645	12	125	7.19E-56	172.035	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#23316 - 	CGI_10001715	superfamily	217293	25	229	1.61E-41	145.468	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#23316 - 	CGI_10001715	superfamily	202474	239	330	3.22E-23	95.4132	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#23318 - 	CGI_10001569	superfamily	241754	230	547	6.01E-136	428.26	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#23319 - 	CGI_10006946	superfamily	245864	1	394	5.59E-50	177.275	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#23321 - 	CGI_10006948	superfamily	247792	38	71	9.15E-07	44.3588	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23323 - 	CGI_10006950	superfamily	241597	166	236	1.31E-20	88.5093	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#23324 - 	CGI_10006951	superfamily	241896	116	317	7.30E-124	356.426	cl00483	UDG_like superfamily	 - 	 - 	"Uracil-DNA glycosylases (UDG) and related enzymes; Uracil-DNA glycosylases (UDG) catalyzes the removal of uracil from DNA, which initiates the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. At least five UDG families have been characterized so far; these families share similar overall folds and common active site motifs. They demonstrate different substrate specificities, but often the function of one enzyme can be complemented by the other. Family 1 enzymes are active against uracil in both ssDNA and dsDNA, and recognize uracil explicitly in an extrahelical conformation via a combination of protein and bound-water interactions. Family 2 enzymes are mismatch specific and explicitly recognize the widowed guanine on the complementary strand, rather than the extrahelical scissile pyrimidine. This allows a broader specificity so that some Family 2 enzymes can excise uracil as well as 3, N(4)-ethenocytosine from mismatches with guanine. A Family 3 UDG from human was first characterized to remove Uracil from ssDNA, hence the name hSMUG (single-strand-selective monofunctional uracil-DNA glycosylase). However, subsequent research has shown that hSMUG1 and its rat ortholog can remove uracil and its oxidized pyrimidine derivatives from both, ssDNA and dsDNA. Enzymes in Families 4 and 5 are both thermostable. Family 4 enzymes specifically recognize uracil in a manner similar to human UDG (Family 1), rather than guanine in the complementary strand DNA, as does E. coli MUG (Family 2). These results suggest that the mechanism by which Family 4 UDGs remove uracils from DNA is similar to that of Family 1 enzyme. Although Family 5 enzymes are close relatives of Family 4, they show different substrate specificities."
Q#23325 - 	CGI_10006952	superfamily	247044	3	138	7.45E-62	200.941	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#23325 - 	CGI_10006952	superfamily	247683	465	518	2.10E-30	112.493	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#23326 - 	CGI_10006953	superfamily	247724	13	208	4.45E-72	234.091	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23326 - 	CGI_10006953	superfamily	243066	471	568	2.62E-14	69.642	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#23328 - 	CGI_10006955	superfamily	247941	173	292	0.00879039	35.5661	cl17387	Methyltransf_21 superfamily	C	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#23332 - 	CGI_10007277	superfamily	245210	1	105	4.95E-56	179.982	cl09938	cond_enzymes superfamily	N	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#23333 - 	CGI_10007278	superfamily	248097	10	123	6.43E-20	79.6166	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23334 - 	CGI_10007279	superfamily	245210	41	237	1.44E-67	215.421	cl09938	cond_enzymes superfamily	C	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#23335 - 	CGI_10007280	superfamily	243096	981	1165	4.64E-29	117.014	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#23335 - 	CGI_10007280	superfamily	247725	1212	1305	2.58E-28	111.988	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23335 - 	CGI_10007280	superfamily	241566	726	771	1.08E-08	54.0352	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#23336 - 	CGI_10007281	superfamily	245201	30	217	4.94E-37	133.029	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23337 - 	CGI_10007282	superfamily	217473	114	205	5.01E-05	43.893	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#23338 - 	CGI_10007283	superfamily	192604	21	96	3.66E-14	66.1686	cl11135	PACT_coil_coil superfamily	 - 	 - 	"Pericentrin-AKAP-450 domain of centrosomal targeting protein; This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly."
Q#23343 - 	CGI_10013128	superfamily	247740	106	155	0.00427014	36.455	cl17186	TIM_phosphate_binding superfamily	NC	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#23346 - 	CGI_10013131	superfamily	241752	643	709	5.09E-20	86.9897	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#23346 - 	CGI_10013131	superfamily	241752	136	188	1.57E-18	82.7525	cl00283	ADP_ribosyl superfamily	C	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#23346 - 	CGI_10013131	superfamily	145501	414	567	0.00346884	37.288	cl03566	Cornifin superfamily	 - 	 - 	Cornifin (SPRR) family; SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. The most characteristic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid.
Q#23348 - 	CGI_10013133	superfamily	241583	247	434	1.67E-59	200.105	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23348 - 	CGI_10013133	superfamily	241571	618	736	4.79E-23	95.557	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23348 - 	CGI_10013133	superfamily	243035	495	610	2.71E-09	55.7037	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23348 - 	CGI_10013133	superfamily	216301	27	216	2.38E-40	146.64	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#23349 - 	CGI_10013134	superfamily	241578	187	358	1.89E-20	90.9165	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#23349 - 	CGI_10013134	superfamily	217211	408	474	4.75E-08	51.9014	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#23351 - 	CGI_10013136	superfamily	248097	66	189	1.04E-14	66.905	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23353 - 	CGI_10013138	superfamily	248097	9	119	1.83E-08	48.0302	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23356 - 	CGI_10013141	superfamily	241831	18	81	5.60E-13	59.4104	cl00386	BolA superfamily	N	 - 	BolA-like protein; This family consist of the morphoprotein BolA from E. coli and its various homologues. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5.
Q#23357 - 	CGI_10009439	superfamily	241600	2	194	1.65E-54	174.736	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23358 - 	CGI_10009440	superfamily	241600	9	153	2.75E-46	163.18	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23358 - 	CGI_10009440	superfamily	241600	372	488	8.49E-28	111.563	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23358 - 	CGI_10009440	superfamily	241600	178	255	4.64E-21	91.9182	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23358 - 	CGI_10009440	superfamily	248275	616	637	0.00491457	35.6336	cl17721	zf-C2H2_jaz superfamily	C	 - 	"Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation."
Q#23360 - 	CGI_10009442	superfamily	241613	632	664	2.69E-06	45.6606	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23361 - 	CGI_10009443	superfamily	241613	438	469	1.64E-11	60.2981	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23362 - 	CGI_10009444	superfamily	243035	113	206	5.05E-08	49.1554	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23373 - 	CGI_10002849	superfamily	110440	484	510	9.62E-05	40.0837	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#23373 - 	CGI_10002849	superfamily	241563	59	95	0.000353698	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#23373 - 	CGI_10002849	superfamily	128778	103	212	0.00981233	35.3183	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#23374 - 	CGI_10002044	superfamily	241600	1	102	2.58E-49	159.328	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23375 - 	CGI_10002045	superfamily	241600	27	197	3.61E-69	212.871	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23376 - 	CGI_10002046	superfamily	247905	39	173	4.87E-07	47.6177	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#23376 - 	CGI_10002046	superfamily	243778	222	296	7.17E-19	80.3459	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#23380 - 	CGI_10015782	superfamily	247856	155	201	4.09E-13	61.7949	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23382 - 	CGI_10015784	superfamily	241599	111	160	1.40E-20	83.0616	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#23382 - 	CGI_10015784	superfamily	217600	218	264	1.42E-05	42.1018	cl04137	TF_Otx superfamily	C	 - 	Otx1 transcription factor; Otx1 transcription factor.  
Q#23383 - 	CGI_10015785	superfamily	221433	484	615	2.13E-35	130.496	cl13553	DUF3585 superfamily	 - 	 - 	Protein of unknown function (DUF3585); This domain is found in eukaryotes. This domain is typically between 135 and 149 amino acids in length and is found associated with pfam00307.
Q#23383 - 	CGI_10015785	superfamily	241559	40	82	0.000346346	39.57	cl00030	CH superfamily	N	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#23384 - 	CGI_10015786	superfamily	247068	80	167	2.56E-13	65.7977	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23384 - 	CGI_10015786	superfamily	247068	185	257	2.53E-08	51.5454	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23386 - 	CGI_10015788	superfamily	217293	27	225	1.72E-45	157.795	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#23386 - 	CGI_10015788	superfamily	202474	232	315	6.01E-10	57.6637	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#23387 - 	CGI_10015789	superfamily	202474	1	164	6.02E-09	51.8857	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#23389 - 	CGI_10015791	superfamily	245206	5	260	6.07E-90	269.702	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23391 - 	CGI_10015793	superfamily	215988	99	199	2.78E-17	74.9856	cl18355	Ligase_CoA superfamily	C	 - 	"CoA-ligase; This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP."
Q#23392 - 	CGI_10015794	superfamily	245206	40	311	6.16E-91	275.114	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23393 - 	CGI_10015795	superfamily	216152	119	398	1.56E-87	272.265	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#23394 - 	CGI_10015796	superfamily	245819	447	630	3.23E-57	192.409	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#23394 - 	CGI_10015796	superfamily	219812	120	353	3.10E-14	71.9536	cl07121	NIT superfamily	 - 	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#23394 - 	CGI_10015796	superfamily	219526	391	432	1.03E-08	54.5475	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#23395 - 	CGI_10015797	superfamily	245819	457	618	3.14E-61	203.58	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#23395 - 	CGI_10015797	superfamily	219812	130	367	3.16E-15	75.0352	cl07121	NIT superfamily	 - 	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#23395 - 	CGI_10015797	superfamily	219526	401	444	4.37E-08	52.6215	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#23397 - 	CGI_10015799	superfamily	248458	47	399	5.92E-19	86.5989	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23398 - 	CGI_10015800	superfamily	247804	36	77	4.20E-06	41.7922	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#23400 - 	CGI_10008880	superfamily	247916	161	278	9.41E-18	79.7522	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#23407 - 	CGI_10003890	superfamily	112929	1	151	5.62E-43	155.815	cl04414	Sec34 superfamily	 - 	 - 	"Sec34-like family; Sec34 and Sec35 form a sub-complex, in a seven protein complex that includes Dor1 (pfam04124). This complex is thought to be important for tether vesicles to the Golgi."
Q#23411 - 	CGI_10014510	superfamily	243035	19	85	1.42E-13	61.4817	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23412 - 	CGI_10014511	superfamily	243035	145	246	4.12E-19	79.9713	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23412 - 	CGI_10014511	superfamily	243035	44	143	4.14E-16	71.4969	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23419 - 	CGI_10014518	superfamily	222150	356	378	0.00128218	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23419 - 	CGI_10014518	superfamily	222150	382	406	0.00158009	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23419 - 	CGI_10014518	superfamily	222150	409	434	0.00940429	34.2897	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23420 - 	CGI_10014520	superfamily	247856	292	354	2.17E-16	73.3509	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23420 - 	CGI_10014520	superfamily	247856	230	282	7.34E-12	60.6393	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23420 - 	CGI_10014520	superfamily	247856	29	90	2.29E-10	56.4021	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23420 - 	CGI_10014520	superfamily	247856	103	164	2.31E-10	56.4021	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23420 - 	CGI_10014520	superfamily	247856	365	417	9.86E-07	46.0017	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23420 - 	CGI_10014520	superfamily	247856	159	219	0.00287496	35.6013	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23421 - 	CGI_10014521	superfamily	247856	24	86	1.06E-18	78.3585	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23421 - 	CGI_10014521	superfamily	247856	198	257	3.21E-09	52.5501	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23421 - 	CGI_10014521	superfamily	247856	98	150	1.36E-06	44.8461	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23421 - 	CGI_10014521	superfamily	247856	265	328	6.34E-05	40.2237	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23422 - 	CGI_10014522	superfamily	247856	26	88	8.43E-18	73.3509	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23422 - 	CGI_10014522	superfamily	247856	99	157	4.79E-09	49.0833	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23423 - 	CGI_10014523	superfamily	242232	68	117	3.32E-12	57.9532	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#23424 - 	CGI_10014524	superfamily	242232	68	117	3.32E-12	57.9532	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#23425 - 	CGI_10014525	superfamily	247856	622	683	3.01E-18	80.2845	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	414	476	3.38E-16	74.1213	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	488	547	3.89E-15	71.0397	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	548	610	1.76E-14	69.4989	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	228	290	1.94E-14	69.1137	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	144	198	4.14E-14	68.3433	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	69	131	1.74E-13	66.4173	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	13	69	2.79E-13	66.0321	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23425 - 	CGI_10014525	superfamily	247856	321	383	3.87E-11	59.8689	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23426 - 	CGI_10026210	superfamily	222090	275	466	1.14E-17	81.5502	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#23427 - 	CGI_10026211	superfamily	241571	64	163	1.46E-07	47.7923	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23427 - 	CGI_10026211	superfamily	241613	169	198	4.75E-06	42.1938	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23430 - 	CGI_10026214	superfamily	243362	109	259	9.86E-42	143.72	cl03262	DnaJ_C superfamily	 - 	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#23430 - 	CGI_10026214	superfamily	243077	7	57	1.42E-24	94.1493	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#23431 - 	CGI_10026215	superfamily	243072	127	240	0.000462666	38.9039	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23434 - 	CGI_10026218	superfamily	218588	1	361	1.22E-154	442.271	cl05147	FIBP superfamily	 - 	 - 	Acidic fibroblast growth factor binding (FIBP); Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF.
Q#23437 - 	CGI_10026221	superfamily	241749	36	64	0.003152	32.7429	cl00280	globin_like superfamily	C	 - 	superfamily containing globins and truncated hemoglobins
Q#23438 - 	CGI_10026222	superfamily	241749	1	79	4.17E-16	68.5665	cl00280	globin_like superfamily	N	 - 	superfamily containing globins and truncated hemoglobins
Q#23439 - 	CGI_10026223	superfamily	146263	454	568	1.09E-33	126.65	cl04138	SK_channel superfamily	 - 	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#23439 - 	CGI_10026223	superfamily	219619	666	725	1.27E-11	61.8399	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#23439 - 	CGI_10026223	superfamily	198825	745	814	0.00483984	36.2377	cl03763	CaMBD superfamily	 - 	 - 	"Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other."
Q#23440 - 	CGI_10026224	superfamily	243092	114	218	0.000736541	38.8552	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23441 - 	CGI_10026225	superfamily	215827	136	316	1.12E-29	117.569	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#23442 - 	CGI_10026226	superfamily	215827	144	320	6.07E-31	121.036	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#23443 - 	CGI_10026227	superfamily	215827	67	245	1.37E-43	157.245	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#23443 - 	CGI_10026227	superfamily	243119	771	805	5.82E-05	41.6606	cl02629	CBM_14 superfamily	N	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#23444 - 	CGI_10026228	superfamily	116798	34	174	8.18E-30	107.763	cl17955	Lipocalin_2 superfamily	 - 	 - 	"Lipocalin-like domain; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel."
Q#23445 - 	CGI_10026229	superfamily	116798	34	179	1.69E-25	96.5918	cl17955	Lipocalin_2 superfamily	 - 	 - 	"Lipocalin-like domain; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel."
Q#23446 - 	CGI_10026230	superfamily	247905	68	151	2.42E-06	46.0769	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#23446 - 	CGI_10026230	superfamily	215827	260	438	1.35E-39	143.378	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#23451 - 	CGI_10026235	superfamily	243035	12	104	1.61E-14	65.3337	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23454 - 	CGI_10026238	superfamily	246680	6	94	6.22E-14	65.5252	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#23455 - 	CGI_10026239	superfamily	202111	95	168	4.76E-32	112.691	cl03448	ODC_AZ superfamily	 - 	 - 	Ornithine decarboxylase antizyme; This family consists of ornithine decarboxylase antizyme proteins. The polyamine biosynthetic enzyme ornithine decarboxylase (ODC) is degraded by the 26 S proteasome via a ubiquitin-independent pathway. Its degradation is greatly accelerated by association with the polyamine-induced regulatory protein antizyme 1 (AZ1).
Q#23456 - 	CGI_10026240	superfamily	241571	347	464	1.63E-10	58.963	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23456 - 	CGI_10026240	superfamily	245213	469	502	4.94E-05	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23456 - 	CGI_10026240	superfamily	241583	119	300	6.24E-31	119.983	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23456 - 	CGI_10026240	superfamily	243051	514	669	2.11E-10	59.2865	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23457 - 	CGI_10026241	superfamily	245836	335	522	1.15E-124	366.881	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#23458 - 	CGI_10026242	superfamily	248097	47	168	1.60E-27	101.188	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23460 - 	CGI_10026244	superfamily	217643	55	331	4.07E-111	331.429	cl04182	Solute_trans_a superfamily	 - 	 - 	"Organic solute transporter Ostalpha; This family is a transmembrane organic solute transport protein. In vertebrates these proteins form a complex with Ostbeta, and function as bile transporters. In plants they may transport brassinosteroid-like compounds and act as regulators of cell death."
Q#23461 - 	CGI_10026245	superfamily	248458	2	205	0.00108752	38.8341	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23462 - 	CGI_10026246	superfamily	247723	16	88	2.70E-37	125.486	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23463 - 	CGI_10026247	superfamily	243088	148	267	5.99E-34	124.577	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#23463 - 	CGI_10026247	superfamily	149621	407	488	1.64E-13	66.9244	cl07303	Nexin_C superfamily	 - 	 - 	Sorting nexin C terminal; This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787.
Q#23465 - 	CGI_10026249	superfamily	247723	28	99	1.64E-25	97.8013	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23468 - 	CGI_10026252	superfamily	247723	357	430	1.18E-41	148.262	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23468 - 	CGI_10026252	superfamily	207684	10	42	2.40E-07	48.9143	cl02640	SAP superfamily	 - 	 - 	"SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins."
Q#23471 - 	CGI_10026255	superfamily	241580	250	327	7.10E-46	156.945	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#23471 - 	CGI_10026255	superfamily	241581	51	138	1.17E-11	62.0186	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#23472 - 	CGI_10026256	superfamily	243092	360	657	2.85E-31	123.599	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23472 - 	CGI_10026256	superfamily	243092	59	480	1.04E-26	110.117	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23473 - 	CGI_10026257	superfamily	241645	32	118	5.72E-43	137.788	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#23474 - 	CGI_10026258	superfamily	244972	169	232	4.47E-06	45.0278	cl08475	PIG-X superfamily	C	 - 	PIG-X / PBN1; Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I. These enzymes are involved in the transfer of sugar molecules.
Q#23476 - 	CGI_10026260	superfamily	243084	2488	2588	1.98E-44	159.257	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#23476 - 	CGI_10026260	superfamily	243137	167	226	1.74E-17	80.3251	cl02674	DDT superfamily	 - 	 - 	"DDT domain; This domain is approximately 60 residues in length, and is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is exclusively associated with nuclear domains, and is thought to be arranged into three alpha helices."
Q#23476 - 	CGI_10026260	superfamily	247999	2367	2414	5.55E-10	58.2708	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#23476 - 	CGI_10026260	superfamily	247999	2425	2471	4.32E-09	55.681	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#23476 - 	CGI_10026260	superfamily	247999	323	367	6.27E-06	46.3296	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#23477 - 	CGI_10026261	superfamily	241748	321	550	1.45E-103	316.425	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#23477 - 	CGI_10026261	superfamily	216431	1	131	0.00235998	37.2625	cl08317	Creatinase_N superfamily	 - 	 - 	Creatinase/Prolidase N-terminal domain; This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.
Q#23478 - 	CGI_10026262	superfamily	241748	11	39	4.60E-09	51.4081	cl00279	APP_MetAP superfamily	N	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#23479 - 	CGI_10026263	superfamily	241748	339	460	7.14E-36	132.685	cl00279	APP_MetAP superfamily	C	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#23479 - 	CGI_10026263	superfamily	216431	64	165	0.000153888	40.3441	cl08317	Creatinase_N superfamily	 - 	 - 	Creatinase/Prolidase N-terminal domain; This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.
Q#23481 - 	CGI_10026265	superfamily	243175	92	213	2.29E-61	189.836	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#23481 - 	CGI_10026265	superfamily	241832	5	76	1.12E-32	114.332	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#23484 - 	CGI_10002806	superfamily	247743	1740	1773	0.00103285	40.3564	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23484 - 	CGI_10002806	superfamily	247743	2140	2179	0.00723678	37.66	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23487 - 	CGI_10002160	superfamily	245210	15	403	0	513.565	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#23489 - 	CGI_10002162	superfamily	199156	213	227	0.00493622	33.5708	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#23492 - 	CGI_10002608	superfamily	247038	422	516	9.65E-22	91.6082	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#23492 - 	CGI_10002608	superfamily	247038	517	614	1.28E-17	79.1905	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#23492 - 	CGI_10002608	superfamily	247042	10	164	6.78E-28	117.34	cl15693	Sema superfamily	N	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#23492 - 	CGI_10002608	superfamily	247038	616	714	5.77E-10	57.4269	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#23492 - 	CGI_10002608	superfamily	243104	371	420	7.77E-07	47.1628	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#23493 - 	CGI_10007575	superfamily	247065	38	85	7.10E-12	57.3546	cl15777	GGCT_like superfamily	N	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#23494 - 	CGI_10007576	superfamily	246669	1571	1747	4.94E-79	259.563	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#23494 - 	CGI_10007576	superfamily	246669	1434	1556	1.34E-61	208.263	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#23494 - 	CGI_10007576	superfamily	203315	62	111	0.00257325	38.2527	cl05335	zf-piccolo superfamily	 - 	 - 	"Piccolo Zn-finger; This (predicted) Zinc finger is found in the bassoon and piccolo proteins. There are eight conserved cysteines, suggesting that it coordinates two zinc ligands."
Q#23495 - 	CGI_10007577	superfamily	247727	268	367	2.18E-15	72.4626	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#23495 - 	CGI_10007577	superfamily	247727	166	307	1.74E-05	45.3044	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#23496 - 	CGI_10007578	superfamily	245202	576	626	2.49E-10	57.9738	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#23496 - 	CGI_10007578	superfamily	245202	237	298	4.03E-10	57.2034	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#23496 - 	CGI_10007578	superfamily	245202	400	462	1.98E-07	49.1142	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#23496 - 	CGI_10007578	superfamily	245202	83	124	0.000110446	41.025	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#23496 - 	CGI_10007578	superfamily	245202	725	788	8.91E-09	53.3715	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#23496 - 	CGI_10007578	superfamily	193374	800	832	0.000416189	39.0716	cl15152	SUZ-C superfamily	 - 	 - 	SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.
Q#23497 - 	CGI_10007579	superfamily	227778	93	281	1.90E-09	54.8143	cl17122	VPS24 superfamily	 - 	 - 	Conserved protein implicated in secretion [Cell motility and secretion]
Q#23500 - 	CGI_10007582	superfamily	241575	934	978	5.60E-08	51.1191	cl00054	DSRM superfamily	C	 - 	"Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases."
Q#23500 - 	CGI_10007582	superfamily	243107	869	909	1.13E-13	67.1472	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#23503 - 	CGI_10007585	superfamily	248097	50	172	1.30E-15	69.2162	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23505 - 	CGI_10007587	superfamily	241977	1	176	7.46E-43	142.939	cl00607	PUA superfamily	 - 	 - 	"PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain."
Q#23506 - 	CGI_10002861	superfamily	243072	100	221	2.05E-15	75.1126	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23506 - 	CGI_10002861	superfamily	243072	302	459	2.15E-13	69.3346	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23506 - 	CGI_10002861	superfamily	243072	398	524	1.96E-12	66.253	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23506 - 	CGI_10002861	superfamily	243072	196	350	3.44E-10	59.7046	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23507 - 	CGI_10002862	superfamily	243034	84	175	1.00E-17	75.8795	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23508 - 	CGI_10002863	superfamily	241748	186	433	4.98E-75	237.856	cl00279	APP_MetAP superfamily	 - 	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#23508 - 	CGI_10002863	superfamily	244955	2	147	5.54E-24	96.925	cl08433	AMP_N superfamily	 - 	 - 	"Aminopeptidase P, N-terminal domain; This domain is structurally very similar to the creatinase N-terminal domain (pfam01321). However, little or no sequence similarity exists between the two families."
Q#23509 - 	CGI_10002864	superfamily	242904	236	517	3.50E-79	251.646	cl02149	CDC73 superfamily	 - 	 - 	"RNA pol II accessory factor, Cdc73 family; RNA pol II accessory factor, Cdc73 family.  "
Q#23510 - 	CGI_10002865	superfamily	241799	14	232	9.32E-85	254.409	cl00339	SugarP_isomerase superfamily	 - 	 - 	"SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway."
Q#23511 - 	CGI_10010628	superfamily	247866	140	282	1.32E-17	79.4188	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#23512 - 	CGI_10010629	superfamily	247866	60	287	1.59E-20	87.8932	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#23513 - 	CGI_10010630	superfamily	245868	65	298	4.44E-81	248.099	cl12093	YIF1 superfamily	 - 	 - 	YIF1; YIF1 (Yip1 interacting factor) is an integral membrane protein that is required for membrane fusion of ER derived vesicles. It also plays a role in the biogenesis of ER derived COPII transport vesicles.
Q#23514 - 	CGI_10010631	superfamily	218605	4	74	5.11E-24	87.3085	cl05186	SRP9-21 superfamily	 - 	 - 	"Signal recognition particle 9 kDa protein (SRP9); This family consists of several eukaryotic SRP9 proteins. SRP9 together with the Alu-homologous region of 7SL RNA and SRP14 comprise the "Alu domain" of SRP, which mediates pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP. This family also contains the homologous fungal SRP21."
Q#23515 - 	CGI_10010632	superfamily	247725	20	127	2.68E-70	219.857	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23515 - 	CGI_10010632	superfamily	204060	379	413	0.000160897	39.3551	cl07401	VASP_tetra superfamily	 - 	 - 	VASP tetramerisation domain; Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure.
Q#23517 - 	CGI_10010634	superfamily	247736	50	108	9.36E-08	45.7297	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#23518 - 	CGI_10010635	superfamily	241607	94	134	1.72E-08	48.4202	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#23519 - 	CGI_10010636	superfamily	243034	436	533	0.000387197	39.2856	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23519 - 	CGI_10010636	superfamily	111114	185	217	5.95E-05	41.3972	cl03482	HAT superfamily	 - 	 - 	HAT (Half-A-TPR) repeat; The HAT (Half A TPR) repeat is found in several RNA processing proteins.
Q#23519 - 	CGI_10010636	superfamily	214642	84	116	0.000277585	39.0694	cl02592	HAT superfamily	 - 	 - 	HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Q#23521 - 	CGI_10010638	superfamily	192535	13	292	1.10E-08	54.139	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#23523 - 	CGI_10010640	superfamily	243053	762	972	1.55E-62	212.113	cl02485	RasGEF superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors."
Q#23523 - 	CGI_10010640	superfamily	243038	205	333	6.19E-62	206.426	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#23523 - 	CGI_10010640	superfamily	241570	355	466	4.41E-21	90.4629	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#23523 - 	CGI_10010640	superfamily	241570	34	134	2.52E-17	79.6774	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#23523 - 	CGI_10010640	superfamily	243067	502	609	5.65E-09	55.1112	cl02520	REM superfamily	 - 	 - 	"Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few."
Q#23528 - 	CGI_10003050	superfamily	247724	17	113	1.63E-59	182.608	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23529 - 	CGI_10003051	superfamily	247723	9	77	6.32E-16	69.6413	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23529 - 	CGI_10003051	superfamily	199156	101	116	0.000955302	35.4968	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#23531 - 	CGI_10002193	superfamily	248022	72	440	1.20E-28	115.838	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#23533 - 	CGI_10005496	superfamily	247999	4	57	0.000499565	37.9618	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#23535 - 	CGI_10005498	superfamily	242274	68	215	3.71E-05	42.0142	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#23537 - 	CGI_10027788	superfamily	220695	9	127	2.33E-05	42.9511	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#23539 - 	CGI_10027790	superfamily	220695	96	236	5.52E-07	48.3439	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#23540 - 	CGI_10027791	superfamily	220695	100	238	4.62E-05	43.3363	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#23543 - 	CGI_10027794	superfamily	243035	177	248	4.27E-05	41.0662	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23545 - 	CGI_10027796	superfamily	241564	8	50	2.02E-10	53.0567	cl00035	BIR superfamily	N	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#23546 - 	CGI_10027797	superfamily	243035	105	179	0.00165238	36.829	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23549 - 	CGI_10027800	superfamily	110440	256	283	0.00936898	33.1501	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#23550 - 	CGI_10027801	superfamily	241563	62	97	2.26E-05	41.504	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#23550 - 	CGI_10027801	superfamily	128778	98	212	0.00783064	34.9331	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#23551 - 	CGI_10027802	superfamily	128778	162	276	0.00314408	36.4739	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#23552 - 	CGI_10027803	superfamily	202638	100	326	2.04E-37	136.569	cl18230	Anp1 superfamily	 - 	 - 	"Anp1; The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localise within the cis Golgi, and that they are physically associated in two distinct complexes."
Q#23553 - 	CGI_10027804	superfamily	245847	250	398	7.55E-36	129.394	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#23554 - 	CGI_10027805	superfamily	243034	529	629	5.86E-16	75.1091	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23554 - 	CGI_10027805	superfamily	243034	420	512	2.36E-13	67.4052	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23554 - 	CGI_10027805	superfamily	243034	751	822	5.78E-07	48.5304	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23554 - 	CGI_10027805	superfamily	243034	598	704	6.23E-06	45.4488	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23554 - 	CGI_10027805	superfamily	149463	255	330	1.48E-29	113.464	cl07144	DUF1736 superfamily	 - 	 - 	Domain of unknown function (DUF1736); This domain of unknown function is found in various hypothetical metazoan proteins.
Q#23554 - 	CGI_10027805	superfamily	247918	90	227	0.00129406	39.097	cl17364	PMT_2 superfamily	 - 	 - 	Dolichyl-phosphate-mannose-protein mannosyltransferase; This family contains members that are not captured by pfam02366.
Q#23555 - 	CGI_10027806	superfamily	246669	192	327	1.44E-35	126.929	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#23556 - 	CGI_10027808	superfamily	243035	155	275	2.73E-22	89.2161	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23556 - 	CGI_10027808	superfamily	243035	68	116	0.0019864	36.0386	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23557 - 	CGI_10027809	superfamily	243035	45	111	8.65E-12	58.7853	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23557 - 	CGI_10027809	superfamily	241592	153	193	4.40E-19	79.9488	cl00074	H2A superfamily	N	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23558 - 	CGI_10027810	superfamily	207411	93	133	2.01E-11	57.8396	cl01438	zf-AN1 superfamily	 - 	 - 	"AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues."
Q#23559 - 	CGI_10027811	superfamily	241570	327	436	3.33E-06	45.3946	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#23560 - 	CGI_10027812	superfamily	221683	20	100	4.61E-25	98.4951	cl15002	UPF0489 superfamily	 - 	 - 	UPF0489 domain; This family is probably an enzyme which is related to the Arginase family.
Q#23561 - 	CGI_10027813	superfamily	222150	297	320	0.0010057	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23562 - 	CGI_10027814	superfamily	243072	137	219	2.53E-13	67.7938	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23563 - 	CGI_10027815	superfamily	207794	136	277	2.95E-44	160.841	cl02948	GH20_hexosaminidase superfamily	N	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#23563 - 	CGI_10027815	superfamily	207794	52	120	2.46E-40	149.67	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#23564 - 	CGI_10027816	superfamily	243109	1	102	3.34E-68	217.812	cl02614	SPRY superfamily	N	 - 	"SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome."
Q#23564 - 	CGI_10027816	superfamily	214806	392	489	3.86E-18	80.0321	cl15966	CRA superfamily	 - 	 - 	"CT11-RanBPM; protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)"
Q#23564 - 	CGI_10027816	superfamily	128914	174	230	5.36E-06	44.099	cl15352	CTLH superfamily	 - 	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#23564 - 	CGI_10027816	superfamily	199226	135	167	0.000440166	38.1844	cl11662	LisH superfamily	 - 	 - 	"LisH; The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex."
Q#23566 - 	CGI_10027818	superfamily	245201	19	335	0	610.135	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23567 - 	CGI_10027819	superfamily	216686	2	175	2.64E-42	144.388	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#23569 - 	CGI_10027821	superfamily	241782	419	667	2.38E-74	246.314	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#23570 - 	CGI_10027822	superfamily	245206	62	286	1.44E-78	242.148	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23571 - 	CGI_10027823	superfamily	241782	2	139	3.24E-27	104.176	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#23572 - 	CGI_10027824	superfamily	241623	570	922	1.46E-169	500.792	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#23572 - 	CGI_10027824	superfamily	246669	256	411	3.85E-37	138.214	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#23572 - 	CGI_10027824	superfamily	241742	453	575	1.48E-22	96.5577	cl00271	PI3Ka superfamily	 - 	 - 	"Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture."
Q#23572 - 	CGI_10027824	superfamily	207610	123	225	4.33E-15	72.7212	cl02484	PI3K_rbd superfamily	 - 	 - 	"PI3-kinase family, ras-binding domain; Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding pfam00788 domains (unpublished observation)."
Q#23572 - 	CGI_10027824	superfamily	198687	34	105	3.97E-08	51.8913	cl02483	PI3K_p85B superfamily	 - 	 - 	"PI3-kinase family, p85-binding domain; PI3-kinase family, p85-binding domain.  "
Q#23573 - 	CGI_10027825	superfamily	247866	44	271	9.64E-16	74.026	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#23574 - 	CGI_10027826	superfamily	243110	123	312	7.56E-11	60.9061	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#23575 - 	CGI_10027827	superfamily	243110	124	336	4.82E-18	83.2477	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#23577 - 	CGI_10027829	superfamily	241563	6	44	2.11E-07	45.4059	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#23579 - 	CGI_10027832	superfamily	118742	51	173	2.83E-37	127.198	cl10907	DUF2054 superfamily	 - 	 - 	"Uncharacterized conserved protein (DUF2054); This entry contains 14 conserved cysteines, three of which are CC-dimers. The region is of approximately 200 residues in length but its function is unknown."
Q#23580 - 	CGI_10027833	superfamily	241600	589	786	1.23E-70	232.516	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23581 - 	CGI_10027834	superfamily	222080	156	291	1.31E-35	128.945	cl16256	Transglut_core2 superfamily	C	 - 	Transglutaminase-like superfamily; Transglutaminase-like superfamily.  
Q#23581 - 	CGI_10027834	superfamily	242575	337	367	0.00131441	36.7911	cl01548	YccV-like superfamily	N	 - 	Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.
Q#23583 - 	CGI_10027836	superfamily	222269	27	285	1.05E-89	270.349	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#23584 - 	CGI_10027837	superfamily	245874	25	117	3.23E-05	42.0282	cl12111	TNFR superfamily	 - 	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#23586 - 	CGI_10027839	superfamily	248020	26	353	1.04E-54	187.672	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#23587 - 	CGI_10027840	superfamily	248020	226	547	5.54E-55	191.909	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#23589 - 	CGI_10027842	superfamily	248458	145	290	1.12E-15	77.3541	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23589 - 	CGI_10027842	superfamily	248458	352	540	2.26E-09	58.0941	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#23590 - 	CGI_10027843	superfamily	247755	490	682	1.51E-49	170.322	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#23590 - 	CGI_10027843	superfamily	247755	327	399	8.34E-36	132.187	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#23590 - 	CGI_10027843	superfamily	247755	176	239	1.31E-14	71.7108	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#23590 - 	CGI_10027843	superfamily	221805	394	455	1.87E-19	84.171	cl14896	ABC_tran_2 superfamily	C	 - 	ABC transporter; This domain is related to pfam00005.
Q#23591 - 	CGI_10027844	superfamily	245201	32	302	4.42E-20	90.7589	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23591 - 	CGI_10027844	superfamily	243092	984	1360	1.44E-13	71.5972	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23592 - 	CGI_10027845	superfamily	217473	192	346	3.73E-25	105.14	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#23593 - 	CGI_10027846	superfamily	217380	225	518	3.92E-44	162.494	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#23596 - 	CGI_10027849	superfamily	151555	34	154	3.56E-31	112.167	cl12666	CENP-M superfamily	N	 - 	"Centromere protein M (CENP-M); The prime candidate for specifying centromere identity is the array of nucleosomes assembles with CENP-A. CENP-A recruits a nucleosome associated complex (NAC) comprised of CENP-M along with two other proteins. Assembly of the CENP-A NAC at centromeres is partly dependant on CENP-M. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival."
Q#23599 - 	CGI_10027852	superfamily	247750	12	28	1.91E-06	43.0479	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#23600 - 	CGI_10027853	superfamily	247856	186	266	0.00573378	34.4457	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23601 - 	CGI_10027854	superfamily	243034	513	607	4.51E-15	72.4127	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#23603 - 	CGI_10027856	superfamily	247727	51	139	2.80E-07	47.266	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#23604 - 	CGI_10027857	superfamily	241995	12	115	1.36E-37	134.383	cl00635	Ntn_Asparaginase_2_like superfamily	C	 - 	"Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and  L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue."
Q#23604 - 	CGI_10027857	superfamily	241995	125	225	1.09E-18	81.6106	cl00635	Ntn_Asparaginase_2_like superfamily	N	 - 	"Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and  L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue."
Q#23605 - 	CGI_10027858	superfamily	241578	140	402	4.93E-153	449.899	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#23605 - 	CGI_10027858	superfamily	247044	622	742	5.55E-78	248.443	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#23605 - 	CGI_10027858	superfamily	218277	531	631	4.33E-40	143.44	cl04773	Sec23_helical superfamily	 - 	 - 	"Sec23/Sec24 helical domain; COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices."
Q#23605 - 	CGI_10027858	superfamily	219707	415	516	9.31E-27	105.291	cl06871	Sec23_BS superfamily	 - 	 - 	Sec23/Sec24 beta-sandwich domain; Sec23/Sec24 beta-sandwich domain.  
Q#23605 - 	CGI_10027858	superfamily	203092	70	110	9.12E-17	75.6747	cl04769	zf-Sec23_Sec24 superfamily	 - 	 - 	"Sec23/Sec24 zinc finger; COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain."
Q#23606 - 	CGI_10027859	superfamily	247856	23	86	1.57E-12	57.5577	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23607 - 	CGI_10027860	superfamily	219896	37	215	3.51E-33	119.228	cl18532	CIA30 superfamily	 - 	 - 	"Complex I intermediate-associated protein 30 (CIA30); This protein is associated with mitochondrial Complex I intermediate-associated protein 30 (CIA30) in human and mouse. The family is also present in Schizosaccharomyces pombe which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits. This means it is possible that this family of protein may not be directly involved in oxidative phosphorylation."
Q#23608 - 	CGI_10027861	superfamily	241984	70	354	5.62E-168	483.3	cl00615	Membrane-FADS-like superfamily	 - 	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#23608 - 	CGI_10027861	superfamily	247736	465	607	7.08E-38	137.144	cl17182	NAT_SF superfamily	 - 	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#23608 - 	CGI_10027861	superfamily	117132	5	85	1.55E-11	59.9797	cl07243	Lipid_DES superfamily	 - 	 - 	Sphingolipid Delta4-desaturase (DES); Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyzes the formation of (E)-sphing-4-enine. Some proteins in this family have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis. This small domain associates with FA_desaturase pfam00487 and appears to be specific to sphingolipid delta 4-desaturase.
Q#23609 - 	CGI_10027862	superfamily	222150	270	295	0.000129789	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23609 - 	CGI_10027862	superfamily	222150	299	326	0.000133036	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23611 - 	CGI_10027864	superfamily	241559	73	154	1.68E-10	56.9355	cl00030	CH superfamily	C	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#23611 - 	CGI_10027864	superfamily	216033	213	304	2.49E-08	50.41	cl16959	Filamin superfamily	N	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#23612 - 	CGI_10027865	superfamily	241568	8	71	0.00161031	35.1312	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#23613 - 	CGI_10027866	superfamily	247856	19	73	3.16E-05	40.2237	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23614 - 	CGI_10027867	superfamily	243060	381	481	4.57E-09	55.4628	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#23614 - 	CGI_10027867	superfamily	243060	710	803	1.40E-06	47.7588	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#23616 - 	CGI_10027869	superfamily	202715	138	237	6.85E-35	121.916	cl04194	Tctex-1 superfamily	 - 	 - 	Tctex-1 family; Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Q#23617 - 	CGI_10027870	superfamily	241570	315	426	1.42E-18	82.7589	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#23617 - 	CGI_10027870	superfamily	219619	184	233	6.96E-11	59.1435	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#23618 - 	CGI_10027871	superfamily	207794	186	310	3.35E-73	237.96	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#23618 - 	CGI_10027871	superfamily	207794	311	413	3.34E-17	81.9544	cl02948	GH20_hexosaminidase superfamily	NC	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#23618 - 	CGI_10027871	superfamily	243574	1	51	2.21E-12	63.888	cl03918	CHB_HEX superfamily	N	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#23619 - 	CGI_10027872	superfamily	247724	14	54	9.94E-05	39.0968	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23621 - 	CGI_10002519	superfamily	242248	82	150	4.93E-11	57.9469	cl01008	DUF423 superfamily	 - 	 - 	Protein of unknown function (DUF423); This family of proteins with unknown function is a possible integral membrane protein from Caenorhabditis elegans. This family of proteins has GO references indicating the protein is involved in nematode larval development and is a positive regulator of growth rate.
Q#23623 - 	CGI_10003191	superfamily	245304	166	471	7.32E-130	391.538	cl10459	Peptidases_S8_S53 superfamily	 - 	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#23623 - 	CGI_10003191	superfamily	201820	551	638	4.12E-30	115.03	cl08326	P_proprotein superfamily	 - 	 - 	Proprotein convertase P-domain; A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Q#23624 - 	CGI_10003192	superfamily	241609	354	433	7.25E-24	95.1375	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#23624 - 	CGI_10003192	superfamily	241583	88	180	5.58E-42	148.488	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23627 - 	CGI_10019365	superfamily	243050	178	223	2.00E-13	62.8588	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#23628 - 	CGI_10019366	superfamily	245603	94	161	7.48E-07	43.8644	cl11403	pepsin_retropepsin_like superfamily	C	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#23628 - 	CGI_10019366	superfamily	199156	24	39	0.000170836	36.6524	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#23630 - 	CGI_10019368	superfamily	241889	46	254	4.29E-64	202.612	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#23631 - 	CGI_10019369	superfamily	241705	79	188	1.30E-45	148.094	cl00228	HIT_like superfamily	 - 	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#23633 - 	CGI_10019371	superfamily	247724	10	165	2.32E-50	162.831	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23634 - 	CGI_10019372	superfamily	241564	27	92	1.62E-22	87.3211	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#23634 - 	CGI_10019372	superfamily	241564	136	202	6.25E-19	77.6911	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#23637 - 	CGI_10019375	superfamily	243035	29	148	8.16E-22	89.2161	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23637 - 	CGI_10019375	superfamily	243035	277	379	8.99E-12	61.4817	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23638 - 	CGI_10019377	superfamily	241568	200	253	0.00122031	36.2868	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#23640 - 	CGI_10019379	superfamily	243035	123	233	3.10E-16	73.8081	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23640 - 	CGI_10019379	superfamily	243035	258	371	1.94E-15	71.4969	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23640 - 	CGI_10019379	superfamily	243035	29	98	0.00014823	39.9106	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23641 - 	CGI_10019380	superfamily	243035	162	233	3.14E-05	41.0662	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23642 - 	CGI_10019381	superfamily	243035	177	290	1.23E-14	68.4153	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23642 - 	CGI_10019381	superfamily	243035	24	135	1.70E-14	68.0301	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#23643 - 	CGI_10019382	superfamily	242274	3	54	0.000663362	34.1334	cl01053	SGNH_hydrolase superfamily	NC	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#23646 - 	CGI_10019385	superfamily	241619	26	82	7.95E-06	40.1457	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#23647 - 	CGI_10019386	superfamily	241655	36	207	3.62E-46	152.543	cl00167	VMO-I superfamily	 - 	 - 	"Vitelline membrane outer layer protein I (VMO-I) domain, VMO-I is one of the proteins found in the outer layer of the vitelline membrane of poultry eggs; VMO-I, lysozyme, and VMO-II are tightly bound to ovomucin; this complex forms the backbone of the outer layer;  VMO-I has three distinct internal repeats;  all three repeats are used to define the domain here; VMO-I has recently been shown to synthesize N-acetylchito-oligosaccharides from N-acetylglucosamine; may be a carbohydrate-binding protein; member of the beta-prism-fold family"
Q#23648 - 	CGI_10019387	superfamily	246751	319	551	1.07E-23	101.399	cl14883	Lipase superfamily	 - 	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#23649 - 	CGI_10019388	superfamily	205803	82	189	1.16E-23	93.3709	cl16326	Helicase_C_3 superfamily	C	 - 	Helicase conserved C-terminal domain; This domain family is found in a wide variety of helicases and helicase-related proteins.
Q#23651 - 	CGI_10019390	superfamily	243689	56	95	3.48E-06	46.0825	cl04271	IBN_N superfamily	N	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#23651 - 	CGI_10019390	superfamily	202500	392	422	0.000131608	40.9641	cl03819	HEAT superfamily	 - 	 - 	HEAT repeat; The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514).
Q#23652 - 	CGI_10019391	superfamily	242137	1	205	4.41E-30	112.801	cl00847	PAC2 superfamily	 - 	 - 	"PAC2 family; This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits."
Q#23653 - 	CGI_10019392	superfamily	247743	358	493	2.29E-24	100.683	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23653 - 	CGI_10019392	superfamily	216502	556	759	2.85E-75	245.579	cl03209	Peptidase_M41 superfamily	 - 	 - 	Peptidase family M41; Peptidase family M41.  
Q#23655 - 	CGI_10005458	superfamily	192997	320	472	6.72E-46	163.907	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#23655 - 	CGI_10005458	superfamily	243092	1048	1270	1.28E-17	84.3088	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23655 - 	CGI_10005458	superfamily	243092	820	875	0.00140583	40.7812	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23659 - 	CGI_10005462	superfamily	248391	23	250	3.11E-63	200.279	cl17837	DUF1295 superfamily	 - 	 - 	Protein of unknown function (DUF1295); This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long.
Q#23660 - 	CGI_10005463	superfamily	243054	321	428	0.00929143	36.6548	cl02488	SPEC superfamily	NC	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#23664 - 	CGI_10006353	superfamily	247692	121	611	3.60E-140	438.416	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#23664 - 	CGI_10006353	superfamily	245206	1141	1375	1.78E-77	257.467	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23664 - 	CGI_10006353	superfamily	245206	755	1052	5.16E-72	243.712	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23664 - 	CGI_10006353	superfamily	245209	636	690	4.23E-10	57.9498	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#23665 - 	CGI_10006354	superfamily	218793	133	349	4.91E-19	83.7349	cl12319	CNPase superfamily	 - 	 - 	"2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase); This family consists of the eukaryotic protein 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins expressed in differentiating oligodendrocytes and Schwann cells. CNP is abundant in the central nervous system and in oligodendrocytes. This protein is also found in mammalian photoreceptor cells, testis and lymphocytes. Although the biological function of CNP is unknown, it is thought to play a significant role in the formation of the myelin sheath, where it comprises 4% of total protein. CNP selectively cleaves 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Although physiologically relevant substrates with 2',3'-cyclic termini are still unknown, numerous cyclic phosphate containing RNAs occur transiently within eukaryotic cells. Other known protein families capable of hydrolysing 2',3'-cyclic nucleotides include tRNA ligases and plant cyclic phosphodiesterases. The catalytic domains from all these proteins contain two tetra-peptide motifs H-X-T/S-X, where X is usually a hydrophobic residue. Mutation of either histidine in CNP abolishes enzymatic activity. CNPases belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT, vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins."
Q#23665 - 	CGI_10006354	superfamily	247807	3	78	4.47E-07	47.2897	cl17253	AAA_17 superfamily	C	 - 	AAA domain; AAA domain.  
Q#23666 - 	CGI_10006355	superfamily	218793	133	349	4.63E-19	83.7349	cl12319	CNPase superfamily	 - 	 - 	"2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase); This family consists of the eukaryotic protein 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins expressed in differentiating oligodendrocytes and Schwann cells. CNP is abundant in the central nervous system and in oligodendrocytes. This protein is also found in mammalian photoreceptor cells, testis and lymphocytes. Although the biological function of CNP is unknown, it is thought to play a significant role in the formation of the myelin sheath, where it comprises 4% of total protein. CNP selectively cleaves 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Although physiologically relevant substrates with 2',3'-cyclic termini are still unknown, numerous cyclic phosphate containing RNAs occur transiently within eukaryotic cells. Other known protein families capable of hydrolysing 2',3'-cyclic nucleotides include tRNA ligases and plant cyclic phosphodiesterases. The catalytic domains from all these proteins contain two tetra-peptide motifs H-X-T/S-X, where X is usually a hydrophobic residue. Mutation of either histidine in CNP abolishes enzymatic activity. CNPases belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT, vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins."
Q#23666 - 	CGI_10006355	superfamily	247807	3	78	7.10E-07	46.5193	cl17253	AAA_17 superfamily	C	 - 	AAA domain; AAA domain.  
Q#23667 - 	CGI_10006356	superfamily	247858	93	275	3.32E-29	110.17	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#23668 - 	CGI_10006357	superfamily	203913	1	131	4.13E-06	44.1301	cl07084	P4Ha_N superfamily	 - 	 - 	"Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known."
Q#23669 - 	CGI_10006358	superfamily	243072	585	704	5.45E-21	90.5206	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23669 - 	CGI_10006358	superfamily	243072	653	799	1.81E-19	86.2834	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23669 - 	CGI_10006358	superfamily	218713	209	316	6.54E-13	67.7524	cl05332	MRG superfamily	NC	 - 	"MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif."
Q#23669 - 	CGI_10006358	superfamily	218713	484	549	1.16E-10	60.8188	cl05332	MRG superfamily	N	 - 	"MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif."
Q#23669 - 	CGI_10006358	superfamily	152153	10	73	1.45E-05	43.7434	cl18050	Tudor-knot superfamily	 - 	 - 	RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilisation of Ht2 is essential for RNA binding.
Q#23670 - 	CGI_10006359	superfamily	247684	328	745	6.30E-89	290.333	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#23671 - 	CGI_10003308	superfamily	245201	28	282	9.70E-61	197.742	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23673 - 	CGI_10003310	superfamily	241550	408	642	1.31E-99	323.415	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#23673 - 	CGI_10003310	superfamily	241550	40	182	7.27E-82	273.724	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#23673 - 	CGI_10003310	superfamily	245839	642	835	1.36E-75	249.776	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#23674 - 	CGI_10003311	superfamily	247639	11	128	3.05E-31	113.71	cl16914	O-FucT_like superfamily	N	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#23675 - 	CGI_10004374	superfamily	248021	7	82	8.39E-36	124.745	cl17467	CTP_transf_1 superfamily	N	 - 	Cytidylyltransferase family; The members of this family are integral membrane protein cytidylyltransferases. The family includes phosphatidate cytidylyltransferase EC:2.7.7.41 as well as Sec59 from yeast. Sec59 is a dolichol kinase EC:2.7.1.108.
Q#23676 - 	CGI_10003560	superfamily	217473	321	586	8.44E-26	108.606	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#23676 - 	CGI_10003560	superfamily	215866	20	104	2.61E-12	65.4244	cl18349	Arrestin_N superfamily	N	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#23677 - 	CGI_10003562	superfamily	218140	394	969	5.16E-133	411.221	cl04579	Anoctamin superfamily	 - 	 - 	"Calcium-activated chloride channel; The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes."
Q#23678 - 	CGI_10003563	superfamily	148752	29	215	2.10E-49	161.934	cl06383	DGCR6 superfamily	 - 	 - 	"DiGeorge syndrome critical region 6 (DGCR6) protein; This family contains DiGeorge syndrome critical region 6 (DGCR6) proteins (approximately 200 residues long) of a number of vertebrates. DGCR6 is a candidate for involvement in the DiGeorge syndrome pathology by playing a role in neural crest cell migration into the third and fourth pharyngeal pouches, the structures from which derive the organs affected in DiGeorge syndrome. Also found in this family is the Drosophila melanogaster gonadal protein gdl."
Q#23679 - 	CGI_10004129	superfamily	247057	40	108	1.99E-29	103.117	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#23680 - 	CGI_10004130	superfamily	222150	59	84	0.00332989	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23681 - 	CGI_10004131	superfamily	201536	212	309	2.27E-39	138.532	cl03053	UDPG_MGDP_dh superfamily	 - 	 - 	"UDP-glucose/GDP-mannose dehydrogenase family, central domain; The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyze the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate."
Q#23681 - 	CGI_10004131	superfamily	248301	331	446	3.02E-32	118.448	cl17747	UDPG_MGDP_dh_C superfamily	 - 	 - 	"UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyze the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate."
Q#23682 - 	CGI_10004132	superfamily	245596	20	236	3.27E-88	277.181	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23682 - 	CGI_10004132	superfamily	247677	508	666	1.38E-45	159.732	cl17013	W2 superfamily	 - 	 - 	"C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon; This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats."
Q#23682 - 	CGI_10004132	superfamily	193687	339	417	2.57E-31	117.679	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#23683 - 	CGI_10004133	superfamily	248097	15	100	4.62E-17	71.9126	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23684 - 	CGI_10004134	superfamily	248097	12	116	2.46E-17	75.7646	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23684 - 	CGI_10004134	superfamily	248097	178	303	2.95E-15	69.9866	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23685 - 	CGI_10004135	superfamily	248097	14	117	1.63E-15	67.6754	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23686 - 	CGI_10007022	superfamily	241546	2450	2571	1.08E-50	178.624	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#23686 - 	CGI_10007022	superfamily	248011	484	529	0.00126599	40.1726	cl17457	PKD superfamily	N	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#23686 - 	CGI_10007022	superfamily	243093	1	59	6.13E-10	59.081	cl02568	WSC superfamily	N	 - 	WSC domain; This domain may be involved in carbohydrate binding.
Q#23686 - 	CGI_10007022	superfamily	243086	2340	2380	4.55E-09	55.8442	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#23686 - 	CGI_10007022	superfamily	248011	77	146	0.0013277	40.0882	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#23686 - 	CGI_10007022	superfamily	248011	1074	1100	0.00753818	37.8158	cl17457	PKD superfamily	N	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#23687 - 	CGI_10007023	superfamily	241832	2	134	3.72E-41	136.491	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#23688 - 	CGI_10007024	superfamily	241832	36	68	4.78E-09	48.2805	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#23690 - 	CGI_10007026	superfamily	242031	5	183	3.47E-57	180.081	cl00689	TYW3 superfamily	 - 	 - 	Methyltransferase TYW3; The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis. yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3' position adjacent the anticodon of phenylalanine tRNA. TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner.
Q#23691 - 	CGI_10007027	superfamily	243037	319	476	2.72E-65	210.121	cl02440	DAGK_acc superfamily	 - 	 - 	Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
Q#23691 - 	CGI_10007027	superfamily	248019	175	300	7.51E-36	129.724	cl17465	DAGK_cat superfamily	 - 	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#23691 - 	CGI_10007027	superfamily	241566	81	133	7.18E-07	46.6787	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#23693 - 	CGI_10007029	superfamily	243064	176	268	0.00702378	34.5775	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#23695 - 	CGI_10007031	superfamily	245596	2	180	9.18E-88	264.32	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#23697 - 	CGI_10007033	superfamily	245240	7	149	3.05E-43	156.344	cl10034	LabA_like/DUF88 superfamily	 - 	 - 	"LabA_like proteins; The LabA-like superfamily is composed of a well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing."
Q#23697 - 	CGI_10007033	superfamily	246749	952	1022	5.28E-38	138.711	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#23697 - 	CGI_10007033	superfamily	247723	167	237	8.01E-22	92.3358	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23697 - 	CGI_10007033	superfamily	246749	795	863	6.22E-33	124.12	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#23697 - 	CGI_10007033	superfamily	247723	495	572	7.41E-27	107.422	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23697 - 	CGI_10007033	superfamily	246749	699	767	6.01E-24	98.5196	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#23697 - 	CGI_10007033	superfamily	246749	868	939	7.59E-19	83.5625	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#23697 - 	CGI_10007033	superfamily	246749	587	643	1.93E-12	64.9091	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#23697 - 	CGI_10007033	superfamily	246749	1169	1237	1.51E-09	56.842	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#23697 - 	CGI_10007033	superfamily	246749	1029	1098	5.23E-09	54.8818	cl14879	LabA_like_C superfamily	 - 	 - 	"C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains)."
Q#23698 - 	CGI_10007034	superfamily	243263	83	235	8.90E-28	111.744	cl02990	ASC superfamily	NC	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#23698 - 	CGI_10007034	superfamily	243263	19	78	4.72E-09	55.1066	cl02990	ASC superfamily	C	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#23699 - 	CGI_10007035	superfamily	243263	16	111	5.61E-21	86.693	cl02990	ASC superfamily	C	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#23701 - 	CGI_10009597	superfamily	241600	140	227	1.46E-38	136.987	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23702 - 	CGI_10009598	superfamily	241750	75	319	7.47E-28	109.294	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#23703 - 	CGI_10009599	superfamily	241600	1	57	1.10E-13	61.4875	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23704 - 	CGI_10009600	superfamily	241600	142	342	4.00E-74	230.59	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23705 - 	CGI_10009601	superfamily	247725	330	471	5.36E-67	217.183	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23705 - 	CGI_10009601	superfamily	243096	147	326	1.28E-28	112.776	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#23707 - 	CGI_10009603	superfamily	247792	18	68	3.60E-06	44.744	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23708 - 	CGI_10009604	superfamily	248054	6	220	5.86E-14	70.0239	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#23710 - 	CGI_10009606	superfamily	245882	36	416	2.05E-174	497.969	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#23713 - 	CGI_10009609	superfamily	243362	304	345	0.00565431	36.2491	cl03262	DnaJ_C superfamily	N	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#23713 - 	CGI_10009609	superfamily	110440	431	457	0.00670749	34.6909	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#23716 - 	CGI_10003716	superfamily	243263	72	424	3.92E-44	160.651	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#23717 - 	CGI_10003717	superfamily	243263	70	430	2.66E-68	226.135	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#23719 - 	CGI_10003958	superfamily	221522	226	573	5.62E-120	362.082	cl18610	KBP_C superfamily	 - 	 - 	KIF-1 binding protein C terminal; This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 365 and 621 amino acids in length. There is a conserved LLP sequence motif. KBP is a binding partner for KIF1Balpha that is a regulator of its transport function and thus represents a type of kinesin interacting protein.
Q#23720 - 	CGI_10003959	superfamily	247725	431	566	1.19E-91	291.901	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23720 - 	CGI_10003959	superfamily	218982	624	717	1.53E-23	97.6211	cl05682	NumbF superfamily	 - 	 - 	NUMB domain; This presumed domain is found in the Numb family of proteins adjacent to the PTB domain..
Q#23720 - 	CGI_10003959	superfamily	218982	1011	1104	1.53E-23	97.6211	cl05682	NumbF superfamily	 - 	 - 	NUMB domain; This presumed domain is found in the Numb family of proteins adjacent to the PTB domain..
Q#23720 - 	CGI_10003959	superfamily	247725	932	953	2.92E-07	50.3808	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23720 - 	CGI_10003959	superfamily	247724	232	293	0.00770896	37.7586	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23721 - 	CGI_10003960	superfamily	241568	666	718	0.000215757	40.9092	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#23721 - 	CGI_10003960	superfamily	241568	589	630	0.0034153	37.4424	cl00043	CCP superfamily	C	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#23721 - 	CGI_10003960	superfamily	111397	718	801	2.33E-12	65.055	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#23721 - 	CGI_10003960	superfamily	219525	1331	1376	1.14E-10	59.3549	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#23721 - 	CGI_10003960	superfamily	111397	1	63	5.59E-10	58.1214	cl03620	HYR superfamily	N	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#23721 - 	CGI_10003960	superfamily	219525	414	454	3.44E-08	52.0361	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#23721 - 	CGI_10003960	superfamily	111397	492	571	1.62E-06	47.7211	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#23721 - 	CGI_10003960	superfamily	219525	1118	1168	0.000334807	40.095	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#23721 - 	CGI_10003960	superfamily	241568	68	119	0.00443967	36.7844	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#23721 - 	CGI_10003960	superfamily	241568	806	857	0.00443967	36.7844	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#23723 - 	CGI_10016614	superfamily	245226	26	221	1.51E-40	143.964	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#23723 - 	CGI_10016614	superfamily	245226	296	369	0.000450435	39.9603	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#23724 - 	CGI_10016615	superfamily	245226	25	191	4.70E-25	100.822	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#23725 - 	CGI_10016616	superfamily	245226	22	106	5.40E-24	91.1919	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#23726 - 	CGI_10016617	superfamily	242406	3	87	3.87E-11	55.2901	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#23727 - 	CGI_10016618	superfamily	246918	265	317	1.87E-15	73.0047	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23727 - 	CGI_10016618	superfamily	246918	436	488	6.98E-15	71.4639	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23727 - 	CGI_10016618	superfamily	216897	17	83	1.18E-14	71.5585	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#23727 - 	CGI_10016618	superfamily	246918	322	374	8.15E-14	68.3823	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23727 - 	CGI_10016618	superfamily	246918	208	260	2.37E-12	64.1451	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23727 - 	CGI_10016618	superfamily	246918	397	430	0.000186547	41.0331	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23727 - 	CGI_10016618	superfamily	246918	101	144	0.00257133	37.5663	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23728 - 	CGI_10016619	superfamily	219621	30	157	4.45E-20	82.4091	cl06777	Rrp15p superfamily	 - 	 - 	Rrp15p; Rrp15p is required for the formation of 60S ribosomal subunits.
Q#23729 - 	CGI_10016620	superfamily	247905	349	461	4.24E-26	103.857	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#23729 - 	CGI_10016620	superfamily	247805	131	337	1.23E-55	187.692	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#23730 - 	CGI_10016621	superfamily	246908	335	435	6.12E-49	164.87	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#23730 - 	CGI_10016621	superfamily	243073	444	491	6.69E-15	69.6355	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#23731 - 	CGI_10016622	superfamily	243092	11	284	2.32E-33	131.303	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23731 - 	CGI_10016622	superfamily	241597	936	999	5.50E-05	42.2208	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#23731 - 	CGI_10016622	superfamily	204888	495	521	8.86E-07	47.0466	cl13738	DUF3639 superfamily	 - 	 - 	"Protein of unknown function (DUF3639); This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam00400. There are two completely conserved residues (E and R) that may be functionally important."
Q#23733 - 	CGI_10016624	superfamily	241789	12	128	5.48E-21	82.524	cl00328	Ribosomal_L14 superfamily	 - 	 - 	Ribosomal protein L14p/L23e; Ribosomal protein L14p/L23e.  
Q#23734 - 	CGI_10016625	superfamily	246925	188	356	1.24E-16	80.0921	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#23735 - 	CGI_10016626	superfamily	241571	222	337	2.67E-34	122.906	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23735 - 	CGI_10016626	superfamily	241583	129	183	9.88E-12	61.8182	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23736 - 	CGI_10016627	superfamily	246597	196	452	5.18E-147	422.795	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#23739 - 	CGI_10016630	superfamily	241548	4	459	0	826.754	cl00013	Lyase_I_like superfamily	 - 	 - 	"Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Lyase class I_like superfamily of enzymes that catalyze beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. This superfamily contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase. The lyase class I family comprises proteins similar to class II fumarase, aspartase, adenylosuccinate lyase, argininosuccinate lyase, and 3-carboxy-cis, cis-muconate lactonizing enzyme which, for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. Histidine or phenylalanine ammonia-lyase catalyze a beta-elimination of ammonia from histidine and phenylalanine, respectively."
Q#23740 - 	CGI_10016631	superfamily	245201	71	183	5.27E-28	108.778	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23741 - 	CGI_10016632	superfamily	247856	499	557	1.58E-08	51.7797	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23741 - 	CGI_10016632	superfamily	246925	158	434	1.50E-28	115.53	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#23742 - 	CGI_10016633	superfamily	246925	141	432	1.98E-25	106.286	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#23745 - 	CGI_10016636	superfamily	193409	408	476	1.78E-17	78.0113	cl15178	Kri1_C superfamily	N	 - 	KRI1-like family C-terminal; The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus. This is the C-terminal domain of the family.
Q#23745 - 	CGI_10016636	superfamily	218482	292	354	6.96E-12	62.2793	cl04969	Kri1 superfamily	C	 - 	KRI1-like family; The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus.
Q#23746 - 	CGI_10008055	superfamily	241591	26	97	1.79E-27	102.314	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#23746 - 	CGI_10008055	superfamily	241592	162	264	5.40E-68	209.376	cl00074	H2A superfamily	N	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23747 - 	CGI_10008056	superfamily	241592	22	101	4.51E-39	127.232	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23748 - 	CGI_10008057	superfamily	241592	33	121	1.27E-51	160.375	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23749 - 	CGI_10008058	superfamily	241592	23	119	7.20E-43	139.007	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23750 - 	CGI_10008059	superfamily	241591	26	97	7.94E-25	93.8399	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#23751 - 	CGI_10008060	superfamily	241592	1	136	5.16E-83	242.503	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23752 - 	CGI_10008061	superfamily	241592	22	101	4.51E-39	127.232	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23753 - 	CGI_10008062	superfamily	241592	25	121	1.52E-51	160.375	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23754 - 	CGI_10008063	superfamily	241592	23	119	7.20E-43	139.007	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23755 - 	CGI_10008064	superfamily	243072	170	216	1.42E-09	55.8526	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23755 - 	CGI_10008064	superfamily	215882	356	480	4.92E-10	57.2906	cl09511	FERM_M superfamily	 - 	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#23755 - 	CGI_10008064	superfamily	247725	461	554	0.000276777	39.8865	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23756 - 	CGI_10008065	superfamily	241592	23	119	7.20E-43	139.007	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23757 - 	CGI_10008066	superfamily	241592	1	136	5.16E-83	242.503	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23758 - 	CGI_10008067	superfamily	241592	22	101	4.51E-39	127.232	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23759 - 	CGI_10008068	superfamily	241592	25	121	1.52E-51	160.375	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23760 - 	CGI_10008069	superfamily	241592	23	119	7.20E-43	139.007	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23761 - 	CGI_10008070	superfamily	241591	23	97	2.26E-26	98.0771	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#23762 - 	CGI_10008071	superfamily	241592	1	136	5.16E-83	242.503	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23763 - 	CGI_10008072	superfamily	241592	22	101	4.51E-39	127.232	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23764 - 	CGI_10008073	superfamily	241592	25	121	1.52E-51	160.375	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23765 - 	CGI_10008074	superfamily	241592	23	119	7.20E-43	139.007	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23766 - 	CGI_10008075	superfamily	241591	23	97	2.26E-26	98.0771	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#23767 - 	CGI_10008076	superfamily	241592	1	136	5.16E-83	242.503	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23768 - 	CGI_10008077	superfamily	241592	22	101	4.51E-39	127.232	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23769 - 	CGI_10008078	superfamily	241592	33	121	6.85E-52	161.145	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23770 - 	CGI_10008079	superfamily	241592	23	119	7.20E-43	139.007	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23771 - 	CGI_10008080	superfamily	241591	23	97	2.26E-26	98.0771	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#23772 - 	CGI_10008081	superfamily	241592	1	136	5.16E-83	242.503	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23773 - 	CGI_10008082	superfamily	241592	22	101	4.51E-39	127.232	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23774 - 	CGI_10008083	superfamily	241592	33	121	6.85E-52	161.145	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23775 - 	CGI_10008084	superfamily	241592	23	119	7.20E-43	139.007	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23776 - 	CGI_10008085	superfamily	241591	23	97	2.32E-26	98.0771	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#23777 - 	CGI_10008086	superfamily	241592	1	157	4.59E-80	235.955	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23778 - 	CGI_10008087	superfamily	241592	22	101	4.51E-39	127.232	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#23780 - 	CGI_10008089	superfamily	247739	21	199	1.91E-40	138.173	cl17185	LPLAT superfamily	 - 	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#23781 - 	CGI_10008090	superfamily	247792	12	55	1.15E-07	48.596	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23782 - 	CGI_10008091	superfamily	247792	14	61	1.67E-07	48.2108	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23783 - 	CGI_10008092	superfamily	247792	11	54	5.44E-08	49.7516	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23784 - 	CGI_10008093	superfamily	247792	465	510	1.19E-06	46.67	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23784 - 	CGI_10008093	superfamily	247792	9	54	1.52E-06	46.67	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23785 - 	CGI_10008094	superfamily	243060	202	273	3.17E-09	54.6924	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#23785 - 	CGI_10008094	superfamily	243060	338	386	0.00670777	35.4324	cl02507	SEA superfamily	C	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#23788 - 	CGI_10005334	superfamily	221377	208	275	1.64E-05	43.2263	cl13449	DUF3504 superfamily	C	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#23790 - 	CGI_10005336	superfamily	241643	159	196	5.57E-06	43.2167	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#23790 - 	CGI_10005336	superfamily	241752	279	348	4.98E-08	50.636	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#23792 - 	CGI_10007932	superfamily	245599	214	424	1.38E-94	286.113	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#23792 - 	CGI_10007932	superfamily	207662	67	158	1.18E-63	202.095	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#23793 - 	CGI_10007933	superfamily	220904	244	332	2.51E-09	54.6105	cl12494	DUF2781 superfamily	N	 - 	Protein of unknown function (DUF2781); This is a eukaryotic family of uncharacterized proteins. Some of the proteins in this family are annotated as membrane proteins.
Q#23795 - 	CGI_10007935	superfamily	246908	146	239	1.39E-53	177.482	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#23795 - 	CGI_10007935	superfamily	247683	22	78	4.22E-30	111.627	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#23795 - 	CGI_10007935	superfamily	246908	88	161	7.13E-17	75.955	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#23795 - 	CGI_10007935	superfamily	245201	255	509	1.66E-154	444.15	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23797 - 	CGI_10007937	superfamily	241546	343	440	2.56E-29	110.828	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#23798 - 	CGI_10007938	superfamily	216363	125	232	4.83E-22	87.9109	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#23800 - 	CGI_10007600	superfamily	241600	1	171	1.20E-55	176.662	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23801 - 	CGI_10007601	superfamily	241600	62	232	1.61E-57	183.981	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23802 - 	CGI_10007602	superfamily	241600	56	225	3.18E-58	185.522	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23803 - 	CGI_10007603	superfamily	241600	58	229	5.53E-55	177.433	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23804 - 	CGI_10007604	superfamily	241600	18	192	2.84E-56	179.359	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#23805 - 	CGI_10007605	superfamily	215647	239	457	3.53E-29	115.784	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#23805 - 	CGI_10007605	superfamily	243029	162	218	1.65E-14	68.9165	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#23806 - 	CGI_10007606	superfamily	245599	237	466	2.65E-54	183.407	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#23806 - 	CGI_10007606	superfamily	207662	83	162	2.46E-45	154.353	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#23808 - 	CGI_10004080	superfamily	216363	63	143	4.79E-09	49.7762	cl08312	UPF0029 superfamily	C	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#23809 - 	CGI_10004081	superfamily	220371	59	198	2.25E-29	107.776	cl10720	Bud13 superfamily	 - 	 - 	"Pre-mRNA-splicing factor of RES complex; This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function."
Q#23811 - 	CGI_10004083	superfamily	241594	32	64	0.00178889	34.2032	cl00077	HECTc superfamily	N	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#23817 - 	CGI_10005825	superfamily	245304	13	484	0	773.765	cl10459	Peptidases_S8_S53 superfamily	 - 	 - 	"Peptidase domain in the S8 and S53 families; Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and  exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.  The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base.   However, the aspartic acid residue that acts as an electrophile is quite different.  In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity.  There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values."
Q#23817 - 	CGI_10005825	superfamily	221649	776	963	1.48E-71	237.529	cl13955	TPPII superfamily	 - 	 - 	"Tripeptidyl peptidase II; This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. The family is found in association with pfam00082. Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides."
Q#23818 - 	CGI_10005826	superfamily	241599	37	93	6.91E-21	82.2912	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#23820 - 	CGI_10005828	superfamily	219502	407	661	2.66E-75	242.35	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#23820 - 	CGI_10005828	superfamily	201962	225	295	2.17E-20	86.2756	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#23820 - 	CGI_10005828	superfamily	219507	304	399	1.06E-13	68.0347	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#23822 - 	CGI_10013776	superfamily	241548	1	222	6.86E-102	305.208	cl00013	Lyase_I_like superfamily	NC	 - 	"Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Lyase class I_like superfamily of enzymes that catalyze beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. This superfamily contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase. The lyase class I family comprises proteins similar to class II fumarase, aspartase, adenylosuccinate lyase, argininosuccinate lyase, and 3-carboxy-cis, cis-muconate lactonizing enzyme which, for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. Histidine or phenylalanine ammonia-lyase catalyze a beta-elimination of ammonia from histidine and phenylalanine, respectively."
Q#23823 - 	CGI_10013777	superfamily	152488	1	82	7.78E-05	37.5877	cl13485	DUF3534 superfamily	C	 - 	Domain of unknown function (DUF3534); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 150 amino acids in length. This domain is found associated with pfam00595. This domain has a conserved GILD sequence motif.
Q#23824 - 	CGI_10013778	superfamily	247856	221	283	1.48E-08	52.1649	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#23826 - 	CGI_10013780	superfamily	217210	587	1103	1.32E-175	531.468	cl10595	Ald_Xan_dh_C2 superfamily	 - 	 - 	Molybdopterin-binding domain of aldehyde dehydrogenase; Molybdopterin-binding domain of aldehyde dehydrogenase.  
Q#23826 - 	CGI_10013780	superfamily	243326	472	579	6.46E-38	139.19	cl03161	Ald_Xan_dh_C superfamily	 - 	 - 	"Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain.  "
Q#23826 - 	CGI_10013780	superfamily	201981	24	77	2.92E-27	107.566	cl08334	Fer2_2 superfamily	N	 - 	[2Fe-2S] binding domain; [2Fe-2S] binding domain.  
Q#23826 - 	CGI_10013780	superfamily	244932	324	422	6.95E-14	69.8377	cl08390	CO_deh_flav_C superfamily	 - 	 - 	CO dehydrogenase flavoprotein C-terminal domain; CO dehydrogenase flavoprotein C-terminal domain.  
Q#23827 - 	CGI_10013781	superfamily	247723	1487	1581	5.88E-58	196.725	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23827 - 	CGI_10013781	superfamily	217210	859	1082	2.50E-79	274.155	cl10595	Ald_Xan_dh_C2 superfamily	N	 - 	Molybdopterin-binding domain of aldehyde dehydrogenase; Molybdopterin-binding domain of aldehyde dehydrogenase.  
Q#23827 - 	CGI_10013781	superfamily	217210	594	857	2.24E-57	209.827	cl10595	Ald_Xan_dh_C2 superfamily	C	 - 	Molybdopterin-binding domain of aldehyde dehydrogenase; Molybdopterin-binding domain of aldehyde dehydrogenase.  
Q#23827 - 	CGI_10013781	superfamily	243326	479	586	5.85E-43	154.213	cl03161	Ald_Xan_dh_C superfamily	 - 	 - 	"Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain.  "
Q#23827 - 	CGI_10013781	superfamily	201981	5	80	3.32E-36	133.76	cl08334	Fer2_2 superfamily	 - 	 - 	[2Fe-2S] binding domain; [2Fe-2S] binding domain.  
Q#23827 - 	CGI_10013781	superfamily	244932	328	428	4.86E-14	70.6081	cl08390	CO_deh_flav_C superfamily	 - 	 - 	CO dehydrogenase flavoprotein C-terminal domain; CO dehydrogenase flavoprotein C-terminal domain.  
Q#23827 - 	CGI_10013781	superfamily	243107	1420	1459	3.19E-09	55.2438	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#23828 - 	CGI_10013782	superfamily	192507	9	89	5.61E-30	111.53	cl10955	WGG superfamily	 - 	 - 	Pre-rRNA-processing protein TSR2; This entry represents the central conserved section of a family of proteins described as pre-rRNA-processing protein TSR2. The region has a distinctive WGG motif but the function is unknown.
Q#23829 - 	CGI_10013783	superfamily	193607	292	423	5.36E-64	212.047	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#23829 - 	CGI_10013783	superfamily	247792	245	283	2.55E-09	54.7592	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#23829 - 	CGI_10013783	superfamily	245213	632	668	9.36E-07	47.2462	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23829 - 	CGI_10013783	superfamily	241554	16	155	6.07E-33	126.616	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#23829 - 	CGI_10013783	superfamily	241554	123	211	1.65E-05	44.8329	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#23831 - 	CGI_10013785	superfamily	219122	2322	2458	1.18E-27	115.855	cl05933	DUF1162 superfamily	C	 - 	Protein of unknown function (DUF1162); This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins.
Q#23831 - 	CGI_10013785	superfamily	204985	6	63	1.05E-08	55.6407	cl14987	Chorein_N superfamily	C	 - 	"N-terminal region of Chorein, a TM vesicle-mediated sorter; Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport."
Q#23832 - 	CGI_10013786	superfamily	219122	3	98	4.60E-06	47.6743	cl05933	DUF1162 superfamily	N	 - 	Protein of unknown function (DUF1162); This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins.
Q#23834 - 	CGI_10013788	superfamily	248097	161	248	0.0016244	37.2446	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23834 - 	CGI_10013788	superfamily	248097	429	514	0.00269832	36.8594	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23835 - 	CGI_10013789	superfamily	247785	42	336	4.51E-77	240.279	cl17231	HpcH_HpaI superfamily	 - 	 - 	"HpcH/HpaI aldolase/citrate lyase family; This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase."
Q#23837 - 	CGI_10013791	superfamily	247999	398	435	0.00310428	35.6506	cl17445	PHD superfamily	C	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#23841 - 	CGI_10013795	superfamily	247723	44	136	6.31E-38	138.97	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23841 - 	CGI_10013795	superfamily	152200	1243	1378	1.55E-17	82.4391	cl13245	N-SET superfamily	 - 	 - 	"COMPASS (Complex proteins associated with Set1p) component N; The n-SET or N-SET domain is a component of the COMPASS complex, associated with SET1, conserved in yeasts and in other eukaryotes up to humans. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes. This domain promotes trimethylation in conjunction with an RRM domain and is necessary for binding of the Spp1 component of COMPASS into the complex."
Q#23842 - 	CGI_10004100	superfamily	247723	118	166	0.00968562	33.5771	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23845 - 	CGI_10004103	superfamily	241568	706	740	0.0011993	37.8276	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#23845 - 	CGI_10004103	superfamily	242059	19	426	6.37E-76	256.134	cl00738	MBOAT superfamily	 - 	 - 	"MBOAT, membrane-bound O-acyltransferase family; The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue."
Q#23848 - 	CGI_10000673	superfamily	218839	7	165	6.57E-53	169.802	cl05501	Med7 superfamily	 - 	 - 	MED7 protein; This family consists of several eukaryotic proteins which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multi-step process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus.
Q#23849 - 	CGI_10001248	superfamily	217859	42	85	9.40E-15	65.7599	cl04376	P34-Arc superfamily	NC	 - 	"Arp2/3 complex, 34 kD subunit p34-Arc; Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. This family represents the p34-Arc subunit."
Q#23851 - 	CGI_10010828	superfamily	241754	10	220	1.69E-86	289.275	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#23852 - 	CGI_10010829	superfamily	241754	2	356	0	632.424	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#23852 - 	CGI_10010829	superfamily	247725	1605	1715	2.54E-41	150.044	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#23852 - 	CGI_10010829	superfamily	241581	472	572	1.70E-06	48.5366	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#23852 - 	CGI_10010829	superfamily	221593	1167	1317	5.59E-44	159.077	cl13857	DUF3694 superfamily	 - 	 - 	"Kinesin protein; This domain family is found in eukaryotes, and is typically between 131 and 151 amino acids in length. The family is found in association with pfam00225, pfam00498. There is a single completely conserved residue W that may be functionally important."
Q#23852 - 	CGI_10010829	superfamily	241754	1737	1848	6.03E-37	144.825	cl00286	Motor_domain superfamily	C	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#23852 - 	CGI_10010829	superfamily	221571	834	880	1.39E-07	50.5791	cl13810	KIF1B superfamily	 - 	 - 	"Kinesin protein 1B; This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00225, pfam00498. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells."
Q#23853 - 	CGI_10010830	superfamily	246925	79	361	6.79E-29	114.375	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#23854 - 	CGI_10010831	superfamily	244840	22	124	6.53E-34	118.043	cl08021	Flavoprotein superfamily	N	 - 	"Flavoprotein; This family contains diverse flavoprotein enzymes. This family includes epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN. This enzyme catalyzes the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance. dipicolinate synthase catalyzes the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenyl-acrylic acid decarboxylase (EC:4.1.1.-)."
Q#23855 - 	CGI_10010832	superfamily	243175	126	251	1.30E-59	187.089	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#23855 - 	CGI_10010832	superfamily	241832	23	93	1.20E-32	115.601	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#23860 - 	CGI_10010837	superfamily	241832	4	73	2.41E-25	96.464	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#23860 - 	CGI_10010837	superfamily	243175	157	271	8.82E-18	76.1222	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#23860 - 	CGI_10010837	superfamily	243175	84	192	4.73E-13	63.0254	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#23861 - 	CGI_10010838	superfamily	241832	4	73	2.37E-27	100.316	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#23861 - 	CGI_10010838	superfamily	243175	84	186	3.43E-12	59.5586	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#23862 - 	CGI_10010839	superfamily	243490	2	48	0.00494575	31.883	cl03656	PS_Dcarbxylase superfamily	NC	 - 	"Phosphatidylserine decarboxylase; This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyze the reaction: Phosphatidyl-L-serine <=> phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine."
Q#23863 - 	CGI_10010840	superfamily	247746	106	213	0.00544196	36.8526	cl17192	ATP-synt_B superfamily	 - 	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#23864 - 	CGI_10010841	superfamily	247750	179	308	8.45E-58	195.201	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#23864 - 	CGI_10010841	superfamily	247750	34	111	3.91E-43	155.91	cl17196	E1_enzyme_family superfamily	NC	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#23864 - 	CGI_10010841	superfamily	202124	84	146	9.03E-12	59.8684	cl08340	UBACT superfamily	 - 	 - 	Repeat in ubiquitin-activating (UBA) protein; Repeat in ubiquitin-activating (UBA) protein.  
Q#23865 - 	CGI_10010842	superfamily	247750	116	308	1.20E-70	229.098	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#23865 - 	CGI_10010842	superfamily	247750	1	48	1.98E-22	96.2043	cl17196	E1_enzyme_family superfamily	NC	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#23866 - 	CGI_10005516	superfamily	218284	49	93	9.18E-13	59.5755	cl04786	SOUL superfamily	C	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#23866 - 	CGI_10005516	superfamily	243051	23	49	0.0010389	34.6337	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23868 - 	CGI_10005518	superfamily	198738	180	264	4.26E-46	155.504	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#23870 - 	CGI_10005520	superfamily	220626	1	198	1.10E-33	125.426	cl18564	GpcrRhopsn4 superfamily	N	 - 	"Rhodopsin-like GPCR transmembrane domain; This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans. GPCRs are integral membrane receptors whose intracellular actions are mediated by signalling pathways involving G proteins and downstream secondary messengers."
Q#23872 - 	CGI_10005522	superfamily	220626	154	410	6.43E-62	205.933	cl18564	GpcrRhopsn4 superfamily	 - 	 - 	"Rhodopsin-like GPCR transmembrane domain; This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans. GPCRs are integral membrane receptors whose intracellular actions are mediated by signalling pathways involving G proteins and downstream secondary messengers."
Q#23873 - 	CGI_10005523	superfamily	245029	308	417	8.53E-06	43.7904	cl09190	MAPEG superfamily	 - 	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#23876 - 	CGI_10025860	superfamily	219542	53	160	2.70E-40	136.603	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#23877 - 	CGI_10025861	superfamily	215647	23	237	1.46E-40	146.214	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#23879 - 	CGI_10025863	superfamily	216363	278	373	3.96E-12	62.1026	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#23879 - 	CGI_10025863	superfamily	242748	148	185	0.00435338	35.2196	cl01853	COG4467 superfamily	C	 - 	"Regulator of replication initiation timing [Replication,    recombination, and repair]"
Q#23881 - 	CGI_10025865	superfamily	216363	7	72	1.60E-15	65.9546	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#23884 - 	CGI_10025868	superfamily	246669	197	277	2.86E-22	89.6394	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#23884 - 	CGI_10025868	superfamily	246669	1	71	2.20E-13	64.5075	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#23885 - 	CGI_10025869	superfamily	238191	27	528	7.14E-105	328.908	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#23886 - 	CGI_10025870	superfamily	243051	688	838	9.87E-34	128.65	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23886 - 	CGI_10025870	superfamily	243051	531	636	4.91E-30	118.249	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23886 - 	CGI_10025870	superfamily	243051	856	1007	1.65E-28	113.627	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23886 - 	CGI_10025870	superfamily	241571	337	459	2.37E-10	59.3482	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23886 - 	CGI_10025870	superfamily	245213	1006	1041	0.000350906	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23886 - 	CGI_10025870	superfamily	243051	1050	1111	1.80E-10	60.4421	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23886 - 	CGI_10025870	superfamily	241583	192	251	1.35E-08	54.4995	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23887 - 	CGI_10025871	superfamily	243051	29	158	8.52E-28	103.997	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23888 - 	CGI_10025872	superfamily	241583	156	336	1.44E-54	188.549	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23888 - 	CGI_10025872	superfamily	243051	919	1070	2.34E-27	110.16	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23888 - 	CGI_10025872	superfamily	243051	520	648	2.90E-19	86.6629	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23888 - 	CGI_10025872	superfamily	241571	391	513	9.45E-11	60.5038	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23888 - 	CGI_10025872	superfamily	245213	651	684	0.000160525	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23888 - 	CGI_10025872	superfamily	245213	783	810	0.000520271	39.157	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23888 - 	CGI_10025872	superfamily	243051	693	773	2.88E-13	68.9165	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23888 - 	CGI_10025872	superfamily	243051	819	876	1.01E-05	45.4466	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23890 - 	CGI_10025874	superfamily	243051	2	35	0.000584709	34.661	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23891 - 	CGI_10025875	superfamily	243051	624	777	1.54E-30	118.634	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23891 - 	CGI_10025875	superfamily	243051	318	470	4.45E-27	108.619	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23891 - 	CGI_10025875	superfamily	243051	186	315	6.59E-20	87.8185	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23891 - 	CGI_10025875	superfamily	245213	588	615	0.000157681	40.3126	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23891 - 	CGI_10025875	superfamily	245213	477	506	0.00066285	38.3866	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23891 - 	CGI_10025875	superfamily	243051	515	575	3.01E-08	52.7653	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	241583	1250	1432	4.98E-53	187.008	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23892 - 	CGI_10025876	superfamily	243051	1613	1758	6.42E-36	136.739	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	243051	929	1082	1.06E-28	115.938	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	243051	2734	2842	6.41E-25	104.767	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	243051	542	662	6.17E-21	93.2113	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	243051	681	788	3.05E-19	88.2037	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	241571	2509	2631	7.41E-12	65.1262	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23892 - 	CGI_10025876	superfamily	241571	373	495	5.00E-11	62.815	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23892 - 	CGI_10025876	superfamily	245213	888	920	3.57E-05	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23892 - 	CGI_10025876	superfamily	245213	791	826	0.00459524	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23892 - 	CGI_10025876	superfamily	243051	2671	2750	7.84E-12	65.8621	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	241583	230	287	5.12E-08	54.1143	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23892 - 	CGI_10025876	superfamily	243051	8	80	8.26E-07	50.4269	cl02479	MAM superfamily	NC	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	241583	2358	2414	8.31E-07	50.6475	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23892 - 	CGI_10025876	superfamily	243051	860	886	1.88E-06	49.2986	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23892 - 	CGI_10025876	superfamily	241571	2020	2079	1.68E-05	45.8663	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#23892 - 	CGI_10025876	superfamily	241583	1869	1922	0.00109409	41.4027	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#23893 - 	CGI_10025877	superfamily	243051	23	131	5.78E-28	103.612	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23894 - 	CGI_10025878	superfamily	243051	91	245	8.20E-25	97.0633	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23894 - 	CGI_10025878	superfamily	243051	1	73	4.67E-16	72.4105	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23895 - 	CGI_10025879	superfamily	243051	209	279	0.000503598	38.4785	cl02479	MAM superfamily	C	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23896 - 	CGI_10025880	superfamily	243051	1	36	0.00865902	35.4041	cl02479	MAM superfamily	NC	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#23897 - 	CGI_10025881	superfamily	245312	150	375	1.20E-06	48.7996	cl10482	KefB superfamily	 - 	 - 	"Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]"
Q#23900 - 	CGI_10025885	superfamily	243045	99	191	3.01E-11	62.6507	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#23900 - 	CGI_10025885	superfamily	241596	15	66	4.51E-08	52.2163	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#23900 - 	CGI_10025885	superfamily	243045	273	349	0.00209482	38.3831	cl02459	PAS superfamily	N	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#23901 - 	CGI_10025887	superfamily	238191	601	1082	1.56E-118	376.672	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#23901 - 	CGI_10025887	superfamily	238191	99	568	3.86E-113	362.035	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#23902 - 	CGI_10025888	superfamily	238191	28	537	3.81E-126	387.843	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#23902 - 	CGI_10025888	superfamily	238012	644	683	0.00466715	35.793	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#23903 - 	CGI_10025889	superfamily	241877	320	346	0.000333899	40.9401	cl00459	MIT_CorA-like superfamily	N	 - 	"metal ion transporter CorA-like divalent cation transporter superfamily; This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport."
Q#23904 - 	CGI_10025890	superfamily	217311	8	391	2.90E-105	325.06	cl18402	DUF229 superfamily	N	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#23905 - 	CGI_10025891	superfamily	241889	1338	1473	2.29E-27	110.798	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#23905 - 	CGI_10025891	superfamily	243066	380	479	1.71E-08	54.1605	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#23908 - 	CGI_10025894	superfamily	247684	17	431	2.83E-93	302.659	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#23908 - 	CGI_10025894	superfamily	178029	564	857	1.48E-116	362.187	cl18093	PLN02407 superfamily	 - 	 - 	diphosphomevalonate decarboxylase
Q#23912 - 	CGI_10025898	superfamily	247907	1963	2144	2.93E-26	108.66	cl17353	LamG superfamily	 - 	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#23912 - 	CGI_10025898	superfamily	247068	1223	1324	5.24E-26	106.244	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	553	655	3.52E-24	100.851	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	889	999	6.36E-23	96.9989	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	338	434	5.60E-17	80.0501	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	1008	1101	6.79E-17	79.6649	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	1333	1430	1.29E-16	78.8945	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	1445	1541	5.65E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	663	761	6.36E-16	76.9685	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	1109	1213	2.08E-12	66.5681	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	446	535	2.12E-12	66.5681	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	245213	2462	2499	2.73E-11	61.8838	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23912 - 	CGI_10025898	superfamily	247907	2241	2331	3.00E-09	57.8133	cl17353	LamG superfamily	C	 - 	"Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules."
Q#23912 - 	CGI_10025898	superfamily	247068	776	873	3.38E-09	56.9382	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	219	324	4.07E-08	53.8566	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	1549	1663	5.71E-08	53.0862	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	110	208	5.33E-07	50.3898	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	245213	1927	1960	0.00285383	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23912 - 	CGI_10025898	superfamily	216265	2549	2652	2.10E-18	85.432	cl03079	Cadherin_C superfamily	 - 	 - 	Cadherin cytoplasmic region; Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
Q#23912 - 	CGI_10025898	superfamily	247068	6	99	0.00272563	38.8338	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23912 - 	CGI_10025898	superfamily	247068	1685	1766	0.00304001	38.4486	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23913 - 	CGI_10025899	superfamily	245201	240	475	1.74E-22	95.7665	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23914 - 	CGI_10025900	superfamily	247692	48	254	6.69E-56	185.032	cl17068	AFD_class_I superfamily	N	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#23916 - 	CGI_10025902	superfamily	247724	1	86	2.41E-22	87.1959	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#23920 - 	CGI_10025906	superfamily	218759	9	136	8.59E-33	113.989	cl05405	DUF842 superfamily	 - 	 - 	"Eukaryotic protein of unknown function (DUF842); This family consists of a number of conserved eukaryotic proteins of unknown function. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation."
Q#23921 - 	CGI_10023479	superfamily	245206	21	264	6.36E-143	410.683	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23921 - 	CGI_10023479	superfamily	242376	334	423	1.96E-23	93.829	cl01225	SCP2 superfamily	 - 	 - 	"SCP-2 sterol transfer family; This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145."
Q#23922 - 	CGI_10023480	superfamily	245210	53	455	1.00E-115	347.714	cl09938	cond_enzymes superfamily	 - 	 - 	"Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products."
Q#23924 - 	CGI_10023482	superfamily	221308	1	101	4.67E-22	85.7586	cl13364	DUF3429 superfamily	N	 - 	Protein of unknown function (DUF3429); This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 147 to 245 amino acids in length.
Q#23925 - 	CGI_10023483	superfamily	248097	778	898	8.36E-23	95.795	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23925 - 	CGI_10023483	superfamily	248097	659	779	2.41E-16	76.9202	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23925 - 	CGI_10023483	superfamily	247743	119	160	0.000761599	39.4904	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#23926 - 	CGI_10023484	superfamily	245201	29	174	6.02E-15	73.0397	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23929 - 	CGI_10023487	superfamily	241763	194	422	5.32E-87	268.37	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#23929 - 	CGI_10023487	superfamily	207618	46	89	0.0013996	36.6442	cl02508	Somatomedin_B superfamily	 - 	 - 	Somatomedin B domain; Somatomedin B domain.  
Q#23930 - 	CGI_10023488	superfamily	217955	685	887	1.34E-65	220.219	cl04442	Utp21 superfamily	 - 	 - 	"Utp21 specific WD40 associated putative domain; Utp21 is a subunit of U3 snoRNP, which is essential for synthesis of 18S rRNA."
Q#23930 - 	CGI_10023488	superfamily	243092	270	604	6.41E-26	108.962	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23930 - 	CGI_10023488	superfamily	243092	92	356	1.35E-21	95.8648	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23931 - 	CGI_10023489	superfamily	241675	119	385	2.39E-49	168.634	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#23932 - 	CGI_10023490	superfamily	247757	22	279	5.81E-67	210.951	cl17203	Fer4_NifH superfamily	 - 	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#23933 - 	CGI_10023491	superfamily	241599	38	94	4.69E-11	55.7125	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#23934 - 	CGI_10023492	superfamily	248020	38	290	1.90E-06	49.3852	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#23935 - 	CGI_10023493	superfamily	222150	706	733	0.00619037	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#23936 - 	CGI_10023494	superfamily	220281	237	491	1.11E-34	135.148	cl12364	Ndc1_Nup superfamily	N	 - 	"Nucleoporin protein Ndc1-Nup; Ndc1 is a nucleoporin protein that is a component of the Nuclear Pore Complex, and, in fungi, also of the Spindle Pole Body. It consists of six transmembrane segments, three lumenal loops, both concentrated at the N-terminus and cytoplasmic domains largely at the C-terminus, all of which are well conserved."
Q#23937 - 	CGI_10023495	superfamily	241622	44	119	3.49E-16	69.5178	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#23938 - 	CGI_10023496	superfamily	216897	43	125	4.13E-26	99.678	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#23938 - 	CGI_10023496	superfamily	243029	139	198	1.43E-08	50.976	cl02422	HRM superfamily	 - 	 - 	Hormone receptor domain; This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain.
Q#23939 - 	CGI_10023497	superfamily	244859	110	315	1.31E-12	66.0309	cl08171	HtrL_YibB superfamily	 - 	 - 	"Bacterial protein of unknown function (HtrL_YibB); The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein."
Q#23942 - 	CGI_10023500	superfamily	220691	5	228	0.00206907	37.5974	cl18569	7TM_GPCR_Srv superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#23943 - 	CGI_10023501	superfamily	241642	405	461	0.000340471	38.6306	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#23944 - 	CGI_10023502	superfamily	192393	13	114	5.56E-29	105.046	cl10788	EAF superfamily	 - 	 - 	RNA polymerase II transcription elongation factor; Members of this family act as transcriptional transactivators of ELL and ELL2 elongation activities. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. The N-terminus of approx 120 residues is globular and highly conserved.
Q#23945 - 	CGI_10023504	superfamily	218200	9	35	1.77E-06	45.8211	cl04660	Glyco_transf_54 superfamily	N	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#23946 - 	CGI_10023505	superfamily	216653	165	305	2.15E-26	101.905	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#23947 - 	CGI_10023506	superfamily	246750	28	143	0.00186933	36.8414	cl14880	CBM6-CBM35-CBM36_like superfamily	 - 	 - 	"Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. This alignment model also contains the C-terminal domains of bacterial insecticidal toxins, where they may be involved in determining insect specificity through carbohydrate binding functionality."
Q#23948 - 	CGI_10023507	superfamily	243353	27	67	1.80E-14	63.2172	cl03225	GRIP superfamily	 - 	 - 	"GRIP domain; The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures in."
Q#23950 - 	CGI_10023509	superfamily	245599	382	540	6.05E-30	116.939	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#23950 - 	CGI_10023509	superfamily	243104	574	617	3.52E-05	42.1469	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#23953 - 	CGI_10023512	superfamily	245201	355	499	1.29E-18	84.9809	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23954 - 	CGI_10023513	superfamily	246921	289	332	1.50E-10	58.5409	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#23954 - 	CGI_10023513	superfamily	246921	214	281	7.38E-05	41.9773	cl15299	FG-GAP superfamily	 - 	 - 	"FG-GAP repeat; This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats."
Q#23955 - 	CGI_10023514	superfamily	241574	8	140	3.02E-37	135.406	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#23955 - 	CGI_10023514	superfamily	241574	186	370	1.56E-22	93.8045	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#23957 - 	CGI_10012621	superfamily	215648	388	609	1.08E-29	117.697	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#23957 - 	CGI_10012621	superfamily	217211	206	261	0.000785652	38.4194	cl03691	Cache_1 superfamily	C	 - 	Cache domain; Cache domain.  
Q#23958 - 	CGI_10012622	superfamily	248022	317	473	6.93E-11	62.6803	cl17468	Aa_trans superfamily	NC	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#23958 - 	CGI_10012622	superfamily	248022	136	185	7.93E-05	43.8055	cl17468	Aa_trans superfamily	C	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#23960 - 	CGI_10012624	superfamily	142634	1021	1340	7.37E-166	500.593	cl11429	RNAP_largest_subunit_C superfamily	 - 	 - 	"Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria."
Q#23960 - 	CGI_10012624	superfamily	245715	246	548	1.21E-139	430.787	cl11591	RNA_pol_Rpb1_2 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion."
Q#23960 - 	CGI_10012624	superfamily	218370	12	354	5.30E-101	326.564	cl04880	RNA_pol_Rpb1_1 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand."
Q#23960 - 	CGI_10012624	superfamily	218361	526	700	8.52E-45	160.864	cl04873	RNA_pol_Rpb1_3 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking."
Q#23960 - 	CGI_10012624	superfamily	218372	725	831	8.14E-37	136.346	cl04881	RNA_pol_Rpb1_4 superfamily	 - 	 - 	"RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors."
Q#23961 - 	CGI_10012625	superfamily	247799	155	272	1.30E-35	128.516	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#23962 - 	CGI_10012626	superfamily	243310	26	226	1.23E-52	176.66	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#23962 - 	CGI_10012626	superfamily	220228	227	275	4.09E-11	58.4512	cl09661	CENP-X superfamily	N	 - 	"CENP-S associating Centromere protein X; The centromere, essential for faithful chromosome segregation during mitosis, has a network of constitutive centromere-associated (CCAN) proteins associating with it during mitosis. So far in vertebrates at least 15 centromere proteins have been identified, which are divided into several subclasses based on functional and biochemical analyses. These provide a platform for the formation of a functional kinetochore during mitosis. CENP-S is one that does not associate with the CENP-H-containing complex but rather interacts with CENP-X to form a stable assembly of outer kinetochore proteins that functions downstream of other components of the CCAN. This complex may directly allow efficient and stable formation of the outer kinetochore on the CCAN platform."
Q#23963 - 	CGI_10012627	superfamily	243310	26	262	1.62E-65	206.321	cl03120	ELO superfamily	 - 	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#23964 - 	CGI_10012628	superfamily	241580	200	277	5.22E-21	87.9946	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#23965 - 	CGI_10012629	superfamily	243092	260	514	2.28E-41	150.563	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23965 - 	CGI_10012629	superfamily	150420	39	185	0.00136772	38.1779	cl18042	Jnk-SapK_ap_N superfamily	N	 - 	JNK_SAPK-associated protein-1; This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end.
Q#23966 - 	CGI_10012630	superfamily	241900	457	762	4.47E-113	354.637	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#23966 - 	CGI_10012630	superfamily	246908	29	132	2.24E-31	119.853	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#23966 - 	CGI_10012630	superfamily	247057	994	1052	1.79E-12	64.6268	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#23967 - 	CGI_10012631	superfamily	245206	20	286	2.27E-91	274.872	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23968 - 	CGI_10012632	superfamily	245206	1	256	1.43E-88	266.783	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23969 - 	CGI_10012633	superfamily	241782	37	294	1.31E-42	150.955	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#23971 - 	CGI_10012635	superfamily	245206	7	252	3.08E-112	325.905	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#23973 - 	CGI_10012637	superfamily	241546	941	1049	8.88E-46	161.938	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#23973 - 	CGI_10012637	superfamily	245670	173	358	1.93E-59	203.558	cl11519	DENN superfamily	 - 	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#23973 - 	CGI_10012637	superfamily	243635	9	109	2.57E-24	99.7164	cl04085	uDENN superfamily	 - 	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#23973 - 	CGI_10012637	superfamily	243142	856	929	1.36E-17	81.5187	cl02689	RUN superfamily	N	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#23973 - 	CGI_10012637	superfamily	208095	484	559	3.45E-14	69.5447	cl04084	dDENN superfamily	 - 	 - 	dDENN domain; This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
Q#23973 - 	CGI_10012637	superfamily	243142	1133	1266	5.45E-08	52.6287	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#23974 - 	CGI_10000408	superfamily	241743	26	190	1.11E-14	67.9834	cl00274	ML superfamily	 - 	 - 	"The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2  and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids."
Q#23975 - 	CGI_10018635	superfamily	246918	224	276	1.54E-16	73.3899	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#23975 - 	CGI_10018635	superfamily	243072	167	212	0.00306055	36.2075	cl02529	ANK superfamily	NC	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#23976 - 	CGI_10018636	superfamily	245847	34	154	1.76E-21	85.6861	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#23978 - 	CGI_10018638	superfamily	241550	363	686	2.80E-126	385.347	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#23978 - 	CGI_10018638	superfamily	245839	695	829	3.55E-17	79.4561	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#23978 - 	CGI_10018638	superfamily	248097	255	371	1.27E-23	98.1062	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23979 - 	CGI_10018639	superfamily	248097	70	192	2.80E-30	109.277	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23980 - 	CGI_10018640	superfamily	248012	5	86	6.21E-10	54.8913	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#23980 - 	CGI_10018640	superfamily	248012	166	279	0.000174084	39.0981	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#23981 - 	CGI_10018641	superfamily	248012	2	86	4.98E-08	46.4169	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#23982 - 	CGI_10018642	superfamily	248097	42	128	3.29E-21	84.239	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#23983 - 	CGI_10018643	superfamily	247068	64	160	1.69E-14	66.5681	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#23984 - 	CGI_10018644	superfamily	247723	102	187	9.50E-27	99.6845	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#23985 - 	CGI_10018645	superfamily	243092	28	369	8.12E-11	61.1968	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#23986 - 	CGI_10018646	superfamily	220695	73	198	0.00483171	37.5583	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#23987 - 	CGI_10018647	superfamily	245201	608	821	2.47E-66	222.797	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#23987 - 	CGI_10018647	superfamily	241584	499	588	0.00184247	37.4759	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#23987 - 	CGI_10018647	superfamily	245213	29	61	0.00514554	35.9154	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23988 - 	CGI_10018648	superfamily	192535	50	323	6.97E-05	42.583	cl18179	7TM_GPCR_Srsx superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#23989 - 	CGI_10018649	superfamily	222032	146	298	2.58E-39	136.608	cl16218	CPSF100_C superfamily	 - 	 - 	"Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex."
Q#23989 - 	CGI_10018649	superfamily	203663	64	101	2.28E-06	43.6323	cl06522	RMMBL superfamily	 - 	 - 	RNA-metabolising metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism.
Q#23990 - 	CGI_10018650	superfamily	241613	629	663	2.82E-09	55.6758	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	1960	1994	3.61E-08	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	2297	2328	6.74E-08	51.8238	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	2090	2123	2.24E-07	50.283	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	245213	2384	2422	6.47E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#23990 - 	CGI_10018650	superfamily	241613	591	623	2.16E-06	47.5866	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	1999	2031	2.55E-06	47.2014	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	2251	2284	5.59E-06	46.0458	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	2127	2159	1.22E-05	45.2754	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	2169	2202	1.31E-05	45.2754	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	682	705	5.52E-05	43.3494	cl00104	LDLa superfamily	N	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	1918	1952	5.61E-05	43.3494	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	2053	2077	0.000457802	40.653	cl00104	LDLa superfamily	N	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	554	586	0.000460554	40.653	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241613	464	498	0.000470317	40.653	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#23990 - 	CGI_10018650	superfamily	241752	2496	2586	4.35E-29	115.88	cl00283	ADP_ribosyl superfamily	N	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#23990 - 	CGI_10018650	superfamily	214531	1766	1806	3.25E-11	61.4636	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	214531	908	951	6.08E-07	49.1373	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	214531	866	906	1.20E-06	48.3669	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	214531	1394	1427	1.76E-05	44.9001	cl18310	LY superfamily	C	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	214531	319	354	1.98E-05	44.5149	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	215683	1739	1781	3.11E-05	44.0831	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#23990 - 	CGI_10018650	superfamily	221695	2364	2387	4.38E-05	43.5978	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#23990 - 	CGI_10018650	superfamily	214531	964	998	0.000618923	40.2777	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	215683	1020	1059	0.00163695	39.0755	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#23990 - 	CGI_10018650	superfamily	214531	1443	1485	0.00523534	37.5813	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	215683	1825	1865	0.00561475	37.5347	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#23990 - 	CGI_10018650	superfamily	214531	1181	1228	0.00639906	37.1961	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23990 - 	CGI_10018650	superfamily	214531	1670	1707	0.00724299	37.1961	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#23991 - 	CGI_10018651	superfamily	189857	23	140	2.91E-23	92.313	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#23992 - 	CGI_10018652	superfamily	243066	136	239	2.80E-06	44.9892	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#23993 - 	CGI_10018653	superfamily	220603	30	82	4.91E-21	85.5263	cl10849	DUF2360 superfamily	C	 - 	Predicted coiled-coil domain-containing protein (DUF2360); This is the conserved 140 amino acid region of a family of proteins conserved from nematodes to humans. One C. elegans member is annotated as a Daf-16-dependent longevity protein 1 but this could not be confirmed. The function is unknown.
Q#23993 - 	CGI_10018653	superfamily	220603	139	179	2.27E-16	72.4295	cl10849	DUF2360 superfamily	N	 - 	Predicted coiled-coil domain-containing protein (DUF2360); This is the conserved 140 amino acid region of a family of proteins conserved from nematodes to humans. One C. elegans member is annotated as a Daf-16-dependent longevity protein 1 but this could not be confirmed. The function is unknown.
Q#23994 - 	CGI_10018654	superfamily	243689	29	95	5.01E-08	51.0901	cl04271	IBN_N superfamily	 - 	 - 	Importin-beta N-terminal domain; Importin-beta N-terminal domain.  
Q#23994 - 	CGI_10018654	superfamily	219817	122	249	1.26E-07	51.0797	cl07129	Xpo1 superfamily	 - 	 - 	"Exportin 1-like protein; The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus."
Q#23995 - 	CGI_10018655	superfamily	246925	93	174	0.000240533	40.4166	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#23998 - 	CGI_10018658	superfamily	217380	314	605	6.49E-62	208.718	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#23999 - 	CGI_10018659	superfamily	241754	170	565	1.73E-108	331.843	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#24000 - 	CGI_10018660	superfamily	247724	77	207	1.54E-13	68.3394	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24000 - 	CGI_10018660	superfamily	217881	201	238	1.25E-10	57.5614	cl04390	Abhydro_lipase superfamily	N	 - 	Partial alpha/beta-hydrolase lipase region; This family corresponds to a N-terminal part of an alpha/beta hydrolase domain.
Q#24000 - 	CGI_10018660	superfamily	218405	221	386	0.00890406	36.7057	cl18455	DUF676 superfamily	C	 - 	Putative serine esterase (DUF676); This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.
Q#24003 - 	CGI_10013015	superfamily	245864	43	280	7.42E-26	105.053	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#24004 - 	CGI_10013016	superfamily	243051	163	242	8.65E-14	65.8349	cl02479	MAM superfamily	NC	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#24012 - 	CGI_10013024	superfamily	243069	209	314	7.92E-08	50.037	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24013 - 	CGI_10013025	superfamily	243058	407	526	1.10E-21	92.7627	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24013 - 	CGI_10013025	superfamily	243058	255	374	1.94E-18	83.5179	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24013 - 	CGI_10013025	superfamily	243058	492	633	4.81E-18	82.3623	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24013 - 	CGI_10013025	superfamily	243058	178	288	2.76E-10	59.2503	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24013 - 	CGI_10013025	superfamily	243069	941	1034	0.000798856	39.2514	cl02525	Band_7 superfamily	N	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24013 - 	CGI_10013025	superfamily	243058	376	436	0.000302679	40.1053	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24014 - 	CGI_10013026	superfamily	222150	713	736	5.47E-09	53.1645	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24014 - 	CGI_10013026	superfamily	222150	683	710	5.60E-07	47.3865	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24014 - 	CGI_10013026	superfamily	246975	728	749	4.13E-05	41.9489	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#24016 - 	CGI_10013028	superfamily	241644	33	178	5.25E-36	124.237	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#24017 - 	CGI_10013029	superfamily	244994	202	285	2.28E-17	74.965	cl08520	Cdc6_C superfamily	 - 	 - 	"Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding; This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases the specificity of the ORC-origins interaction. Further studies suggest that hydrolysis of Cdc6-bound ATP promotes the association of the replication licensing factor Cdt1 with origins through an interaction with Orc6 and this in turn promotes the loading of MCM2-7 helicase onto chromatin. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication.  S-Cdk (S-phase cyclin and cyclin-dependent kinase complex) prevents rereplication by causing the Cdc6 protein to dissociate from ORC and prevents the Cdc6 and MCM proteins from reassembling at any origin. By phosphorylating Cdc6, S-Cdk also triggers Cdc6's ubiquitination.  The Cdc6 protein is composed of three domains, an N-terminal AAA+ domain with Walker A and B, and Sensor-1 and -2 motifs. The central region contains a conserved nucleotide binding/ATPase domain and is a member of the ATPase superfamily. The C-terminal domain (Cdc6_C) is a conserved winged-helix domain that possibly mediates protein-protein interactions or direct DNA interactions. Cdc6 is conserved in eukaryotes, and related genes are found in Archaea. The winged helix fold structure of Cdc6_C is similar to the structures of other eukaryotic replication initiators without apparent sequence similarity."
Q#24017 - 	CGI_10013029	superfamily	247743	21	71	0.000418847	38.3497	cl17189	AAA superfamily	N	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#24018 - 	CGI_10013030	superfamily	241900	227	536	5.03E-77	248.372	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#24020 - 	CGI_10013032	superfamily	241610	10	63	2.02E-13	58.8006	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#24022 - 	CGI_10001355	superfamily	243161	4	69	9.02E-06	41.9962	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#24028 - 	CGI_10001842	superfamily	241578	11	181	1.26E-06	47.1754	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24029 - 	CGI_10001843	superfamily	190706	28	240	5.09E-21	92.0788	cl04201	Glyco_hydro_79n superfamily	 - 	 - 	"Glycosyl hydrolase family 79, N-terminal domain; Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment. Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesised as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form. Experimental evidence suggests that heparanase may facilitate both tumour cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity."
Q#24029 - 	CGI_10001843	superfamily	190706	292	322	0.00358929	37.7657	cl04201	Glyco_hydro_79n superfamily	N	 - 	"Glycosyl hydrolase family 79, N-terminal domain; Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment. Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesised as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form. Experimental evidence suggests that heparanase may facilitate both tumour cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity."
Q#24032 - 	CGI_10001846	superfamily	247866	3	133	4.30E-26	100.605	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#24034 - 	CGI_10014237	superfamily	216152	39	321	1.29E-49	170.958	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#24035 - 	CGI_10014238	superfamily	241637	18	76	4.28E-07	48.0734	cl00146	TFIIS_I superfamily	 - 	 - 	N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Q#24035 - 	CGI_10014238	superfamily	219215	548	634	4.60E-21	89.704	cl06096	Elongin_A superfamily	 - 	 - 	"RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin."
Q#24036 - 	CGI_10014239	superfamily	242156	1	62	7.44E-29	100.171	cl00869	PTH2_family superfamily	N	 - 	"Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes."
Q#24037 - 	CGI_10014240	superfamily	248011	386	471	0.000445352	39.3566	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#24038 - 	CGI_10014241	superfamily	243069	266	317	9.89E-14	67.9426	cl02525	Band_7 superfamily	C	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24039 - 	CGI_10014242	superfamily	243069	60	275	1.41E-86	260.542	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24040 - 	CGI_10014243	superfamily	243069	31	246	9.11E-80	245.52	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24040 - 	CGI_10014243	superfamily	243069	250	345	1.00E-28	111.085	cl02525	Band_7 superfamily	N	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24041 - 	CGI_10014244	superfamily	243069	58	272	4.36E-84	253.994	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24042 - 	CGI_10014245	superfamily	241619	27	98	1.20E-09	54.3981	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#24042 - 	CGI_10014245	superfamily	241619	289	351	1.57E-08	50.9313	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#24042 - 	CGI_10014245	superfamily	241619	106	178	4.22E-08	49.7757	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#24042 - 	CGI_10014245	superfamily	241619	205	267	0.00131641	36.6789	cl00112	PAN_APPLE superfamily	N	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#24043 - 	CGI_10014246	superfamily	241571	1	108	4.54E-24	96.3274	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24043 - 	CGI_10014246	superfamily	241571	114	188	6.46E-16	73.6006	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24044 - 	CGI_10014247	superfamily	247725	122	215	4.16E-15	72.2501	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24044 - 	CGI_10014247	superfamily	247725	15	117	3.25E-06	46.1269	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24045 - 	CGI_10014248	superfamily	148425	65	238	1.63E-13	67.4734	cl06049	NPDC1 superfamily	N	 - 	Neural proliferation differentiation control-1 protein (NPDC1); This family consists of several neural proliferation differentiation control-1 (NPDC1) proteins. NPDC1 plays a role in the control of neural cell proliferation and differentiation. It has been suggested that NPDC1 may be involved in the development of several secretion glands. This family also contains the C-terminal region of the C. elegans protein CAB-1 which is known to interact with AEX-3.
Q#24046 - 	CGI_10014249	superfamily	248281	38	122	1.72E-15	70.7623	cl17727	GT1 superfamily	 - 	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#24047 - 	CGI_10014250	superfamily	245864	76	438	3.24E-69	229.087	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#24048 - 	CGI_10014251	superfamily	245864	27	495	8.26E-101	313.061	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#24049 - 	CGI_10014252	superfamily	245847	237	394	3.33E-35	132.091	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#24049 - 	CGI_10014252	superfamily	245814	612	669	1.83E-05	44.0171	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24049 - 	CGI_10014252	superfamily	245814	517	592	0.0080258	35.5427	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24049 - 	CGI_10014252	superfamily	245814	706	769	2.34E-09	55.1055	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24051 - 	CGI_10014254	superfamily	243077	282	336	1.67E-20	83.7489	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#24051 - 	CGI_10014254	superfamily	242232	3	50	7.69E-12	59.8792	cl00984	TM2 superfamily	 - 	 - 	"TM2 domain; This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts."
Q#24052 - 	CGI_10014255	superfamily	247724	22	178	2.22E-58	182.656	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24053 - 	CGI_10014256	superfamily	247683	10	60	1.24E-06	46.6871	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#24053 - 	CGI_10014256	superfamily	219574	514	694	2.67E-29	116.227	cl06698	DC_STAMP superfamily	 - 	 - 	"DC-STAMP-like protein; This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family."
Q#24053 - 	CGI_10014256	superfamily	221781	170	256	0.00559776	38.3308	cl15101	FUSC-like superfamily	C	 - 	FUSC-like inner membrane protein yccS; This family has similarities to the fusaric acid resistance protein family. The proteins are lodged in the inner membrane.
Q#24054 - 	CGI_10014257	superfamily	243069	52	232	2.05E-08	51.2144	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#24056 - 	CGI_10014259	superfamily	247905	248	359	5.76E-11	59.9441	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#24056 - 	CGI_10014259	superfamily	247805	38	183	7.41E-10	56.5768	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#24058 - 	CGI_10014261	superfamily	243016	47	174	5.44E-42	139.388	cl02384	NOT2_3_5 superfamily	 - 	 - 	"NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5."
Q#24061 - 	CGI_10014264	superfamily	241578	51	207	1.13E-20	91.5076	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24063 - 	CGI_10014266	superfamily	241550	17	70	8.16E-28	106.711	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#24064 - 	CGI_10014267	superfamily	241550	1	223	1.17E-81	249.423	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#24066 - 	CGI_10014269	superfamily	241600	197	349	7.48E-48	162.41	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24066 - 	CGI_10014269	superfamily	241600	74	193	2.81E-35	128.897	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24067 - 	CGI_10006828	superfamily	246918	147	206	3.25E-10	54.9003	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24067 - 	CGI_10006828	superfamily	246918	94	141	2.16E-05	41.0331	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24068 - 	CGI_10006829	superfamily	248097	63	186	3.16E-27	100.803	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24068 - 	CGI_10006829	superfamily	217473	13	64	0.000138655	40.041	cl03978	Mab-21 superfamily	NC	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#24070 - 	CGI_10024664	superfamily	114259	12	194	7.39E-70	212.975	cl05211	DUF758 superfamily	 - 	 - 	"Domain of unknown function (DUF758); Family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor."
Q#24071 - 	CGI_10024665	superfamily	241566	1513	1561	7.51E-11	60.5836	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#24071 - 	CGI_10024665	superfamily	241754	157	668	0	769.06	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#24071 - 	CGI_10024665	superfamily	243095	1624	1812	1.43E-75	251.589	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#24071 - 	CGI_10024665	superfamily	241754	806	936	1.35E-54	205.128	cl00286	Motor_domain superfamily	N	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#24071 - 	CGI_10024665	superfamily	241645	31	126	4.50E-14	70.79	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#24071 - 	CGI_10024665	superfamily	210118	984	1005	0.000269484	40.7719	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#24073 - 	CGI_10024667	superfamily	241684	477	882	0	668.104	cl00205	HMG-CoA_reductase superfamily	 - 	 - 	"Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR) is a tightly regulated enzyme, which catalyzes the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. In mammals, this is the rate limiting committed step in cholesterol biosynthesis. Bacteria, such as Pseudomonas mevalonii, which rely solely on mevalonate for their carbon source, catalyze the reverse reaction, using an NAD-dependent HMGR to deacetylate mevalonate into 3-hydroxy-3-methylglutaryl-CoA. There are two classes of HMGR: class I enzymes which are found predominantly in eukaryotes and contain N-terminal membrane regions and class II enzymes which are found primarily in prokaryotes and are soluble as they lack the membrane region. With the exception of Archaeoglobus fulgidus, most archeae are assigned to class I, based on sequence similarity of the active site, even though they lack membrane regions. Yeast and human HMGR are divergent in their N-terminal regions, but are conserved in their active site. In contrast, human and bacterial HMGR differ in their active site architecture. While the prokaryotic enzyme is a homodimer, the eukaryotic enzyme is a homotetramer."
Q#24073 - 	CGI_10024667	superfamily	192997	119	249	7.42E-14	70.3031	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#24074 - 	CGI_10024668	superfamily	243066	1	99	1.19E-18	80.3541	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24074 - 	CGI_10024668	superfamily	198867	114	214	1.27E-11	60.818	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#24077 - 	CGI_10024671	superfamily	241564	138	204	2.09E-27	105.04	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#24077 - 	CGI_10024671	superfamily	241564	5	69	2.16E-13	65.7499	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#24077 - 	CGI_10024671	superfamily	247792	337	375	0.000800774	37.4252	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24077 - 	CGI_10024671	superfamily	247792	477	516	0.0019258	36.2696	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24079 - 	CGI_10024673	superfamily	205992	219	260	2.25E-16	70.7217	cl16421	DUF4187 superfamily	N	 - 	"Domain of unknown function (DUF4187); This family is found at the very C-terminus of proteins that carry a G-patch domain, pfam01585. The domain is short and cysteine-rich."
Q#24079 - 	CGI_10024673	superfamily	243107	67	111	3.02E-14	64.8738	cl02611	G-patch superfamily	 - 	 - 	"G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines."
Q#24084 - 	CGI_10024678	superfamily	247723	28	104	3.22E-54	167.023	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24086 - 	CGI_10024680	superfamily	217962	91	244	1.77E-17	76.9156	cl09558	TPD52 superfamily	N	 - 	"Tumour protein D52 family; The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other."
Q#24091 - 	CGI_10024685	superfamily	246925	85	300	1.60E-23	98.9669	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#24093 - 	CGI_10024687	superfamily	247858	139	324	2.44E-32	120.571	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#24094 - 	CGI_10024688	superfamily	243175	168	284	1.91E-62	195.493	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#24094 - 	CGI_10024688	superfamily	241832	97	153	2.19E-22	88.3959	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#24095 - 	CGI_10024689	superfamily	247918	1	215	5.29E-44	157.874	cl17364	PMT_2 superfamily	 - 	 - 	Dolichyl-phosphate-mannose-protein mannosyltransferase; This family contains members that are not captured by pfam02366.
Q#24095 - 	CGI_10024689	superfamily	197746	310	365	3.93E-09	53.4991	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#24095 - 	CGI_10024689	superfamily	197746	378	426	3.08E-06	45.4099	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#24095 - 	CGI_10024689	superfamily	197746	243	299	0.000458728	38.8615	cl02624	MIR superfamily	 - 	 - 	Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.  
Q#24096 - 	CGI_10024690	superfamily	243175	52	104	0.000129991	37.176	cl02776	GST_C_family superfamily	C	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#24096 - 	CGI_10024690	superfamily	241832	8	37	0.000429706	34.8531	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#24097 - 	CGI_10024691	superfamily	245598	934	1239	1.49E-176	528.511	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#24097 - 	CGI_10024691	superfamily	241570	610	717	6.48E-21	90.8481	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24097 - 	CGI_10024691	superfamily	241570	485	596	1.28E-16	78.1366	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24097 - 	CGI_10024691	superfamily	241570	177	298	8.37E-15	72.7438	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24098 - 	CGI_10024692	superfamily	207662	261	336	6.17E-32	119.144	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#24098 - 	CGI_10024692	superfamily	207662	174	241	8.21E-27	104.566	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#24098 - 	CGI_10024692	superfamily	245599	517	663	7.49E-16	75.8649	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#24099 - 	CGI_10024693	superfamily	247684	98	241	7.97E-07	47.1983	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24101 - 	CGI_10024695	superfamily	246962	85	368	2.93E-19	88.2343	cl15430	Nucleoside_tran superfamily	C	 - 	"Nucleoside transporter; This is a family of nucleoside transporters. In mammalian cells nucleoside transporters transport nucleoside across the plasma membrane and are essential for nucleotide synthesis via the salvage pathways for cells that lack their own de novo synthesis pathways. Also in this family is mouse and human nucleolar protein HNP36, a protein of unknown function; although it has been hypothesised to be a plasma membrane nucleoside transporter."
Q#24102 - 	CGI_10024696	superfamily	243092	8	231	5.71E-24	102.028	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24102 - 	CGI_10024696	superfamily	217837	442	549	1.30E-13	68.0029	cl04367	Utp12 superfamily	 - 	 - 	Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.
Q#24104 - 	CGI_10024698	superfamily	217210	687	1255	0	665.903	cl10595	Ald_Xan_dh_C2 superfamily	 - 	 - 	Molybdopterin-binding domain of aldehyde dehydrogenase; Molybdopterin-binding domain of aldehyde dehydrogenase.  
Q#24104 - 	CGI_10024698	superfamily	243326	573	679	7.88E-42	150.861	cl03161	Ald_Xan_dh_C superfamily	 - 	 - 	"Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain.  "
Q#24104 - 	CGI_10024698	superfamily	201981	72	146	6.65E-33	123.745	cl08334	Fer2_2 superfamily	 - 	 - 	[2Fe-2S] binding domain; [2Fe-2S] binding domain.  
Q#24104 - 	CGI_10024698	superfamily	244932	406	508	5.58E-25	102.194	cl08390	CO_deh_flav_C superfamily	 - 	 - 	CO dehydrogenase flavoprotein C-terminal domain; CO dehydrogenase flavoprotein C-terminal domain.  
Q#24105 - 	CGI_10024699	superfamily	241777	9	167	0.00107303	38.4356	cl00316	Cation_efflux superfamily	C	 - 	"Cation efflux family; Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells."
Q#24106 - 	CGI_10024700	superfamily	243100	285	338	5.07E-07	46.0677	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#24107 - 	CGI_10024701	superfamily	218899	129	281	3.57E-25	100.818	cl05570	DUF947 superfamily	 - 	 - 	Domain of unknown function (DUF947); Family of eukaryotic proteins with unknown function.
Q#24107 - 	CGI_10024701	superfamily	218899	297	423	4.57E-17	78.0916	cl05570	DUF947 superfamily	 - 	 - 	Domain of unknown function (DUF947); Family of eukaryotic proteins with unknown function.
Q#24108 - 	CGI_10024702	superfamily	243092	21	346	7.02E-19	83.9236	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24109 - 	CGI_10024703	superfamily	247912	9	264	1.70E-23	102.58	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#24109 - 	CGI_10024703	superfamily	216290	908	1026	5.36E-21	91.1957	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#24109 - 	CGI_10024703	superfamily	217685	1041	1122	9.51E-12	64.2776	cl04225	Cu2_monoox_C superfamily	C	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#24109 - 	CGI_10024703	superfamily	247912	373	482	1.33E-08	56.7409	cl17358	Beta-lactamase superfamily	C	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#24109 - 	CGI_10024703	superfamily	247912	510	645	7.77E-05	44.7997	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#24112 - 	CGI_10024706	superfamily	247746	14	124	0.00354878	36.4674	cl17192	ATP-synt_B superfamily	 - 	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#24113 - 	CGI_10024707	superfamily	110440	395	419	0.00949093	33.9205	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#24114 - 	CGI_10008451	superfamily	243072	70	200	2.34E-15	74.3422	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24114 - 	CGI_10008451	superfamily	149414	214	276	1.06E-21	90.7938	cl07091	TRP_2 superfamily	 - 	 - 	Transient receptor ion channel II; This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023).
Q#24115 - 	CGI_10008452	superfamily	112708	134	224	9.47E-19	78.2323	cl04323	Sec20 superfamily	 - 	 - 	Sec20; Sec20 is a membrane glycoprotein associated with secretory pathway.
Q#24116 - 	CGI_10008453	superfamily	240667	18	198	3.90E-52	176.329	cl18929	TIN2_N superfamily	 - 	 - 	"N-terminal domain of TRF-interacting nuclear factor 2; shelterin complex protein of telomeres; TIN2 is one of the six proteins of shelterin complex, which acts to protect telomeres from DNA damage repair machinery. TIN2 binds directly to TRF1 and TRF2 and stabilizes TRF2 complex-telomere binding by tethering it to the TRF1 complex. TIN2 binding to TRF2 is primarily via the TRF binding motif (TBM) region and the N-terminus, while the far C-terminal region has lower affinity. The TIN2 TBM, but not the N-terminal region, is involved in TIN2 binding to TRF1. Truncation of the TIN2 N-terminus in mouse results in telomere elongation, suggesting a negative regulatory function of this region. Three shelterin components (TRF1, TRF2, POT1) bind DNA and 3 components (TIN2, RAP1, TPP1) are recruited by these DNA binding factors. TRF1 activity at telomeres is regulated in part by selective ubiquitination and degradation. Ubiquitination of TRF1 is mediated by Fbx4, which binds TRF1 in the TRFH domain, via a small GTPase module. When bound to telomeres, TIN2 acts to protect TRF1 from SCF-Fbx4 mediated ubiquitination. F-box proteins act in substrate recognition as part of Skp1-Cul1-Rbx1-F- box (SCF) protein complexes. Tankyrase-mediated ADP-ribosylation releases TRF1 from telomeres, rendering them susceptible to ubiquitination and degradation, promoting telomere elongation. TIN2 also binds PIP1, which recruits POT1 to telomeres."
Q#24117 - 	CGI_10008454	superfamily	241874	842	1376	0	803.8	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24117 - 	CGI_10008454	superfamily	241600	1744	1961	2.39E-86	283.362	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24117 - 	CGI_10008454	superfamily	245213	1627	1663	1.10E-12	65.3506	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24117 - 	CGI_10008454	superfamily	245213	1589	1624	6.55E-10	57.2614	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24117 - 	CGI_10008454	superfamily	245213	1667	1701	9.79E-09	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24117 - 	CGI_10008454	superfamily	245213	1552	1586	8.56E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24117 - 	CGI_10008454	superfamily	245213	1703	1729	4.27E-05	43.3942	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24117 - 	CGI_10008454	superfamily	241874	429	690	1.74E-118	387.43	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24117 - 	CGI_10008454	superfamily	241874	270	428	2.41E-63	227.957	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24118 - 	CGI_10008455	superfamily	241578	25	184	1.14E-48	174.017	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24118 - 	CGI_10008455	superfamily	241578	213	379	8.97E-43	157.005	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24118 - 	CGI_10008455	superfamily	248289	3002	3065	0.00970296	37.1104	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#24121 - 	CGI_10001859	superfamily	247805	37	168	8.88E-07	44.6356	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#24123 - 	CGI_10001861	superfamily	248097	45	127	8.84E-13	60.7418	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24127 - 	CGI_10007048	superfamily	241554	716	852	1.58E-24	101.568	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#24129 - 	CGI_10007050	superfamily	247750	305	560	1.07E-134	412.068	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24129 - 	CGI_10007050	superfamily	247750	628	785	1.76E-72	246.432	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24129 - 	CGI_10007050	superfamily	247750	41	159	5.39E-55	192.097	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24129 - 	CGI_10007050	superfamily	202124	533	595	1.00E-10	59.098	cl08340	UBACT superfamily	 - 	 - 	Repeat in ubiquitin-activating (UBA) protein; Repeat in ubiquitin-activating (UBA) protein.  
Q#24130 - 	CGI_10007051	superfamily	110440	311	337	0.00126976	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#24131 - 	CGI_10007052	superfamily	247750	44	201	1.07E-76	241.039	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24133 - 	CGI_10007054	superfamily	247750	39	196	2.14E-78	244.891	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24133 - 	CGI_10007054	superfamily	247750	3	67	0.00104388	38.1293	cl17196	E1_enzyme_family superfamily	NC	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24136 - 	CGI_10007057	superfamily	247750	346	631	1.99E-155	465.611	cl17196	E1_enzyme_family superfamily	C	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24136 - 	CGI_10007057	superfamily	247750	33	173	1.45E-73	244.099	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24136 - 	CGI_10007057	superfamily	247750	699	856	4.86E-72	244.891	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24136 - 	CGI_10007057	superfamily	247750	269	311	1.63E-19	89.2489	cl17196	E1_enzyme_family superfamily	N	 - 	"Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS."
Q#24136 - 	CGI_10007057	superfamily	202124	605	666	2.63E-09	54.8608	cl08340	UBACT superfamily	 - 	 - 	Repeat in ubiquitin-activating (UBA) protein; Repeat in ubiquitin-activating (UBA) protein.  
Q#24137 - 	CGI_10007058	superfamily	217316	111	185	0.00107319	37.606	cl03832	DUF234 superfamily	 - 	 - 	Archaea bacterial proteins of unknown function; Archaea bacterial proteins of unknown function.  
Q#24137 - 	CGI_10007058	superfamily	110440	481	507	0.0038662	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#24138 - 	CGI_10005341	superfamily	217249	182	325	3.72E-81	245.994	cl03742	Prp18 superfamily	 - 	 - 	"Prp18 domain; The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles."
Q#24138 - 	CGI_10005341	superfamily	207680	75	104	6.61E-09	51.2047	cl02632	PRP4 superfamily	 - 	 - 	pre-mRNA processing factor 4 (PRP4) like; This small domain is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing.
Q#24140 - 	CGI_10005343	superfamily	243212	179	294	8.11E-10	55.4278	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#24141 - 	CGI_10005344	superfamily	241613	2058	2092	3.56E-09	56.061	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2861	2894	5.03E-09	55.6758	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	384	417	8.42E-09	54.9054	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2775	2807	9.68E-09	54.5202	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	302	336	1.04E-08	54.5202	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2099	2133	3.41E-08	52.9794	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2947	2981	6.25E-08	52.209	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	262	293	1.26E-07	51.4386	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2817	2851	1.68E-07	51.0534	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	183	217	1.93E-07	51.0534	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2569	2603	2.11E-07	50.6682	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2527	2564	2.16E-07	50.6682	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2904	2936	9.89E-07	48.7422	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	1730	1762	4.15E-06	47.2014	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	2691	2724	5.24E-06	46.8162	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	1810	1846	5.29E-06	46.8162	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	341	376	0.000128418	42.579	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	245213	546	579	0.000146077	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24141 - 	CGI_10005344	superfamily	241613	2024	2049	0.000291531	41.4234	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	241613	468	501	0.0037813	38.3418	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24141 - 	CGI_10005344	superfamily	214531	1571	1613	3.40E-12	64.9304	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	745	787	1.37E-11	63.0044	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	215683	721	762	3.69E-11	61.8023	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#24141 - 	CGI_10005344	superfamily	214531	2376	2416	1.07E-09	57.6116	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	981	1015	3.22E-09	56.0709	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	2286	2328	8.67E-09	54.9153	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	658	697	8.47E-08	52.2189	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	215683	1548	1588	5.56E-07	49.4759	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#24141 - 	CGI_10005344	superfamily	215683	2350	2391	6.31E-07	49.4759	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#24141 - 	CGI_10005344	superfamily	214531	24	59	1.29E-06	48.7521	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	3233	3274	2.14E-06	47.9817	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	3152	3182	4.59E-06	46.8261	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	1401	1442	5.42E-06	46.8261	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	3186	3230	6.84E-06	46.4409	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	2246	2284	1.80E-05	45.2853	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	221695	2156	2179	9.30E-05	42.8274	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#24141 - 	CGI_10005344	superfamily	221695	3008	3031	0.000212083	42.057	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#24141 - 	CGI_10005344	superfamily	214531	1498	1528	0.000242004	41.8185	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	214531	2417	2458	0.002686	38.7369	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24141 - 	CGI_10005344	superfamily	245213	2176	2216	0.00348874	38.382	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24141 - 	CGI_10005344	superfamily	245213	3028	3060	0.00397568	38.382	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24141 - 	CGI_10005344	superfamily	215683	633	673	0.00582345	37.9199	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#24141 - 	CGI_10005344	superfamily	245213	2134	2169	0.00919747	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24142 - 	CGI_10005345	superfamily	241613	9	43	2.43E-09	53.7498	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24142 - 	CGI_10005345	superfamily	245213	125	156	0.00151249	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24142 - 	CGI_10005345	superfamily	214531	278	323	3.48E-09	53.3745	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24142 - 	CGI_10005345	superfamily	214531	326	366	1.42E-06	46.0557	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24142 - 	CGI_10005345	superfamily	214531	235	271	4.68E-05	41.4333	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24142 - 	CGI_10005345	superfamily	215683	209	250	0.000291329	39.0755	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#24142 - 	CGI_10005345	superfamily	241613	47	80	0.000628272	37.9981	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24142 - 	CGI_10005345	superfamily	214531	565	600	0.00187236	36.8109	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24142 - 	CGI_10005345	superfamily	214531	368	405	0.00425452	35.6553	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24143 - 	CGI_10005346	superfamily	215821	37	129	3.51E-42	140.453	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#24145 - 	CGI_10006969	superfamily	241613	51	86	3.42E-05	39.1122	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24146 - 	CGI_10006970	superfamily	247724	18	188	7.77E-54	171.958	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24147 - 	CGI_10006971	superfamily	246597	1	112	4.09E-47	159.361	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#24147 - 	CGI_10006971	superfamily	145792	202	227	2.88E-07	45.3295	cl10597	Antistasin superfamily	 - 	 - 	Antistasin family; Members of this family are inhibitors of trypsin family proteases. This domain is highly disulphide bonded. The domain is also found in some large extracellular proteins in multiple copies.
Q#24156 - 	CGI_10021509	superfamily	220695	37	238	8.74E-06	45.2623	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#24157 - 	CGI_10021510	superfamily	202351	289	402	4.86E-17	77.9223	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#24157 - 	CGI_10021510	superfamily	202351	32	155	1.21E-10	59.0476	cl03662	Na_Pi_cotrans superfamily	C	 - 	Na+/Pi-cotransporter; This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule.
Q#24158 - 	CGI_10021511	superfamily	245206	150	217	9.23E-11	58.064	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#24159 - 	CGI_10021512	superfamily	148662	3	81	3.54E-47	147.08	cl06288	SF3b10 superfamily	 - 	 - 	Splicing factor 3B subunit 10 (SF3b10); This family consists of several eukaryotic splicing factor 3B subunit 10 (SF3b10) proteins. SF3b10 is a 10 kDa subunit of the splicing factor SF3b. SF3b associates with the splicing factor SF3a and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex. SF3b10 and SF3b14b are also thought to facilitate the interaction of U2 with the branch site.
Q#24160 - 	CGI_10021513	superfamily	217473	96	320	4.91E-28	113.999	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#24161 - 	CGI_10021514	superfamily	201217	284	333	1.87E-11	59.4616	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#24161 - 	CGI_10021514	superfamily	201217	386	437	6.68E-11	57.9208	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#24161 - 	CGI_10021514	superfamily	201217	110	159	6.75E-08	49.0612	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#24161 - 	CGI_10021514	superfamily	201217	59	107	1.48E-06	45.2092	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#24161 - 	CGI_10021514	superfamily	201217	162	211	4.57E-06	44.0536	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#24161 - 	CGI_10021514	superfamily	201217	337	383	5.61E-05	40.5868	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#24161 - 	CGI_10021514	superfamily	205718	198	227	0.000824553	37.0846	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#24166 - 	CGI_10021519	superfamily	241597	2	64	6.99E-07	42.9912	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#24167 - 	CGI_10021520	superfamily	241874	748	1261	0	563.258	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24168 - 	CGI_10021521	superfamily	241874	24	576	0	554.013	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24170 - 	CGI_10021523	superfamily	241599	127	181	3.78E-21	84.2172	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#24170 - 	CGI_10021523	superfamily	146451	248	262	0.00271964	34.6423	cl08404	OAR superfamily	 - 	 - 	OAR domain; OAR domain.  
Q#24172 - 	CGI_10021525	superfamily	243066	7	62	3.98E-09	53.7109	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24172 - 	CGI_10021525	superfamily	219619	362	419	5.66E-08	49.8988	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#24173 - 	CGI_10021526	superfamily	219619	324	379	9.71E-08	49.1284	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#24173 - 	CGI_10021526	superfamily	243066	1	27	0.000959056	37.1473	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24174 - 	CGI_10021527	superfamily	198867	284	383	5.41E-20	86.6264	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#24174 - 	CGI_10021527	superfamily	243066	168	275	1.29E-15	73.8057	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24174 - 	CGI_10021527	superfamily	243146	616	662	1.38E-09	54.975	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#24174 - 	CGI_10021527	superfamily	243146	578	627	2.73E-06	45.6271	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#24175 - 	CGI_10021528	superfamily	247684	7	436	9.55E-92	290.333	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24176 - 	CGI_10021529	superfamily	100116	271	319	1.07E-10	58.5108	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#24176 - 	CGI_10021529	superfamily	100116	377	425	1.77E-10	58.1256	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#24176 - 	CGI_10021529	superfamily	100116	456	504	2.13E-10	57.7404	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#24176 - 	CGI_10021529	superfamily	100116	324	372	1.47E-09	55.4292	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#24176 - 	CGI_10021529	superfamily	100116	216	261	6.52E-06	44.6436	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#24176 - 	CGI_10021529	superfamily	100116	661	711	0.00825406	35.3988	cl10082	NF-X1-zinc-finger superfamily	 - 	 - 	"Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms."
Q#24177 - 	CGI_10021530	superfamily	241594	249	600	2.95E-146	429.678	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#24178 - 	CGI_10021531	superfamily	247805	517	656	1.08E-26	108.579	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#24178 - 	CGI_10021531	superfamily	247905	791	922	4.38E-26	106.168	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#24178 - 	CGI_10021531	superfamily	247792	215	260	6.41E-12	62.8484	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24178 - 	CGI_10021531	superfamily	244870	47	122	1.06E-10	60.9926	cl08238	PA superfamily	N	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#24178 - 	CGI_10021531	superfamily	247804	1163	1202	5.16E-06	45.6442	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#24178 - 	CGI_10021531	superfamily	220113	1217	1327	2.41E-48	169.684	cl07653	SLIDE superfamily	 - 	 - 	"SLIDE; The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (pfam00249) repeats or homeodomains."
Q#24178 - 	CGI_10021531	superfamily	220112	1061	1139	1.06E-18	84.2504	cl07652	HAND superfamily	C	 - 	"HAND; The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein."
Q#24179 - 	CGI_10021532	superfamily	243555	20	182	1.23E-15	70.4978	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#24181 - 	CGI_10021534	superfamily	243072	38	82	2.21E-11	60.0898	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24183 - 	CGI_10021536	superfamily	241782	267	660	2.18E-130	391.181	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#24183 - 	CGI_10021536	superfamily	241659	7	46	0.00500433	35.9587	cl00175	alpha-crystallin-Hsps_p23-like superfamily	C	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#24185 - 	CGI_10021538	superfamily	110440	213	239	0.00199074	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#24186 - 	CGI_10021540	superfamily	241563	68	109	4.40E-07	47.0888	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24189 - 	CGI_10000776	superfamily	242881	8	184	6.60E-116	334.156	cl02099	CK_II_beta superfamily	 - 	 - 	Casein kinase II regulatory subunit; Casein kinase II regulatory subunit.  
Q#24197 - 	CGI_10014699	superfamily	241563	35	66	0.00940683	33.6068	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24198 - 	CGI_10014700	superfamily	241570	250	359	6.91E-17	77.7514	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24199 - 	CGI_10014701	superfamily	247723	43	169	3.85E-45	149.423	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24199 - 	CGI_10014701	superfamily	245716	172	196	0.000651843	36.4533	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#24199 - 	CGI_10014701	superfamily	245716	13	39	0.00148981	35.2267	cl11592	zf-CCCH superfamily	 - 	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#24200 - 	CGI_10014702	superfamily	241546	21	108	4.23E-27	106.591	cl00011	PLAT superfamily	N	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#24201 - 	CGI_10014703	superfamily	147799	1	74	1.50E-08	46.4219	cl05422	Apc13p superfamily	 - 	 - 	Apc13p protein; The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc13p.
Q#24202 - 	CGI_10014704	superfamily	241739	82	286	1.81E-58	202.411	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#24202 - 	CGI_10014704	superfamily	241739	688	817	5.24E-49	175.832	cl00268	class_II_aaRS-like_core superfamily	N	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#24202 - 	CGI_10014704	superfamily	241546	602	686	6.28E-23	95.8056	cl00011	PLAT superfamily	C	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#24202 - 	CGI_10014704	superfamily	245205	2	67	4.95E-11	60.2717	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#24202 - 	CGI_10014704	superfamily	243086	481	521	2.42E-09	54.3034	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#24206 - 	CGI_10014709	superfamily	241698	102	320	1.43E-79	244.481	cl00220	cysteine_hydrolases superfamily	 - 	 - 	"Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function."
Q#24206 - 	CGI_10014709	superfamily	247856	24	88	3.64E-09	52.5501	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#24207 - 	CGI_10014710	superfamily	247792	6	59	1.22E-09	54.7592	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24207 - 	CGI_10014710	superfamily	128778	160	278	0.000285129	39.9407	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#24207 - 	CGI_10014710	superfamily	241563	105	129	0.0040291	35.918	cl00034	BBOX superfamily	C	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24209 - 	CGI_10014712	superfamily	221425	1240	1533	4.84E-80	267.694	cl13536	Nup96 superfamily	 - 	 - 	Nuclear protein 96; Nup96 (often known by the name of its yeast homolog Nup145C) is part of the Nup84 heptameric complex in the nuclear pore complex. Nup96 complexes with Sec13 in the middle of the heptamer. The function of the heptamer is to coat the curvature of the nuclear pore complex between the inner and outer nuclear membranes. Nup96 is predicted to be an alpha helical solenoid. The interaction between Nup96 and Sec13 is the point of curvature in the heptameric complex.
Q#24209 - 	CGI_10014712	superfamily	202886	706	846	1.99E-56	193.979	cl04399	Nucleoporin2 superfamily	 - 	 - 	Nucleoporin autopeptidase; Nucleoporin autopeptidase.  
Q#24209 - 	CGI_10014712	superfamily	222274	110	177	1.56E-05	45.1696	cl18658	Nucleoporin_FG superfamily	C	 - 	"Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145."
Q#24209 - 	CGI_10014712	superfamily	222274	226	323	0.00766887	36.6952	cl18658	Nucleoporin_FG superfamily	 - 	 - 	"Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145."
Q#24210 - 	CGI_10014713	superfamily	243088	53	161	4.97E-09	53.566	cl02563	PX_domain superfamily	 - 	 - 	"The Phox Homology domain, a phosphoinositide binding module; The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting."
Q#24210 - 	CGI_10014713	superfamily	245835	250	294	1.25E-06	47.1161	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#24211 - 	CGI_10014714	superfamily	245206	4	255	6.75E-90	269.281	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#24212 - 	CGI_10014715	superfamily	241884	47	242	8.04E-107	325.294	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#24212 - 	CGI_10014715	superfamily	245595	405	696	3.19E-101	314.459	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#24212 - 	CGI_10014715	superfamily	216944	309	381	1.45E-10	58.3627	cl03496	Propep_M14 superfamily	 - 	 - 	"Carboxypeptidase activation peptide; Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme."
Q#24213 - 	CGI_10014716	superfamily	217293	37	235	1.24E-36	133.912	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#24213 - 	CGI_10014716	superfamily	202474	242	297	7.32E-05	42.6409	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#24214 - 	CGI_10000941	superfamily	245670	86	267	1.01E-60	198.574	cl11519	DENN superfamily	 - 	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#24214 - 	CGI_10000941	superfamily	208095	304	369	8.54E-17	74.9375	cl04084	dDENN superfamily	 - 	 - 	dDENN domain; This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
Q#24214 - 	CGI_10000941	superfamily	243635	4	79	4.29E-15	70.8264	cl04085	uDENN superfamily	 - 	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#24215 - 	CGI_10025581	superfamily	248097	77	181	2.83E-14	65.7494	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24218 - 	CGI_10025584	superfamily	245847	2	92	1.42E-07	44.855	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#24220 - 	CGI_10025586	superfamily	203031	105	164	5.33E-07	46.1672	cl04548	FLYWCH superfamily	 - 	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#24221 - 	CGI_10025587	superfamily	247856	106	159	0.000367049	37.1421	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#24222 - 	CGI_10025588	superfamily	244539	110	334	3.53E-36	132.814	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#24222 - 	CGI_10025588	superfamily	203841	250	423	6.98E-25	99.3344	cl17716	NAD_binding_6 superfamily	 - 	 - 	Ferric reductase NAD binding domain; Ferric reductase NAD binding domain.  
Q#24222 - 	CGI_10025588	superfamily	242267	21	72	1.15E-07	49.596	cl01043	Ferric_reduct superfamily	N	 - 	"Ferric reductase like transmembrane component; This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease."
Q#24225 - 	CGI_10025591	superfamily	248097	128	256	5.38E-19	80.0018	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24227 - 	CGI_10025593	superfamily	241760	287	331	2.49E-15	72.2925	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#24227 - 	CGI_10025593	superfamily	243157	27	83	1.25E-08	53.6965	cl02720	PB1 superfamily	N	 - 	"The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants."
Q#24228 - 	CGI_10025594	superfamily	247044	7	121	1.85E-50	172.793	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24228 - 	CGI_10025594	superfamily	247044	619	716	5.72E-39	140.51	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24228 - 	CGI_10025594	superfamily	247044	391	491	1.54E-38	139.328	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24228 - 	CGI_10025594	superfamily	247044	521	604	1.03E-29	114.251	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24228 - 	CGI_10025594	superfamily	247044	252	350	4.97E-29	112.343	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24228 - 	CGI_10025594	superfamily	247044	134	207	1.81E-26	105.012	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24228 - 	CGI_10025594	superfamily	207613	784	819	4.47E-08	50.7805	cl02491	VHP superfamily	 - 	 - 	Villin headpiece domain; Villin headpiece domain.  
Q#24230 - 	CGI_10025596	superfamily	243077	623	682	1.03E-19	84.1341	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#24230 - 	CGI_10025596	superfamily	243034	505	595	2.26E-16	75.8795	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#24230 - 	CGI_10025596	superfamily	243034	297	369	1.37E-10	58.9308	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#24230 - 	CGI_10025596	superfamily	243034	340	484	7.38E-08	50.8416	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#24230 - 	CGI_10025596	superfamily	241547	37	289	3.59E-94	295.862	cl00012	alpha_CA superfamily	 - 	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#24233 - 	CGI_10025599	superfamily	217293	1	38	1.30E-06	44.5459	cl03788	Neur_chan_LBD superfamily	NC	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#24234 - 	CGI_10025600	superfamily	217293	315	509	5.59E-38	140.846	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#24234 - 	CGI_10025600	superfamily	217293	33	222	1.79E-32	125.438	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#24234 - 	CGI_10025600	superfamily	202474	517	612	2.44E-05	44.9521	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#24234 - 	CGI_10025600	superfamily	202474	230	280	0.00473856	38.0185	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#24235 - 	CGI_10025601	superfamily	248097	155	283	5.60E-13	63.4382	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24236 - 	CGI_10025602	superfamily	247724	7	173	7.95E-75	224.714	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24237 - 	CGI_10025603	superfamily	243072	74	194	5.75E-22	88.5946	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24237 - 	CGI_10025603	superfamily	243073	230	275	1.64E-06	43.9981	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#24238 - 	CGI_10025604	superfamily	189332	49	283	1.59E-76	252.623	cl14874	Luminal_IRE1_like superfamily	 - 	 - 	"The Luminal domain, a dimerization domain, of Inositol-requiring protein 1-like proteins; The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), eukaryotic translation Initiation Factor 2-Alpha Kinase 3  (EIF2AK3), and similar proteins. IRE1 and EIF2AK3 are serine/threonine protein kinases (STKs) and are type I transmembrane proteins that are localized in the endoplasmic reticulum (ER). They are kinase receptors that are activated through the release of BiP, a chaperone bound to their luminal domains under unstressed conditions. This results in dimerization through their luminal domains, allowing trans-autophosphorylation of their kinase domains and activation. They play roles in the signaling of the unfolded protein response (UPR), which is activated when protein misfolding is detected in the ER in order to decrease the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), contains an endoribonuclease domain in its cytoplasmic side and acts as an ER stress sensor. It is the oldest and most conserved component of the UPR in eukaryotes. Its activation results in the cleavage of its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans, promoting a splicing event that enables translation into a transcription factor which activates the UPR. EIF2AK3, also called PKR-like Endoplasmic Reticulum Kinase (PERK), phosphorylates the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. It functions as the central regulator of translational control during the UPR pathway. In addition to the eIF-2 alpha subunit, EIF2AK3 also phosphorylates Nrf2, a leucine zipper transcription factor which regulates cellular redox status and promotes cell survival during the UPR."
Q#24238 - 	CGI_10025604	superfamily	246937	745	870	2.79E-62	206.668	cl15368	RNase_Ire1_like superfamily	 - 	 - 	"RNase domain (also known as the kinase extension nuclease domain) of Ire1 and RNase L; This RNase domain is found in the multi-functional protein Ire1; Ire1 also contains a type I transmembrane serine/threonine protein kinase (STK) domain, and a Luminal dimerization domain. Ire1 is essential for the endoplasmic reticulum (ER) unfolded protein response (UPR). The UPR is activated when protein misfolding is detected in the ER in order to reduce the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1 acts as an ER stress sensor; IRE1 dimerizes through its N-terminal luminal domain and forms oligomers, promoting trans-autophosphorylation by its cytosolic kinase domain which stimulates its endoribonuclease (RNase) activity and results in the cleavage of its mRNA substrate, Hac1 in yeast and Xbp1 in metazoans, thus promoting a splicing event that enables translation into a transcription factor which activates the UPR. This RNase domain is also found in Ribonuclease L (RNase L), sometimes referred to as the 2-5A-dependent RNase. RNase L is a highly regulated, latent endoribonuclease widely expressed in most mammalian tissues. It is involved in the mediation of the antiviral and pro-apoptotic activities of the interferon-inducible 2-5A system; the interferon (IFN)-inducible 2'-5'-oligoadenylate synthetase (OAS)/RNase L pathway blocks infections by certain types of viruses through cleavage of viral and cellular single-stranded RNA. RNase L has been shown to have an impact on the pathogenesis of prostate cancer; the RNase L gene, RNASEL, has been identified as a strong candidate for the hereditary prostate cancer 1 (HPC1) allele."
Q#24238 - 	CGI_10025604	superfamily	245201	490	739	1.47E-47	168.954	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24240 - 	CGI_10025606	superfamily	189332	58	84	1.80E-06	43.0745	cl14874	Luminal_IRE1_like superfamily	C	 - 	"The Luminal domain, a dimerization domain, of Inositol-requiring protein 1-like proteins; The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), eukaryotic translation Initiation Factor 2-Alpha Kinase 3  (EIF2AK3), and similar proteins. IRE1 and EIF2AK3 are serine/threonine protein kinases (STKs) and are type I transmembrane proteins that are localized in the endoplasmic reticulum (ER). They are kinase receptors that are activated through the release of BiP, a chaperone bound to their luminal domains under unstressed conditions. This results in dimerization through their luminal domains, allowing trans-autophosphorylation of their kinase domains and activation. They play roles in the signaling of the unfolded protein response (UPR), which is activated when protein misfolding is detected in the ER in order to decrease the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), contains an endoribonuclease domain in its cytoplasmic side and acts as an ER stress sensor. It is the oldest and most conserved component of the UPR in eukaryotes. Its activation results in the cleavage of its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans, promoting a splicing event that enables translation into a transcription factor which activates the UPR. EIF2AK3, also called PKR-like Endoplasmic Reticulum Kinase (PERK), phosphorylates the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. It functions as the central regulator of translational control during the UPR pathway. In addition to the eIF-2 alpha subunit, EIF2AK3 also phosphorylates Nrf2, a leucine zipper transcription factor which regulates cellular redox status and promotes cell survival during the UPR."
Q#24241 - 	CGI_10025607	superfamily	192522	625	714	7.42E-27	106.103	cl10974	DUF2404 superfamily	 - 	 - 	Putative integral membrane protein conserved region (DUF2404); This domain is conserved from plants to humans. The function is not known.
Q#24242 - 	CGI_10025608	superfamily	221329	31	183	1.85E-40	137.53	cl13389	DUF3456 superfamily	 - 	 - 	"TLR4 regulator and MIR-interacting MSAP; This family of proteins, found from plants to humans, is PRAT4 (A and B), a Protein Associated with Toll-like receptor 4. The Toll family of receptors - TLRs - plays an essential role in innate recognition of microbial products, the first line of defence against bacterial infection. PRAT4A influences the subcellular distribution and the strength of TLR responses and alters the relative activity of each TLR. PRAT4B regulates TLR4 trafficking to the cell surface and the extent of its expression there. TLR4 recognizes lipopolysaccharide (LPS), one of the most immuno-stimulatory glycolipids constituting the outer membrane of the Gram-negative bacteria. This family has also been described as a SAP-like MIR-interacting protein family."
Q#24243 - 	CGI_10025609	superfamily	243092	45	354	2.15E-18	82.768	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24244 - 	CGI_10025610	superfamily	243507	125	322	7.86E-86	270.38	cl03728	Alpha_kinase superfamily	 - 	 - 	"Alpha-kinase family; This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains."
Q#24245 - 	CGI_10025611	superfamily	247723	1198	1252	0.00197591	39.2105	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24246 - 	CGI_10025612	superfamily	243072	324	379	4.53E-09	55.8526	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24246 - 	CGI_10025612	superfamily	241584	458	543	4.00E-08	52.4987	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#24246 - 	CGI_10025612	superfamily	241645	1116	1203	2.54E-06	46.9076	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#24248 - 	CGI_10025614	superfamily	220679	174	247	4.13E-09	54.6405	cl18567	Methyltransf_16 superfamily	C	 - 	Putative methyltransferase; Putative methyltransferase.  
Q#24248 - 	CGI_10025614	superfamily	220679	337	417	0.000721822	38.8473	cl18567	Methyltransf_16 superfamily	N	 - 	Putative methyltransferase; Putative methyltransferase.  
Q#24249 - 	CGI_10025615	superfamily	247723	111	134	1.78E-10	54.8691	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24250 - 	CGI_10025616	superfamily	198867	101	181	3.01E-10	57.5535	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#24250 - 	CGI_10025616	superfamily	243066	2	75	4.53E-08	51.0789	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24250 - 	CGI_10025616	superfamily	243146	313	359	0.00193573	36.6574	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#24251 - 	CGI_10025617	superfamily	240425	1	156	3.87E-59	187.331	cl18912	PTZ00464 superfamily	C	 - 	SNF-7-like protein; Provisional
Q#24252 - 	CGI_10025618	superfamily	241644	551	690	4.62E-49	168.92	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#24252 - 	CGI_10025618	superfamily	248054	12	78	4.71E-08	50.9336	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#24252 - 	CGI_10025618	superfamily	248054	223	269	0.00511682	36.8045	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#24253 - 	CGI_10025619	superfamily	217046	37	174	1.18E-09	53.3512	cl03599	Reticulon superfamily	 - 	 - 	"Reticulon; Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of the three reticulon isoforms and their homologues."
Q#24254 - 	CGI_10025620	superfamily	241832	26	71	2.89E-10	53.2743	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#24254 - 	CGI_10025620	superfamily	243175	132	189	8.68E-10	52.6828	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#24255 - 	CGI_10025621	superfamily	245209	49	123	1.41E-08	48.541	cl09936	PP-binding superfamily	N	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#24256 - 	CGI_10025622	superfamily	247724	3	176	1.36E-134	381.853	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24256 - 	CGI_10025622	superfamily	247724	190	288	1.68E-69	215.832	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24259 - 	CGI_10025625	superfamily	247684	23	442	1.62E-78	256.435	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24264 - 	CGI_10001184	superfamily	110440	255	280	0.00423951	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#24265 - 	CGI_10001185	superfamily	241563	60	98	3.40E-06	44.2503	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24267 - 	CGI_10001283	superfamily	192535	49	145	0.000112454	41.0422	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#24270 - 	CGI_10006705	superfamily	216456	41	178	0.00162264	37.6882	cl03182	RYDR_ITPR superfamily	N	 - 	"RIH domain; The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3."
Q#24271 - 	CGI_10006706	superfamily	241563	43	78	5.04E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24271 - 	CGI_10006706	superfamily	110440	504	531	0.00933903	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#24273 - 	CGI_10006708	superfamily	243097	123	256	6.74E-30	115.82	cl02572	PIPKc superfamily	C	 - 	"Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs."
Q#24273 - 	CGI_10006708	superfamily	243097	364	412	1.28E-09	57.2692	cl02572	PIPKc superfamily	N	 - 	"Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment  includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs."
Q#24274 - 	CGI_10006709	superfamily	247727	69	174	0.000694576	37.7095	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#24277 - 	CGI_10006712	superfamily	151147	12	70	2.19E-11	58.2537	cl11240	DUF2475 superfamily	 - 	 - 	Protein of unknown function (DUF2475); This family of proteins has no known function.
Q#24277 - 	CGI_10006712	superfamily	151147	264	289	0.00043857	37.453	cl11240	DUF2475 superfamily	C	 - 	Protein of unknown function (DUF2475); This family of proteins has no known function.
Q#24278 - 	CGI_10006713	superfamily	241570	186	349	3.05E-10	58.1062	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24278 - 	CGI_10006713	superfamily	241570	37	168	2.99E-06	45.7798	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24279 - 	CGI_10006714	superfamily	246669	161	281	2.07E-26	100.792	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#24282 - 	CGI_10002019	superfamily	245213	50	83	0.000113784	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24282 - 	CGI_10002019	superfamily	245213	89	120	0.000222311	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24282 - 	CGI_10002019	superfamily	245213	341	372	0.000777743	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24282 - 	CGI_10002019	superfamily	245213	302	335	0.00299523	35.305	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24288 - 	CGI_10002401	superfamily	241609	38	113	2.46E-20	82.4259	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#24288 - 	CGI_10002401	superfamily	241609	121	198	2.72E-18	76.6479	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#24288 - 	CGI_10002401	superfamily	241613	3	28	0.00016003	37.9566	cl00104	LDLa superfamily	N	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24288 - 	CGI_10002401	superfamily	241613	196	226	0.000912847	35.6454	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24293 - 	CGI_10005923	superfamily	245205	66	143	1.11E-06	44.1509	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#24297 - 	CGI_10005927	superfamily	248264	6	54	0.000430113	38.3722	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#24298 - 	CGI_10005928	superfamily	220379	66	117	6.90E-18	78.6259	cl10734	DRY_EERY superfamily	C	 - 	"Alternative splicing regulator; This entry represents the conserved N-terminal region of SWAP (suppressor-of-white-apricot protein) proteins. This region contains two highly conserved motifs, viz: DRY and EERY, which appear to be the sites for alternative splicing of exons 2 and 3 of the SWAP mRNA. These proteins are thus thought to be involved in auto-regulation of pre-mRNA splicing. Most family members are associated with two Surp domains pfam01805 and an Arginine- serine-rich binding region towards the C-terminus."
Q#24300 - 	CGI_10005930	superfamily	245206	26	291	3.56E-90	272.176	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#24301 - 	CGI_10005931	superfamily	247058	48	251	4.90E-53	182.375	cl15762	crotonase-like superfamily	 - 	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#24302 - 	CGI_10005932	superfamily	248264	48	94	0.000924846	34.9054	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#24303 - 	CGI_10002673	superfamily	241563	297	333	5.76E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24304 - 	CGI_10002674	superfamily	248097	140	265	2.33E-31	114.285	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24304 - 	CGI_10002674	superfamily	248097	2	122	5.80E-23	91.5578	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24305 - 	CGI_10002675	superfamily	241563	65	97	3.38E-05	41.5539	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24307 - 	CGI_10017694	superfamily	241766	52	327	9.83E-126	364.126	cl00303	PNP_UDP_1 superfamily	 - 	 - 	Phosphorylase superfamily; Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Q#24309 - 	CGI_10017696	superfamily	152459	290	519	1.02E-71	234.588	cl13461	DUF3512 superfamily	 - 	 - 	Domain of unknown function (DUF3512); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 231 to 249 amino acids in length. This domain is found associated with pfam00439.
Q#24309 - 	CGI_10017696	superfamily	243084	139	235	2.73E-48	164.891	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#24311 - 	CGI_10017698	superfamily	241580	85	162	1.33E-48	163.108	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#24313 - 	CGI_10017701	superfamily	241580	70	147	6.83E-51	166.96	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#24314 - 	CGI_10017702	superfamily	245206	10	339	0	536.025	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#24315 - 	CGI_10017703	superfamily	245603	174	247	0.000672922	37.316	cl11403	pepsin_retropepsin_like superfamily	 - 	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#24315 - 	CGI_10017703	superfamily	247057	9	63	3.29E-07	46.9077	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#24315 - 	CGI_10017703	superfamily	247057	74	134	2.52E-06	44.5933	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#24316 - 	CGI_10017704	superfamily	244895	21	483	9.15E-127	381.124	cl08294	Peptidase_M17 superfamily	 - 	 - 	"Cytosol aminopeptidase family, N-terminal and catalytic domains.  Family M17 contains zinc- and manganese-dependent exopeptidases ( EC  3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants."
Q#24317 - 	CGI_10017705	superfamily	198867	158	251	1.24E-18	82.004	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#24317 - 	CGI_10017705	superfamily	243066	32	150	5.55E-12	63.0201	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24317 - 	CGI_10017705	superfamily	243146	392	438	1.07E-08	52.2786	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#24317 - 	CGI_10017705	superfamily	243146	356	403	1.68E-08	51.4051	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#24317 - 	CGI_10017705	superfamily	243146	452	498	8.90E-07	46.3975	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#24317 - 	CGI_10017705	superfamily	243146	487	540	0.00475513	35.7151	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#24318 - 	CGI_10017706	superfamily	112128	212	415	4.50E-92	279.37	cl03992	TF_AP-2 superfamily	 - 	 - 	Transcription factor AP-2; Transcription factor AP-2.  
Q#24319 - 	CGI_10017707	superfamily	242902	222	390	2.66E-41	145.927	cl02144	TLD superfamily	 - 	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#24320 - 	CGI_10017708	superfamily	244906	116	186	2.97E-12	61.8324	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#24320 - 	CGI_10017708	superfamily	244906	217	278	1.65E-07	48.3504	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#24320 - 	CGI_10017708	superfamily	207637	310	384	0.000213476	39.1282	cl02541	CIDE_N superfamily	 - 	 - 	"CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein."
Q#24321 - 	CGI_10017709	superfamily	243082	672	955	8.58E-40	148.444	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#24321 - 	CGI_10017709	superfamily	244906	113	185	1.26E-15	73.3884	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#24321 - 	CGI_10017709	superfamily	244906	467	538	3.30E-13	66.4548	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#24321 - 	CGI_10017709	superfamily	244906	229	290	6.50E-06	44.8836	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#24322 - 	CGI_10017710	superfamily	242883	25	206	2.77E-64	200.314	cl02103	Maf1 superfamily	 - 	 - 	Maf1 regulator; Maf1 is a negative regulator of RNA polymerase III. It targets the initiation factor TFIIIB.
Q#24323 - 	CGI_10017711	superfamily	247792	675	717	0.00558591	35.8844	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24323 - 	CGI_10017711	superfamily	241645	288	359	5.89E-13	65.6504	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#24324 - 	CGI_10017712	superfamily	247724	16	164	6.99E-77	230.008	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24325 - 	CGI_10017713	superfamily	245201	243	504	2.77E-49	170.11	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24325 - 	CGI_10017713	superfamily	247725	119	215	2.46E-23	94.8349	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24326 - 	CGI_10017714	superfamily	248100	1088	1148	3.19E-07	49.0748	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#24326 - 	CGI_10017714	superfamily	248100	925	985	1.63E-05	44.0672	cl17546	PQ-loop superfamily	 - 	 - 	"PQ loop repeat; Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue."
Q#24327 - 	CGI_10017715	superfamily	243092	13	307	4.38E-73	231.455	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24328 - 	CGI_10017716	superfamily	222150	563	588	1.88E-06	45.4605	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24328 - 	CGI_10017716	superfamily	222150	535	559	3.92E-05	41.6085	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24329 - 	CGI_10017717	superfamily	241597	259	319	4.39E-16	73.4219	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#24330 - 	CGI_10017718	superfamily	218660	8	152	3.36E-38	130.147	cl05277	DUF788 superfamily	 - 	 - 	Protein of unknown function (DUF788); This family consists of several eukaryotic proteins of unknown function.
Q#24332 - 	CGI_10017720	superfamily	243034	29	126	2.80E-08	51.2268	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#24332 - 	CGI_10017720	superfamily	243034	172	248	1.96E-07	48.5304	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#24333 - 	CGI_10017721	superfamily	215733	333	590	9.80E-12	64.8939	cl02811	E1-E2_ATPase superfamily	 - 	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#24333 - 	CGI_10017721	superfamily	222006	695	803	3.07E-09	55.6914	cl16182	Hydrolase_like2 superfamily	 - 	 - 	Putative hydrolase of sodium-potassium ATPase alpha subunit; This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.
Q#24334 - 	CGI_10017722	superfamily	244906	58	127	3.18E-19	79.1664	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#24336 - 	CGI_10017724	superfamily	241826	20	49	1.94E-05	37.5413	cl00380	Ribosomal_L36 superfamily	 - 	 - 	Ribosomal protein L36; Ribosomal protein L36.  
Q#24338 - 	CGI_10017726	superfamily	215686	5	135	3.38E-06	42.4045	cl18340	Lipocalin superfamily	 - 	 - 	"Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel."
Q#24341 - 	CGI_10017729	superfamily	248012	82	175	0.00311852	35.3768	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#24342 - 	CGI_10017730	superfamily	247866	10	128	5.62E-05	41.284	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#24343 - 	CGI_10002729	superfamily	245882	21	396	8.83E-164	470.235	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#24344 - 	CGI_10002730	superfamily	217701	71	164	7.10E-06	43.4809	cl04237	Retrotrans_gag superfamily	 - 	 - 	"Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved."
Q#24347 - 	CGI_10002733	superfamily	220964	47	123	0.00496917	35.6545	cl12630	DUF2869 superfamily	NC	 - 	Protein of unknown function (DUF2869); This bacterial family of proteins has no known function.
Q#24350 - 	CGI_10015678	superfamily	216411	1069	1189	9.03E-19	84.6358	cl15974	MARVEL superfamily	N	 - 	"Membrane-associating domain; MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis."
Q#24351 - 	CGI_10015679	superfamily	247692	128	480	2.26E-44	160.149	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#24351 - 	CGI_10015679	superfamily	247692	1	153	3.94E-06	47.9746	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#24352 - 	CGI_10015680	superfamily	247692	128	480	1.23E-40	149.749	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#24352 - 	CGI_10015680	superfamily	247692	1	65	5.89E-06	47.1398	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#24353 - 	CGI_10015681	superfamily	247692	128	480	1.58E-35	135.111	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#24353 - 	CGI_10015681	superfamily	247692	1	65	8.52E-06	46.7546	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#24358 - 	CGI_10015686	superfamily	248458	40	376	1.34E-07	51.9309	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24360 - 	CGI_10015688	superfamily	148067	294	385	7.88E-30	111.595	cl05643	DUF1011 superfamily	 - 	 - 	Protein of unknown function (DUF1011); Family of uncharacterized eukaryotic proteins.
Q#24361 - 	CGI_10015689	superfamily	241578	276	433	6.85E-37	133.571	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24362 - 	CGI_10015690	superfamily	245201	46	235	2.52E-55	181.281	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24363 - 	CGI_10015691	superfamily	241645	43	97	5.24E-16	72.9103	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#24364 - 	CGI_10015692	superfamily	216167	153	292	4.06E-32	123.466	cl02999	DNA_photolyase superfamily	 - 	 - 	DNA photolyase; This domain binds a light harvesting cofactor.
Q#24365 - 	CGI_10015693	superfamily	220692	37	338	2.24E-08	53.7473	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#24366 - 	CGI_10015694	superfamily	220692	43	335	6.79E-24	99.2009	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#24367 - 	CGI_10015695	superfamily	201362	8	112	8.47E-36	124.785	cl08277	Motile_Sperm superfamily	 - 	 - 	MSP (Major sperm protein) domain; Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
Q#24372 - 	CGI_10015700	superfamily	241578	762	938	6.60E-47	167.392	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24372 - 	CGI_10015700	superfamily	207701	519	635	2.30E-38	140.893	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#24372 - 	CGI_10015700	superfamily	241578	32	208	5.84E-30	118.472	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24373 - 	CGI_10015701	superfamily	217473	1	73	8.77E-08	51.9821	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#24376 - 	CGI_10007241	superfamily	248279	63	181	3.83E-38	139.009	cl17725	zf-HC5HC2H superfamily	 - 	 - 	"PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH."
Q#24376 - 	CGI_10007241	superfamily	247999	20	54	2.26E-10	57.2703	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#24382 - 	CGI_10003314	superfamily	245213	511	546	6.02E-09	53.7946	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24382 - 	CGI_10003314	superfamily	245213	359	394	7.54E-09	53.4094	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24382 - 	CGI_10003314	superfamily	245213	549	584	1.83E-07	49.1722	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24382 - 	CGI_10003314	superfamily	245213	435	470	2.43E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24382 - 	CGI_10003314	superfamily	245213	397	432	2.89E-07	48.787	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24382 - 	CGI_10003314	superfamily	245213	473	508	3.09E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24382 - 	CGI_10003314	superfamily	245213	321	357	0.000159523	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24382 - 	CGI_10003314	superfamily	241583	649	846	4.65E-50	178.336	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#24383 - 	CGI_10003315	superfamily	245213	38	73	3.74E-09	49.5574	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24383 - 	CGI_10003315	superfamily	245213	76	111	2.54E-06	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24384 - 	CGI_10004837	superfamily	243072	14	150	2.36E-29	106.699	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24386 - 	CGI_10004839	superfamily	218771	2	142	7.60E-08	47.1944	cl05420	Synaphin superfamily	 - 	 - 	"Synaphin protein; This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerisation of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles. Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin transmembrane regions that reside in opposing membranes prior to fusion."
Q#24388 - 	CGI_10004841	superfamily	241583	249	444	1.42E-67	227.113	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#24388 - 	CGI_10004841	superfamily	245321	461	537	3.14E-33	125.045	cl10507	Disintegrin superfamily	 - 	 - 	Disintegrin; Disintegrin.  
Q#24388 - 	CGI_10004841	superfamily	246968	540	685	6.32E-33	125.935	cl15456	ADAM_CR superfamily	 - 	 - 	ADAM cysteine-rich; ADAMs are membrane-anchored proteases that proteolytically modify cell surface and extracellular matrix (ECM) in order to alter cell behaviour. It has been shown that the cysteine-rich domain of ADAM13 regulates the protein's metalloprotease activity.
Q#24388 - 	CGI_10004841	superfamily	216572	70	219	2.22E-20	89.2562	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#24391 - 	CGI_10001742	superfamily	245814	81	142	6.92E-09	48.9423	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24391 - 	CGI_10001742	superfamily	245814	4	63	0.0012159	35.1737	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24393 - 	CGI_10003776	superfamily	241841	11	124	9.75E-43	139.575	cl00399	MoaE superfamily	 - 	 - 	"MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits."
Q#24394 - 	CGI_10003777	superfamily	240441	1430	1484	4.64E-23	95.7095	cl18913	Na_channel_gate superfamily	 - 	 - 	Inactivation gate of the voltage-gated sodium channel alpha subunits; This region is part of the intracellular linker between domains III and IV of the alpha subunits of voltage-gated sodium channels. It is responsible for fast inactivation of the channel and essential for proper physiological function.
Q#24394 - 	CGI_10003777	superfamily	219069	1126	1176	5.03E-05	45.4458	cl05828	Na_trans_assoc superfamily	N	 - 	"Sodium ion transport-associated; Members of this family contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of pfam00520 and, less often, one copy of pfam00612."
Q#24395 - 	CGI_10003778	superfamily	247065	6	116	7.11E-13	61.2066	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#24397 - 	CGI_10006787	superfamily	245847	27	152	6.49E-07	44.4156	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#24398 - 	CGI_10006788	superfamily	248012	131	231	7.72E-24	93.4112	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#24398 - 	CGI_10006788	superfamily	243058	21	123	0.00210027	36.1384	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24399 - 	CGI_10006789	superfamily	217403	141	245	2.61E-14	66.6774	cl18408	2OG-FeII_Oxy superfamily	 - 	 - 	"2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalyzing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB."
Q#24399 - 	CGI_10006789	superfamily	222608	11	88	0.000198434	38.7747	cl18680	DIOX_N superfamily	N	 - 	non-haem dioxygenase in morphine synthesis N-terminal; This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.
Q#24400 - 	CGI_10006790	superfamily	201664	5	175	4.25E-54	177.035	cl18216	NAD_Gly3P_dh_N superfamily	 - 	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.
Q#24400 - 	CGI_10006790	superfamily	116100	194	343	9.01E-53	173.153	cl08454	NAD_Gly3P_dh_C superfamily	 - 	 - 	NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain.
Q#24401 - 	CGI_10006791	superfamily	243054	177	373	0.000331716	41.6624	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#24401 - 	CGI_10006791	superfamily	219569	686	751	0.00759299	37.5176	cl06693	MFMR superfamily	NC	 - 	"G-box binding protein MFMR; This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals."
Q#24402 - 	CGI_10006792	superfamily	245010	957	1068	8.21E-26	105.004	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#24402 - 	CGI_10006792	superfamily	245201	18	305	1.56E-97	325.679	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24402 - 	CGI_10006792	superfamily	245201	452	917	1.89E-67	239.779	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24403 - 	CGI_10006793	superfamily	243058	626	747	4.17E-26	105.859	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24403 - 	CGI_10006793	superfamily	243058	925	1046	1.03E-16	78.5103	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24404 - 	CGI_10006794	superfamily	247057	333	372	0.000292483	38.4537	cl15755	SAM_superfamily superfamily	C	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#24405 - 	CGI_10006795	superfamily	247057	501	539	0.000144799	39.9153	cl15755	SAM_superfamily superfamily	C	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#24406 - 	CGI_10006796	superfamily	245213	816	850	1.42E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1825	1859	1.42E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	646	680	0.000108109	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1655	1689	0.000108109	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	520	554	0.000262631	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1529	1563	0.000262631	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	344	380	0.000559912	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	944	980	0.000648207	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1953	1989	0.000648207	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	900	943	0.000840541	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1909	1952	0.000840541	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	246	284	0.00121324	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1486	1528	0.00184683	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	477	519	0.00184683	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1570	1611	8.76E-05	42.7212	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	561	602	8.76E-05	42.7212	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	731	766	0.000122553	42.336	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1740	1775	0.000122553	42.336	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	205157	1445	1481	0.000313163	40.9839	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#24406 - 	CGI_10006796	superfamily	205157	436	472	0.000313163	40.9839	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#24406 - 	CGI_10006796	superfamily	205157	1785	1823	0.000469316	40.5987	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#24406 - 	CGI_10006796	superfamily	205157	776	814	0.000469316	40.5987	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#24406 - 	CGI_10006796	superfamily	205157	208	244	0.00120772	39.4431	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#24406 - 	CGI_10006796	superfamily	245213	1866	1905	0.00146475	39.2544	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	857	896	0.00146475	39.2544	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	1696	1732	0.00241119	38.484	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24406 - 	CGI_10006796	superfamily	245213	687	723	0.00241119	38.484	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24408 - 	CGI_10016843	superfamily	243179	46	161	7.31E-05	39.4383	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#24409 - 	CGI_10016844	superfamily	247684	8	42	6.42E-11	55.8147	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24410 - 	CGI_10016845	superfamily	247684	68	221	1.20E-64	209.895	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	NC	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24411 - 	CGI_10016846	superfamily	247684	9	208	4.32E-71	226.458	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24412 - 	CGI_10016847	superfamily	243179	111	211	8.32E-11	56.7723	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#24413 - 	CGI_10016848	superfamily	243179	137	255	2.89E-11	58.6983	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#24414 - 	CGI_10016849	superfamily	245847	150	305	2.24E-32	122.076	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#24414 - 	CGI_10016849	superfamily	243035	316	452	3.49E-22	92.7529	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#24414 - 	CGI_10016849	superfamily	216897	30	108	1.26E-13	66.9361	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#24415 - 	CGI_10016850	superfamily	217293	24	227	1.28E-32	122.741	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#24418 - 	CGI_10016854	superfamily	219605	37	240	3.83E-51	167.121	cl06746	DUF1637 superfamily	 - 	 - 	"Protein of unknown function (DUF1637); This family contains many eukaryotic hypothetical proteins. The region featured in this family is approximately 120 residues long. According to InterPro annotation, some members of this family may belong to the cupin superfamily."
Q#24419 - 	CGI_10016855	superfamily	199166	83	175	5.35E-06	45.396	cl15308	AMN1 superfamily	N	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#24420 - 	CGI_10016856	superfamily	247727	61	163	8.38E-08	47.8099	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#24421 - 	CGI_10016857	superfamily	245202	74	165	4.65E-33	118.036	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#24421 - 	CGI_10016857	superfamily	206550	24	63	7.30E-13	61.6424	cl16842	ECR1_N superfamily	 - 	 - 	Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.
Q#24422 - 	CGI_10016858	superfamily	245201	248	510	4.12E-179	531.348	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24422 - 	CGI_10016858	superfamily	246908	136	229	2.81E-57	193.759	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#24422 - 	CGI_10016858	superfamily	247683	77	131	1.43E-24	99.409	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#24422 - 	CGI_10016858	superfamily	198904	1161	1265	2.89E-10	59.4309	cl07494	F_actin_bind superfamily	 - 	 - 	"F-actin binding; The F-actin binding domain forms a compact bundle of four antiparallel alpha-helices, which are arranged in a left-handed topology. Binding of F-actin to the F-actin binding domain may result in cytoplasmic retention and subcellular distribution of the protein, as well as possible inhibition of protein function."
Q#24423 - 	CGI_10016859	superfamily	220621	167	302	2.31E-09	54.1794	cl18563	DUF2358 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2358); DUF2358 is a family of conserved proteins found from plants to humans. The function is unknown.
Q#24424 - 	CGI_10016860	superfamily	216554	64	255	6.28E-36	128.366	cl15977	zf-DHHC superfamily	 - 	 - 	DHHC palmitoyltransferase; This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.
Q#24425 - 	CGI_10016861	superfamily	216254	44	117	3.41E-11	55.3318	cl08303	Recep_L_domain superfamily	C	 - 	Receptor L domain; The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
Q#24426 - 	CGI_10016862	superfamily	241832	29	126	3.74E-37	135.089	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#24426 - 	CGI_10016862	superfamily	242886	404	502	2.13E-22	93.1394	cl02107	Evr1_Alr superfamily	 - 	 - 	Erv1 / Alr family; Biogenesis of Fe/S clusters involves a number of essential mitochondrial proteins. Erv1p of Saccharomyces cerevisiae mitochondria is required for the maturation of Fe/S proteins in the cytosol. The ALR (augmenter of liver regeneration) represents a mammalian orthologue of yeast Erv1p. Both Erv1p and full-length ALR are located in the mitochondrial intermembrane an d it thought to operate downstream of the mitochondrial ABC transporter.
Q#24427 - 	CGI_10016863	superfamily	245201	670	935	1.11E-120	371.099	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24427 - 	CGI_10016863	superfamily	245814	417	490	7.44E-10	57.1139	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24427 - 	CGI_10016863	superfamily	245814	186	264	2.27E-07	49.4099	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24427 - 	CGI_10016863	superfamily	245213	484	519	2.46E-06	45.7054	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24427 - 	CGI_10016863	superfamily	245213	524	559	4.22E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24427 - 	CGI_10016863	superfamily	245814	72	165	0.000355467	39.7961	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24428 - 	CGI_10016864	superfamily	217838	197	374	1.85E-53	184.303	cl04368	Leo1 superfamily	NC	 - 	Leo1-like protein; Members of this family are part of the Paf1/RNA polymerase II complex. The Paf1 complex probably functions during the elongation phase of transcription. The Leo1 subunit of the yeast Paf1-complex binds RNA and contributes to complex recruitment. The subunit acts by co-ordinating co-transcriptional chromain modifications and helping recruitment of mRNA 3prime-end processing factors.
Q#24429 - 	CGI_10016865	superfamily	199168	201	221	0.00726791	33.8644	cl15310	LRR_TYP superfamily	 - 	 - 	"Leucine-rich repeats, typical (most populated) subfamily; Leucine-rich repeats, typical (most populated) subfamily.  "
Q#24430 - 	CGI_10016866	superfamily	218176	66	282	2.19E-29	112.453	cl14959	Pex19 superfamily	 - 	 - 	Pex19 protein family; Pex19 protein family.  
Q#24431 - 	CGI_10016867	superfamily	245201	23	268	1.40E-77	255.137	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24433 - 	CGI_10016869	superfamily	217895	29	136	0.00473408	36.0819	cl04401	CD20 superfamily	C	 - 	"CD20-like family; This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton."
Q#24434 - 	CGI_10016870	superfamily	243128	478	659	3.08E-27	112.038	cl02652	MIF4G superfamily	 - 	 - 	"MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA."
Q#24434 - 	CGI_10016870	superfamily	243129	765	871	8.83E-22	93.4721	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#24435 - 	CGI_10016871	superfamily	241920	107	197	5.04E-23	90.6467	cl00519	Oligomerisation superfamily	 - 	 - 	"Oligomerisation domain; In yeasts, this domain is required for the oligomerisation of ATP synthase subunit 9 into a ring structure."
Q#24436 - 	CGI_10016872	superfamily	243267	458	821	1.19E-101	321.1	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#24436 - 	CGI_10016872	superfamily	241782	44	402	3.35E-28	116.486	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#24437 - 	CGI_10016873	superfamily	243267	445	808	6.52E-101	318.789	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#24437 - 	CGI_10016873	superfamily	241782	55	389	8.44E-28	115.331	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#24438 - 	CGI_10016874	superfamily	243267	32	421	2.30E-68	224.03	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#24439 - 	CGI_10016875	superfamily	241578	403	544	2.00E-16	77.717	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24439 - 	CGI_10016875	superfamily	241578	548	646	3.42E-13	68.087	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24439 - 	CGI_10016875	superfamily	241578	208	374	4.52E-08	52.4568	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24443 - 	CGI_10016879	superfamily	241578	93	202	1.21E-10	58.457	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24444 - 	CGI_10016880	superfamily	241578	23	192	1.75E-26	102.306	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24445 - 	CGI_10016881	superfamily	241578	14	170	5.72E-29	109.689	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24446 - 	CGI_10004043	superfamily	241600	108	244	1.86E-43	152.395	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24446 - 	CGI_10004043	superfamily	241600	251	407	2.85E-43	151.624	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24448 - 	CGI_10004045	superfamily	216897	33	99	1.40E-14	66.1657	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#24448 - 	CGI_10004045	superfamily	246918	125	160	4.43E-05	39.4923	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24449 - 	CGI_10006075	superfamily	218118	85	149	2.14E-10	55.3129	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#24449 - 	CGI_10006075	superfamily	218118	180	249	2.27E-06	44.1421	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#24449 - 	CGI_10006075	superfamily	218118	142	184	0.000810051	36.4381	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#24450 - 	CGI_10006076	superfamily	218118	46	111	4.15E-16	68.4096	cl04552	CD225 superfamily	 - 	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#24451 - 	CGI_10006077	superfamily	218118	73	126	1.12E-09	51.4609	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#24454 - 	CGI_10006081	superfamily	247769	83	195	4.93E-11	59.6605	cl17215	HDc superfamily	C	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#24455 - 	CGI_10010687	superfamily	222445	61	134	1.69E-10	55.0722	cl16466	R3H-assoc superfamily	C	 - 	"R3H-associated N-terminal domain; This family is found at the N-terminus of R3H, pfam01424, domain-containing proteins. The function is not known."
Q#24456 - 	CGI_10010688	superfamily	241571	24	138	6.23E-36	122.136	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24459 - 	CGI_10010691	superfamily	243035	63	130	5.17E-13	61.0965	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#24459 - 	CGI_10010691	superfamily	241568	30	55	0.00265289	32.82	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#24460 - 	CGI_10010693	superfamily	243035	9	124	8.45E-29	102.698	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#24461 - 	CGI_10010695	superfamily	238012	73	121	2.59E-12	61.2162	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#24466 - 	CGI_10010813	superfamily	165418	23	85	0.0091106	32.224	cl14511	PHA03147 superfamily	C	 - 	hypothetical protein; Provisional
Q#24468 - 	CGI_10010815	superfamily	243066	131	184	5.42E-12	58.7185	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24473 - 	CGI_10010820	superfamily	245814	219	292	1.16E-06	45.9431	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24474 - 	CGI_10010821	superfamily	219727	150	410	2.04E-139	421.249	cl18522	BOP1NT superfamily	 - 	 - 	BOP1NT (NUC169) domain; This N terminal domain is found in BOP1-like WD40 proteins.
Q#24474 - 	CGI_10010821	superfamily	243092	416	751	4.41E-24	103.569	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24475 - 	CGI_10010822	superfamily	241756	8	202	7.92E-68	210.856	cl00289	FIG superfamily	 - 	 - 	"FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule Inositol-1,4,5-triphosphate. Many of these enzymes are inhibited by Li+."
Q#24477 - 	CGI_10010824	superfamily	216981	159	283	2.13E-28	106.463	cl17087	OTU superfamily	 - 	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#24478 - 	CGI_10010825	superfamily	247724	6	174	5.05E-96	299.666	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24478 - 	CGI_10010825	superfamily	247724	253	420	1.00E-93	293.503	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24478 - 	CGI_10010825	superfamily	243185	455	537	5.45E-33	122.971	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#24478 - 	CGI_10010825	superfamily	243185	209	239	5.19E-09	54.4054	cl02787	Translation_Factor_II_like superfamily	C	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#24479 - 	CGI_10010826	superfamily	148541	96	225	7.22E-13	62.4521	cl06160	DUF1301 superfamily	 - 	 - 	Protein of unknown function (DUF1301); This family contains a number of eukaryotic proteins of unknown function that are approximately 160 residues long.
Q#24481 - 	CGI_10008150	superfamily	241571	397	513	5.55E-11	60.5038	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24481 - 	CGI_10008150	superfamily	245213	522	551	0.00142614	37.231	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24481 - 	CGI_10008150	superfamily	241583	169	350	5.47E-33	125.376	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#24482 - 	CGI_10008151	superfamily	241683	16	340	6.02E-171	497.423	cl00204	PFK superfamily	C	 - 	"Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases. Some members evolved by gene duplication and thus have a large C-terminal/N-terminal extension comprising a second PFK domain. Generally, ATP-PFKs are allosteric homotetramers, and  PPi-PFKs are dimeric and nonallosteric except for plant PPi-PFKs which are allosteric heterotetramers."
Q#24483 - 	CGI_10008152	superfamily	241709	4	159	1.29E-60	188.713	cl00232	Ribosomal_L19e superfamily	 - 	 - 	"Ribosomal protein L19e.  L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit.  The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits."
Q#24485 - 	CGI_10008154	superfamily	243066	52	142	4.03E-16	76.1169	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24486 - 	CGI_10008155	superfamily	241992	445	870	0	663.157	cl00628	Piwi-like superfamily	 - 	 - 	"Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism."
Q#24486 - 	CGI_10008155	superfamily	241765	280	400	1.63E-38	140.53	cl00301	PAZ superfamily	 - 	 - 	"PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain."
Q#24486 - 	CGI_10008155	superfamily	219976	228	280	4.12E-20	86.0725	cl07356	DUF1785 superfamily	 - 	 - 	Domain of unknown function (DUF1785); This region is found in argonaute proteins and often co-occurs with pfam02179 and pfam02171.
Q#24486 - 	CGI_10008155	superfamily	219677	935	963	0.00116116	38.1876	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#24487 - 	CGI_10008156	superfamily	217437	59	171	1.95E-26	100.099	cl03944	GILT superfamily	 - 	 - 	"Gamma interferon inducible lysosomal thiol reductase (GILT); This family includes the two characterized human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences. It also contains several other eukaryotic putative proteins with similarity to GILT. The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction."
Q#24488 - 	CGI_10008157	superfamily	217437	55	166	1.27E-23	92.3953	cl03944	GILT superfamily	 - 	 - 	"Gamma interferon inducible lysosomal thiol reductase (GILT); This family includes the two characterized human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences. It also contains several other eukaryotic putative proteins with similarity to GILT. The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction."
Q#24489 - 	CGI_10008158	superfamily	243100	624	685	1.83E-10	58.7295	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#24489 - 	CGI_10008158	superfamily	243100	945	1006	1.83E-10	58.7295	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#24491 - 	CGI_10003006	superfamily	220545	241	279	7.34E-18	74.9698	cl15332	DUF2296 superfamily	C	 - 	"Predicted integral membrane metal-binding protein (DUF2296); This domain, found in various hypothetical bacterial and eukaryotic metal-binding proteins, has no known function."
Q#24492 - 	CGI_10003007	superfamily	245225	349	778	1.22E-39	152.397	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#24492 - 	CGI_10003007	superfamily	245225	4	301	1.04E-17	85.3723	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	N	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#24494 - 	CGI_10011255	superfamily	241874	29	601	0	579.134	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24495 - 	CGI_10011256	superfamily	241622	152	233	4.08E-14	65.2806	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#24500 - 	CGI_10011261	superfamily	241622	264	308	2.41E-06	44.938	cl00117	PDZ superfamily	C	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#24500 - 	CGI_10011261	superfamily	247792	18	53	0.00171209	35.8844	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24505 - 	CGI_10011266	superfamily	243175	152	254	1.31E-50	164.669	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#24505 - 	CGI_10011266	superfamily	241832	57	134	4.58E-13	62.2337	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#24507 - 	CGI_10011268	superfamily	245213	333	368	5.01E-09	52.639	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24507 - 	CGI_10011268	superfamily	245213	292	330	0.000163803	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24511 - 	CGI_10005439	superfamily	248264	2	136	1.75E-13	66.4917	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#24520 - 	CGI_10003178	superfamily	241600	7	82	4.50E-20	80.3623	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24524 - 	CGI_10003231	superfamily	247684	15	94	0.000352035	41.5084	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24524 - 	CGI_10003231	superfamily	241563	152	185	0.00612224	34.7624	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24526 - 	CGI_10002108	superfamily	246597	137	426	4.57E-94	290.329	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#24528 - 	CGI_10004333	superfamily	241815	1	174	1.32E-31	115.371	cl00361	Transcrip_reg superfamily	C	 - 	"Transcriptional regulator; This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region."
Q#24529 - 	CGI_10004334	superfamily	247085	219	335	7.24E-30	111.443	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#24529 - 	CGI_10004334	superfamily	245596	76	206	1.05E-69	222.08	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#24530 - 	CGI_10004335	superfamily	247085	442	558	5.89E-28	108.747	cl15820	RICIN superfamily	 - 	 - 	"Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture."
Q#24530 - 	CGI_10004335	superfamily	245596	193	396	4.76E-101	310.675	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#24530 - 	CGI_10004335	superfamily	245596	104	153	1.00E-15	76.4741	cl11394	Glyco_tranf_GTA_type superfamily	NC	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#24530 - 	CGI_10004335	superfamily	245596	28	102	1.55E-13	69.9257	cl11394	Glyco_tranf_GTA_type superfamily	NC	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#24534 - 	CGI_10009043	superfamily	247941	144	294	3.22E-13	65.4348	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#24535 - 	CGI_10009044	superfamily	214507	138	188	0.000185995	37.4096	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#24535 - 	CGI_10009044	superfamily	243030	33	59	0.00609023	33.0599	cl02423	LRRNT superfamily	 - 	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#24536 - 	CGI_10009045	superfamily	215827	218	395	1.53E-37	139.526	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#24537 - 	CGI_10009046	superfamily	248097	87	172	1.06E-18	77.6906	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24537 - 	CGI_10009046	superfamily	243100	42	82	1.58E-05	39.8548	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#24538 - 	CGI_10009047	superfamily	248097	13	145	1.13E-22	87.7058	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24539 - 	CGI_10009048	superfamily	248097	63	195	6.74E-24	92.3282	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24540 - 	CGI_10009049	superfamily	248097	63	195	4.82E-22	87.3206	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24541 - 	CGI_10015759	superfamily	243035	1	72	1.54E-12	58.0149	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#24544 - 	CGI_10015762	superfamily	248097	77	202	3.46E-24	93.0986	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24545 - 	CGI_10015763	superfamily	248097	52	153	1.53E-16	73.8386	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24550 - 	CGI_10015768	superfamily	243066	36	132	3.98E-17	73.8792	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24551 - 	CGI_10015769	superfamily	243066	238	334	6.95E-15	70.0272	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24551 - 	CGI_10015769	superfamily	243066	1	71	5.81E-05	41.1373	cl02518	BTB superfamily	N	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24553 - 	CGI_10015771	superfamily	243066	36	132	6.14E-17	73.494	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24556 - 	CGI_10015774	superfamily	241578	209	397	3.78E-16	78.1582	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24556 - 	CGI_10015774	superfamily	217211	473	533	3.72E-07	49.5902	cl03691	Cache_1 superfamily	 - 	 - 	Cache domain; Cache domain.  
Q#24556 - 	CGI_10015774	superfamily	219821	142	182	6.44E-05	42.7434	cl07136	VWA_N superfamily	N	 - 	"VWA N-terminal; This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits."
Q#24558 - 	CGI_10015776	superfamily	241874	9	534	0	647.7	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24559 - 	CGI_10015777	superfamily	241874	191	758	0	670.311	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24560 - 	CGI_10015778	superfamily	222150	1012	1036	0.000341318	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24560 - 	CGI_10015778	superfamily	222150	1155	1175	0.000398031	40.0677	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24560 - 	CGI_10015778	superfamily	222150	1124	1149	0.00241841	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24560 - 	CGI_10015778	superfamily	222150	1043	1065	0.00247716	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24561 - 	CGI_10005629	superfamily	197448	26	84	1.85E-15	68.6689	cl15240	Reelin_subrepeat_like superfamily	N	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#24563 - 	CGI_10008252	superfamily	216939	15	73	2.91E-06	39.9537	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#24564 - 	CGI_10008253	superfamily	216939	24	66	5.73E-05	36.4869	cl03492	PC4 superfamily	N	 - 	Transcriptional Coactivator p15 (PC4); p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Q#24566 - 	CGI_10008255	superfamily	191243	12	34	0.00186434	32.7995	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#24571 - 	CGI_10008260	superfamily	247724	24	62	8.94E-07	42.919	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24572 - 	CGI_10008261	superfamily	243056	373	517	4.21E-33	126.267	cl02495	RabGAP-TBC superfamily	N	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#24574 - 	CGI_10013480	superfamily	241568	192	255	6.80E-05	39.7536	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#24574 - 	CGI_10013480	superfamily	241568	12	66	0.000951348	36.2868	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#24575 - 	CGI_10013481	superfamily	245814	1813	1882	2.71E-11	63.2771	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	2541	2607	8.24E-11	61.7363	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1909	1975	1.69E-10	60.9659	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	2095	2164	2.89E-10	60.1955	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	2358	2425	6.56E-10	59.0399	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	704	769	7.98E-10	59.0399	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1720	1784	2.15E-09	57.4991	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1057	1124	3.32E-09	57.1139	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1625	1694	4.01E-09	56.7287	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245213	3762	3802	8.55E-09	54.9502	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24575 - 	CGI_10013481	superfamily	245213	3493	3532	4.00E-07	50.3278	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24575 - 	CGI_10013481	superfamily	245814	435	500	7.75E-07	50.1803	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	525	587	8.42E-07	49.7951	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	241578	34	192	1.80E-06	49.8718	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24575 - 	CGI_10013481	superfamily	245814	2286	2338	2.63E-06	48.6395	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245213	3577	3611	2.84E-05	44.935	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24575 - 	CGI_10013481	superfamily	245213	3660	3689	8.89E-05	43.3942	cl09941	EGF_CA superfamily	C	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24575 - 	CGI_10013481	superfamily	245213	3617	3655	0.000140351	42.6238	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24575 - 	CGI_10013481	superfamily	245213	3533	3568	0.00166489	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24575 - 	CGI_10013481	superfamily	241668	3255	3478	2.29E-42	158.375	cl00186	nidG2 superfamily	 - 	 - 	"Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a potential role in the assembly and connection of networks. Nidogen consists of 3 globular domains (G1-G3), G3 is the lamin-binding domain, while G2 binds collagen IV and perlecan. Also found in hemicentin, a protein which functions at various cell-cell and cell-matrix junctions and might assist in refining broad regions of cell contact into oriented, line-shaped junctions. Nidogen G2 consists of an N-terminal EGF-like domain (excluded from this alignment model) and an 11-stranded beta-barrel with a central helix, a topology that exhibits high structural similarity to the green flourescent proteins of Cnidaria."
Q#24575 - 	CGI_10013481	superfamily	246918	3092	3144	3.64E-17	79.5531	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24575 - 	CGI_10013481	superfamily	246918	2978	3030	7.87E-16	75.7011	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24575 - 	CGI_10013481	superfamily	245814	1330	1412	1.52E-14	72.9232	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	246918	2922	2973	7.03E-14	70.3083	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24575 - 	CGI_10013481	superfamily	245814	604	682	7.78E-14	70.9972	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	246918	3206	3256	2.39E-13	68.7675	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24575 - 	CGI_10013481	superfamily	245814	2186	2252	6.33E-13	67.8171	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	958	1035	7.06E-13	68.3008	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	778	863	1.22E-12	67.6498	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	2769	2830	2.58E-12	65.8911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	2629	2706	3.26E-12	65.9896	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1234	1305	8.10E-12	65.1089	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1140	1210	8.25E-12	65.1089	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1998	2071	8.65E-12	64.7132	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	2447	2511	9.58E-12	64.3878	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1425	1508	7.49E-11	62.1376	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	880	959	5.79E-10	59.4412	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	1529	1592	7.59E-10	58.5723	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	245814	2865	2905	6.62E-07	50.0979	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24575 - 	CGI_10013481	superfamily	246918	3050	3086	3.25E-05	44.8851	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24575 - 	CGI_10013481	superfamily	246918	3167	3201	0.000209734	42.5739	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#24576 - 	CGI_10013482	superfamily	217473	195	447	4.98E-31	122.859	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#24577 - 	CGI_10013483	superfamily	246664	81	557	8.07E-155	457.542	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#24578 - 	CGI_10013484	superfamily	241563	13	58	0.00727187	33.8499	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24579 - 	CGI_10013485	superfamily	245848	15	227	6.98E-22	91.1789	cl12043	Amidinotransf superfamily	 - 	 - 	"Amidinotransferase; This family contains glycine (EC:2.1.4.1) and inosamine (EC:2.1.4.2) amidinotransferases, enzymes involved in creatine and streptomycin biosynthesis respectively. This family also includes arginine deiminases, EC:3.5.3.6. These enzymes catalyze the reaction: arginine + H2O <=> citrulline + NH3. Also found in this family is the Streptococcus anti tumour glycoprotein."
Q#24580 - 	CGI_10013486	superfamily	245848	15	272	1.29E-24	100.424	cl12043	Amidinotransf superfamily	 - 	 - 	"Amidinotransferase; This family contains glycine (EC:2.1.4.1) and inosamine (EC:2.1.4.2) amidinotransferases, enzymes involved in creatine and streptomycin biosynthesis respectively. This family also includes arginine deiminases, EC:3.5.3.6. These enzymes catalyze the reaction: arginine + H2O <=> citrulline + NH3. Also found in this family is the Streptococcus anti tumour glycoprotein."
Q#24584 - 	CGI_10013490	superfamily	246710	24	161	7.40E-38	138.789	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#24584 - 	CGI_10013490	superfamily	246710	586	707	1.33E-27	109.9	cl14783	DOMON_like superfamily	 - 	 - 	"Domon-like ligand-binding domains; DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases."
Q#24584 - 	CGI_10013490	superfamily	216290	184	311	4.77E-33	125.093	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#24584 - 	CGI_10013490	superfamily	217685	328	485	1.03E-29	116.28	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#24584 - 	CGI_10013490	superfamily	217685	705	789	1.20E-24	101.642	cl04225	Cu2_monoox_C superfamily	N	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#24586 - 	CGI_10013492	superfamily	222070	201	347	6.44E-18	78.8736	cl18634	DDE_3 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#24587 - 	CGI_10011531	superfamily	245847	116	247	2.06E-19	81.8341	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#24587 - 	CGI_10011531	superfamily	245847	1	122	1.57E-12	62.1889	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#24591 - 	CGI_10011536	superfamily	245847	27	72	0.000804648	34.4546	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#24593 - 	CGI_10011538	superfamily	245603	110	191	4.73E-06	43.3792	cl11403	pepsin_retropepsin_like superfamily	 - 	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#24594 - 	CGI_10011539	superfamily	241563	61	97	9.71E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24595 - 	CGI_10007963	superfamily	218328	141	330	1.91E-99	296.183	cl04844	XAP5 superfamily	 - 	 - 	"XAP5, circadian clock regulator; This protein is found in a wide range of eukaryotes. It is a nuclear protein and is suggested to be DNA binding. In plants, this family is essential for correct circadian clock functioning by acting as a light-quality regulator coordinating the activities of blue and red light signalling pathways during plant growth - inhibiting growth in red light but promoting growth in blue light."
Q#24597 - 	CGI_10007965	superfamily	247999	26	70	3.27E-08	46.8214	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#24601 - 	CGI_10007969	superfamily	248264	8	49	0.000273184	38.7574	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#24602 - 	CGI_10007970	superfamily	247905	567	620	1.04E-09	56.8625	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#24602 - 	CGI_10007970	superfamily	247805	406	550	2.90E-09	55.4212	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#24602 - 	CGI_10007970	superfamily	248264	321	381	0.0042336	37.2166	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#24604 - 	CGI_10024240	superfamily	248318	274	322	4.41E-18	76.7057	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#24605 - 	CGI_10024241	superfamily	247725	216	257	2.74E-06	44.2278	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24605 - 	CGI_10024241	superfamily	149853	19	78	4.55E-06	43.2093	cl07491	Phe_ZIP superfamily	 - 	 - 	"Phenylalanine zipper; The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS, SH2-B and Lnk."
Q#24606 - 	CGI_10024242	superfamily	246908	30	125	1.79E-63	194.562	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#24607 - 	CGI_10024245	superfamily	247724	285	559	9.50E-156	453.156	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24608 - 	CGI_10024246	superfamily	247724	543	810	1.59E-139	418.102	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24608 - 	CGI_10024246	superfamily	247724	314	545	3.09E-114	352.233	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24609 - 	CGI_10024247	superfamily	248054	5	218	3.46E-14	70.7943	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#24610 - 	CGI_10024248	superfamily	241640	589	798	1.08E-67	227.159	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#24610 - 	CGI_10024248	superfamily	241571	386	486	2.85E-25	102.876	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24610 - 	CGI_10024248	superfamily	241571	27	133	2.99E-22	94.0162	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24610 - 	CGI_10024248	superfamily	241571	226	329	5.61E-21	90.5494	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24610 - 	CGI_10024248	superfamily	241613	516	550	1.13E-11	61.4537	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24610 - 	CGI_10024248	superfamily	243051	924	1066	2.73E-09	56.5901	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#24610 - 	CGI_10024248	superfamily	243051	799	916	1.34E-06	48.143	cl02479	MAM superfamily	N	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#24613 - 	CGI_10024251	superfamily	149750	182	207	1.15E-09	52.9472	cl07409	NHR2 superfamily	NC	 - 	NHR2 domain like; The NHR2 (Nervy homology 2) domain is found in the ETO protein where it mediates oligomerisation and protein-protein interactions. It forms an alpha-helical tetramer.
Q#24615 - 	CGI_10024253	superfamily	241578	64	230	1.53E-41	146.219	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24615 - 	CGI_10024253	superfamily	241578	278	431	1.72E-05	43.4342	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24617 - 	CGI_10024255	superfamily	241573	80	383	1.01E-106	325.441	cl00051	CysPc superfamily	 - 	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#24617 - 	CGI_10024255	superfamily	241653	406	553	6.26E-39	139.741	cl00165	Calpain_III superfamily	 - 	 - 	"Calpain, subdomain III. Calpains are  calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains."
Q#24619 - 	CGI_10024257	superfamily	244539	243	608	4.61E-124	376.182	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#24619 - 	CGI_10024257	superfamily	241863	67	193	6.90E-21	90.1443	cl00438	Flavodoxin_2 superfamily	 - 	 - 	Flavodoxin-like fold; This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
Q#24620 - 	CGI_10024258	superfamily	247725	195	331	1.21E-77	247.837	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24620 - 	CGI_10024258	superfamily	247725	333	429	2.28E-46	160.352	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24620 - 	CGI_10024258	superfamily	241597	560	610	5.26E-14	68.4233	cl00082	HMG-box superfamily	C	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#24621 - 	CGI_10024259	superfamily	248469	455	578	0.000444903	39.6607	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#24621 - 	CGI_10024259	superfamily	217255	124	310	1.70E-41	150.597	cl03746	DDHD superfamily	 - 	 - 	"DDHD domain; The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3). This suggests that this region is involved in functionally important interactions in other members of this family."
Q#24622 - 	CGI_10024260	superfamily	241578	15	251	8.09E-84	269.626	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24622 - 	CGI_10024260	superfamily	234316	438	488	1.18E-05	44.0128	cl14012	Rhs_assc_core superfamily	C	 - 	"RHS repeat-associated core domain; This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (pfam01839) class, and an RHS repeat (pfam05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain."
Q#24624 - 	CGI_10024262	superfamily	241874	23	591	0	819.238	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#24625 - 	CGI_10024263	superfamily	245029	27	134	5.37E-20	80.3843	cl09190	MAPEG superfamily	 - 	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#24626 - 	CGI_10024264	superfamily	245206	6	204	8.49E-36	131.09	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#24627 - 	CGI_10024265	superfamily	245029	58	148	3.33E-17	73.0656	cl09190	MAPEG superfamily	 - 	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#24629 - 	CGI_10024267	superfamily	247723	781	857	3.27E-46	160.254	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24629 - 	CGI_10024267	superfamily	247723	674	755	2.21E-40	144.284	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24629 - 	CGI_10024267	superfamily	247723	555	626	9.05E-40	142.129	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24629 - 	CGI_10024267	superfamily	247723	370	448	1.42E-41	147.552	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24629 - 	CGI_10024267	superfamily	247723	28	92	2.02E-25	101.616	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24629 - 	CGI_10024267	superfamily	247723	258	322	8.49E-17	76.6362	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24630 - 	CGI_10024268	superfamily	242880	4	239	1.41E-143	405.028	cl02098	14-3-3 superfamily	 - 	 - 	"14-3-3 domain; 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 14-3-3 proteins play important roles in many biological processes that are regulated by phosphorylation, including cell cycle regulation, cell proliferation, protein trafficking, metabolic regulation and apoptosis.  More than 300 binding partners of the 14-3-3 domain have been identified in all subcellular compartments and include transcription factors, signaling molecules, tumor suppressors, biosynthetic enzymes, cytoskeletal proteins and apoptosis factors. 14-3-3 binding can alter the conformation, localization, stability, phosphorylation state, activity as well as molecular interactions of a target protein. They function only as dimers, some preferring strictly homodimeric interaction, while others form heterodimers. Binding of the 14-3-3 domain to its target occurs in a phosphospecific manner where it binds to one of two consensus sequences of their target proteins; RSXpSXP (mode-1) and RXXXpSXP (mode-2). In some instances, 14-3-3 domain containing proteins are involved in regulation and signaling of a number of cellular processes in phosphorylation-independent manner. Many organisms express multiple isoforms: there are seven mammalian 14-3-3 family members (beta, gamma, eta, theta, epsilon, sigma, zeta), each encoded by a distinct gene, while plants contain up to 13 isoforms. The flexible C-terminal segment of 14-3-3 isoforms shows the highest sequence variability and may significantly contribute to individual isoform uniqueness by playing an important regulatory role by occupying the ligand binding groove and blocking the binding of inappropriate ligands in a distinct manner. Elevated amounts of 14-3-3 proteins are found in the cerebrospinal fluid of patients with Creutzfeldt-Jakob disease. In protozoa, like Plasmodium or Cryptosporidium parvum 14-3-3 proteins play an important role in key steps of parasite development."
Q#24631 - 	CGI_10024269	superfamily	243166	51	241	4.73E-26	101.601	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#24632 - 	CGI_10024270	superfamily	203013	269	296	7.14E-09	50.7022	cl04519	zf-HIT superfamily	 - 	 - 	HIT zinc finger; This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) that specifically interacts with the ligand binding domain of the thyroid receptor.
Q#24633 - 	CGI_10024271	superfamily	222150	183	206	1.03E-05	41.2233	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24633 - 	CGI_10024271	superfamily	222150	153	180	0.000986726	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24634 - 	CGI_10024272	superfamily	148805	2	175	1.12E-39	138.738	cl06443	NICE-3 superfamily	 - 	 - 	NICE-3 protein; This family consists of several eukaryotic NICE-3 and related proteins. The gene coding for NICE-3 is part of the epidermal differentiation complex (EDC) which comprises a large number of genes that are of crucial importance for the maturation of the human epidermis. The function of NICE-3 is unknown.
Q#24636 - 	CGI_10024274	superfamily	241677	34	199	2.25E-75	227.14	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#24638 - 	CGI_10024276	superfamily	242323	149	263	1.48E-12	62.526	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#24639 - 	CGI_10024277	superfamily	183292	151	194	3.69E-05	44.042	cl18135	PRK11728 superfamily	NC	 - 	hydroxyglutarate oxidase; Provisional
Q#24639 - 	CGI_10024277	superfamily	183782	2	34	0.000307738	41.4223	cl18137	PRK12834 superfamily	C	 - 	putative FAD-binding dehydrogenase; Reviewed
Q#24640 - 	CGI_10024278	superfamily	183782	2	34	0.000247619	41.0371	cl18137	PRK12834 superfamily	C	 - 	putative FAD-binding dehydrogenase; Reviewed
Q#24641 - 	CGI_10024279	superfamily	241739	1	201	3.36E-128	370.342	cl00268	class_II_aaRS-like_core superfamily	N	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#24641 - 	CGI_10024279	superfamily	241738	201	291	4.14E-28	104.893	cl00266	HGTP_anticodon superfamily	 - 	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#24643 - 	CGI_10024281	superfamily	248458	123	251	1.72E-10	61.5609	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24643 - 	CGI_10024281	superfamily	248458	363	548	6.77E-06	46.9233	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24644 - 	CGI_10024282	superfamily	248458	122	242	6.65E-09	56.5533	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24644 - 	CGI_10024282	superfamily	248458	360	535	0.000437501	41.1453	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24645 - 	CGI_10024283	superfamily	243309	1	128	9.60E-59	189.98	cl03119	FpgNei_N superfamily	 - 	 - 	"N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins."
Q#24645 - 	CGI_10024283	superfamily	150080	247	285	2.16E-11	58.6478	cl07797	Neil1-DNA_bind superfamily	 - 	 - 	"Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding."
Q#24645 - 	CGI_10024283	superfamily	115485	135	201	1.13E-08	51.941	cl06065	H2TH superfamily	C	 - 	Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.
Q#24647 - 	CGI_10024285	superfamily	247792	500	543	0.000212299	40.1216	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24648 - 	CGI_10024286	superfamily	243082	1084	1408	1.32E-166	503.381	cl02553	Peptidase_C19 superfamily	 - 	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#24648 - 	CGI_10024286	superfamily	247725	36	154	1.40E-34	130.436	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24648 - 	CGI_10024286	superfamily	246669	216	332	9.19E-13	67.2094	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#24649 - 	CGI_10024287	superfamily	242205	1	160	2.58E-60	186.356	cl00937	Ribosomal_L21e superfamily	 - 	 - 	Ribosomal protein L21e; Ribosomal protein L21e.  
Q#24650 - 	CGI_10024288	superfamily	243066	14	102	1.62E-11	58.3333	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24651 - 	CGI_10024289	superfamily	242194	18	99	1.08E-30	116.515	cl00921	Ribosomal_L31e superfamily	 - 	 - 	"Eukaryotic/archaeal ribosomal protein L31; Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. It is a component of the eukaryotic 60S (large) ribosomal subunit, and the archaeal 50S (large) ribosomal subunit."
Q#24653 - 	CGI_10024291	superfamily	243035	134	246	2.15E-07	47.6146	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#24654 - 	CGI_10024292	superfamily	245814	38	116	0.00923442	32.8625	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24655 - 	CGI_10024293	superfamily	247684	8	433	3.83E-116	353.891	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24656 - 	CGI_10024294	superfamily	247684	12	110	5.20E-21	85.7919	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24657 - 	CGI_10024295	superfamily	247684	1	313	1.21E-77	249.887	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24658 - 	CGI_10024296	superfamily	247684	5	428	6.74E-106	326.927	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24659 - 	CGI_10024297	superfamily	243238	182	684	0	666.232	cl02915	Voltage_gated_ClC superfamily	 - 	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#24659 - 	CGI_10024297	superfamily	246936	715	852	6.44E-34	126.598	cl15354	CBS_pair superfamily	 - 	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#24660 - 	CGI_10024298	superfamily	246681	3	224	1.82E-128	366.581	cl14643	SRPBCC superfamily	 - 	 - 	"START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins."
Q#24661 - 	CGI_10024299	superfamily	241570	171	256	4.53E-09	54.6394	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24662 - 	CGI_10024300	superfamily	241570	298	408	1.87E-19	85.0701	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24668 - 	CGI_10024306	superfamily	241570	258	335	4.37E-05	41.9278	cl00047	CAP_ED superfamily	C	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#24669 - 	CGI_10024307	superfamily	243092	305	616	7.38E-52	183.69	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24669 - 	CGI_10024307	superfamily	217837	753	860	1.54E-20	88.8037	cl04367	Utp12 superfamily	 - 	 - 	Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.
Q#24669 - 	CGI_10024307	superfamily	243092	58	200	2.30E-09	58.1152	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24670 - 	CGI_10024308	superfamily	241883	11	116	1.92E-34	118.258	cl00466	ATP-synt_C superfamily	 - 	 - 	ATP synthase subunit C; ATP synthase subunit C.  
Q#24670 - 	CGI_10024308	superfamily	241883	108	150	5.81E-05	38.1992	cl00466	ATP-synt_C superfamily	N	 - 	ATP synthase subunit C; ATP synthase subunit C.  
Q#24671 - 	CGI_10024309	superfamily	241593	45	160	1.20E-08	53.0342	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#24672 - 	CGI_10026329	superfamily	243096	504	635	1.86E-28	113.932	cl02571	RhoGEF superfamily	C	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#24672 - 	CGI_10026329	superfamily	248318	799	853	3.93E-22	91.7285	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#24672 - 	CGI_10026329	superfamily	247725	656	754	3.58E-17	78.6458	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24672 - 	CGI_10026329	superfamily	247725	870	956	2.94E-16	75.8747	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24673 - 	CGI_10026330	superfamily	248318	36	88	8.50E-18	74.3945	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#24673 - 	CGI_10026330	superfamily	247725	112	195	1.41E-14	66.2447	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24674 - 	CGI_10026331	superfamily	243072	6	95	9.17E-09	48.5338	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24675 - 	CGI_10026332	superfamily	243072	6	95	1.02E-08	48.1486	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24677 - 	CGI_10026334	superfamily	241600	121	333	3.87E-88	266.028	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24678 - 	CGI_10026335	superfamily	243082	84	276	6.90E-20	85.1104	cl02553	Peptidase_C19 superfamily	C	 - 	"Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome."
Q#24679 - 	CGI_10026336	superfamily	245201	14	288	2.34E-56	189.653	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24680 - 	CGI_10026337	superfamily	247724	13	209	2.67E-80	240.925	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24681 - 	CGI_10026338	superfamily	243066	845	945	1.40E-06	47.6856	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24682 - 	CGI_10026339	superfamily	241782	152	551	2.08E-119	359.21	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#24683 - 	CGI_10026340	superfamily	246722	1545	1721	5.20E-80	263.463	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#24683 - 	CGI_10026340	superfamily	220722	968	1074	1.38E-20	90.5565	cl11040	EST1 superfamily	 - 	 - 	Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerisation.
Q#24686 - 	CGI_10026343	superfamily	243051	26	173	3.93E-12	63.5237	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#24687 - 	CGI_10026344	superfamily	191444	21	93	0.0063329	31.5257	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#24688 - 	CGI_10026345	superfamily	243119	60	112	1.34E-05	38.9541	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#24688 - 	CGI_10026345	superfamily	243119	3	52	0.000474979	34.7169	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#24689 - 	CGI_10026346	superfamily	241810	96	198	5.49E-58	181.977	cl00354	KOW superfamily	C	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#24691 - 	CGI_10026348	superfamily	241740	9	122	2.34E-36	123.881	cl00269	cytidine_deaminase-like superfamily	 - 	 - 	"Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes.  All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate."
Q#24692 - 	CGI_10026349	superfamily	215691	191	249	9.44E-05	40.2618	cl15766	Pyr_redox superfamily	C	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#24694 - 	CGI_10026351	superfamily	247984	24	200	2.34E-53	182.425	cl17430	FtsJ superfamily	 - 	 - 	"FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping."
Q#24694 - 	CGI_10026351	superfamily	221275	230	314	1.49E-27	109.298	cl13325	DUF3381 superfamily	C	 - 	"Domain of unknown function (DUF3381); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728."
Q#24694 - 	CGI_10026351	superfamily	219572	532	680	5.39E-26	106.609	cl06696	Spb1_C superfamily	 - 	 - 	Spb1 C-terminal domain; This presumed domain is found at the C-terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis.
Q#24696 - 	CGI_10026353	superfamily	247755	1156	1376	2.56E-118	370.671	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#24696 - 	CGI_10026353	superfamily	247755	566	707	1.02E-54	191.143	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#24696 - 	CGI_10026353	superfamily	216049	840	1107	1.04E-25	108.913	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#24696 - 	CGI_10026353	superfamily	216049	290	518	3.60E-24	104.29	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#24699 - 	CGI_10026356	superfamily	248022	341	590	6.46E-10	59.9839	cl17468	Aa_trans superfamily	N	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#24699 - 	CGI_10026356	superfamily	248022	149	230	1.46E-07	52.6651	cl17468	Aa_trans superfamily	C	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#24700 - 	CGI_10026357	superfamily	243092	434	619	0.00282846	39.2404	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24702 - 	CGI_10026359	superfamily	243854	1	154	1.29E-97	282.966	cl04709	ASF1_hist_chap superfamily	 - 	 - 	ASF1 like histone chaperone; This family includes the yeast and human ASF1 protein. These proteins have histone chaperone activity. ASF1 participates in both the replication-dependent and replication-independent pathways. The structure three-dimensional has been determined as a a compact immunoglobulin-like beta sandwich fold topped by three helical linkers.
Q#24704 - 	CGI_10026361	superfamily	242465	282	319	7.22E-05	42.0436	cl01378	LicD superfamily	C	 - 	"LicD family; The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent. These proteins are part of the nucleotidyltransferase superfamily."
Q#24705 - 	CGI_10026362	superfamily	217390	158	299	1.29E-26	107.646	cl18407	TPT superfamily	 - 	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#24705 - 	CGI_10026362	superfamily	217473	435	662	1.75E-25	107.836	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#24705 - 	CGI_10026362	superfamily	248313	21	148	5.65E-08	52.2334	cl17759	EamA superfamily	 - 	 - 	EamA-like transporter family; This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.
Q#24706 - 	CGI_10026363	superfamily	220691	206	316	0.00982061	36.827	cl18569	7TM_GPCR_Srv superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srv; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#24707 - 	CGI_10026365	superfamily	241677	142	299	5.66E-108	313.81	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#24707 - 	CGI_10026365	superfamily	247723	9	81	1.18E-48	158.54	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24708 - 	CGI_10026366	superfamily	247755	56	213	6.72E-42	153.523	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#24708 - 	CGI_10026366	superfamily	247755	986	1032	1.69E-22	97.2834	cl17201	ABC_ATPase superfamily	NC	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#24711 - 	CGI_10026369	superfamily	217473	325	552	3.77E-25	107.066	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#24711 - 	CGI_10026369	superfamily	217473	1036	1137	5.37E-13	69.7013	cl03978	Mab-21 superfamily	NC	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#24712 - 	CGI_10026370	superfamily	248012	515	643	2.58E-13	66.8325	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#24712 - 	CGI_10026370	superfamily	248012	340	450	1.28E-10	59.1285	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#24712 - 	CGI_10026370	superfamily	247057	253	318	5.67E-09	53.46	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#24712 - 	CGI_10026370	superfamily	248012	75	190	0.00225983	36.7869	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#24713 - 	CGI_10026371	superfamily	217925	11	120	4.85E-27	99.1177	cl04417	Ctr superfamily	 - 	 - 	"Ctr copper transporter family; The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport."
Q#24714 - 	CGI_10026372	superfamily	217925	48	92	0.00308086	34.7893	cl04417	Ctr superfamily	N	 - 	"Ctr copper transporter family; The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport."
Q#24716 - 	CGI_10026374	superfamily	248097	60	183	1.04E-13	64.2086	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24717 - 	CGI_10026375	superfamily	248097	220	343	1.34E-14	69.2162	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24717 - 	CGI_10026375	superfamily	248097	73	159	1.21E-12	63.4382	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24718 - 	CGI_10026376	superfamily	248097	59	182	1.01E-12	61.127	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24719 - 	CGI_10026377	superfamily	248097	118	241	2.40E-18	78.0758	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24720 - 	CGI_10026378	superfamily	222429	7	85	2.50E-14	65.3396	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#24721 - 	CGI_10026379	superfamily	248097	59	184	5.77E-18	76.1498	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24722 - 	CGI_10026380	superfamily	243077	10	65	1.78E-20	85.6749	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#24722 - 	CGI_10026380	superfamily	248275	309	334	1.32E-08	51.4268	cl17721	zf-C2H2_jaz superfamily	 - 	 - 	"Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation."
Q#24724 - 	CGI_10026382	superfamily	247683	268	337	1.73E-05	42.1096	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#24725 - 	CGI_10026383	superfamily	246908	504	609	3.12E-56	189.457	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#24725 - 	CGI_10026383	superfamily	214269	614	765	1.07E-38	141.978	cl17108	iSH2_PI3K_IA_R superfamily	 - 	 - 	"Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits."
Q#24725 - 	CGI_10026383	superfamily	243095	298	471	7.19E-28	111.625	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#24725 - 	CGI_10026383	superfamily	241566	214	263	5.86E-09	53.65	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#24725 - 	CGI_10026383	superfamily	247057	121	170	2.94E-08	51.8565	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#24725 - 	CGI_10026383	superfamily	246908	782	884	5.29E-26	104.033	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#24725 - 	CGI_10026383	superfamily	241566	45	86	0.000155676	40.5155	cl00040	C1 superfamily	C	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#24726 - 	CGI_10026385	superfamily	245206	6	333	0	549.445	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#24728 - 	CGI_10026387	superfamily	243690	127	287	1.31E-16	75.8233	cl04276	Mtp superfamily	N	 - 	Golgi 4-transmembrane spanning transporter; Golgi 4-transmembrane spanning transporter.  
Q#24730 - 	CGI_10026389	superfamily	248012	279	421	1.06E-22	93.9272	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#24731 - 	CGI_10026390	superfamily	245213	45	82	2.54E-05	42.2386	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#24733 - 	CGI_10026392	superfamily	247724	111	146	0.000594677	38.8564	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24736 - 	CGI_10026395	superfamily	247725	121	264	2.10E-37	137.835	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24736 - 	CGI_10026395	superfamily	243095	365	559	1.11E-97	311.257	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#24739 - 	CGI_10026398	superfamily	220666	73	156	2.26E-18	80.0966	cl10951	Tmemb_185A superfamily	N	 - 	"Transmembrane Fragile-X-F protein; This is a family of conserved transmembrane proteins that appear in humans to be expressed from a region upstream of the FragileXF site and to be intimately linked with the Fragile-X syndrome. Absence of TMEM185A does not necessarily lead to developmental delay, but might in combination with other, yet unknown, factors. Otherwise, the lack of the TMEM185A protein is either disposable (redundant) or its function can be complemented by the highly similar chromosome 2 retro-pseudogene product, TMEM185B."
Q#24741 - 	CGI_10026400	superfamily	245201	1	136	3.03E-46	157.123	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24744 - 	CGI_10000799	superfamily	215691	160	241	5.65E-08	49.8918	cl15766	Pyr_redox superfamily	 - 	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#24746 - 	CGI_10000801	superfamily	217572	337	400	5.78E-11	59.0684	cl08392	NIR_SIR_ferr superfamily	 - 	 - 	Nitrite/Sulfite reductase ferredoxin-like half domain; Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidized anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain.
Q#24747 - 	CGI_10000803	superfamily	245203	11	515	0	712.845	cl09928	Molybdopterin-Binding superfamily	 - 	 - 	"Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a  large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is the eukaryotic/eubacterial protein domain family of the 75-kDa subunit/Nad11/NuoG (second domain) of respiratory complex 1/NADH-quinone oxidoreductase which is postulated to have lost an ancestral formate dehydrogenase activity and only vestigial sequence evidence remains of a molybdopterin binding site."
Q#24747 - 	CGI_10000803	superfamily	245204	522	645	1.62E-55	187.01	cl09929	MopB_CT superfamily	 - 	 - 	"Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a  large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is the eukaryotic/eubacterial protein domain family of the 75-kDa subunit/Nad11/NuoG (second domain) of respiratory complex 1/NADH-quinone oxidoreductase which is postulated to have lost an ancestral formate dehydrogenase activity and only vestigial sequence evidence remains of a molybdopterin binding site. This hierarchy is of the conserved MopB_CT domain present in many, but not all, MopB homologs."
Q#24747 - 	CGI_10000803	superfamily	242297	772	823	5.50E-13	65.3851	cl01093	Fer2_BFD superfamily	 - 	 - 	"BFD-like [2Fe-2S] binding domain; The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as Bacterioferritin-associated ferredoxin (BFD). The function of BFD is not known, but it may may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria. This domain is also found in nitrate reductase proteins in association with Nitrite and sulphite reductase 4Fe-4S domain (pfam01077), Nitrite/Sulfite reductase ferredoxin-like half domain (pfam03460) and Pyridine nucleotide-disulphide oxidoreductase (pfam00070). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N terminal domain (pfam01592) and NifU-like domain (pfam01106)."
Q#24748 - 	CGI_10014146	superfamily	218787	8	145	1.45E-61	189.404	cl05443	ESCRT-II superfamily	 - 	 - 	"ESCRT-II complex subunit; This family of conserved eukaryotic proteins are subunits of the endosome associated complex ESCRT-II which recruits transport machinery for protein sorting at the multivesicular body (MVB). This protein complex transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo."
Q#24749 - 	CGI_10014147	superfamily	243092	420	675	3.90E-68	226.833	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24749 - 	CGI_10014147	superfamily	208922	93	225	5.85E-51	173.919	cl08418	TAF5_NTD2 superfamily	 - 	 - 	"TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID); The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs.  In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. TAF5 has a paralog gene (TAF5L) which has a redundant function. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. C-terminus of TAF5 contains six WD40 repeats that likely form a closed beta propeller structure and may be involved in protein-protein interaction. The first part of the TAF5 N-terminal (TAF5_NTD1) homodimerizes in the absence of other TAFs. The second conserved N-terminal part of TAF5 (TAF5_NTD2) has an alpha-helical domain. One study has shown that TAF5_NTD2 homodimerizes only at high concentration of calcium but not any other metals. No dimerization was observed in other structural studies of TAF_NTD2. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. However, TAF5 does not have a HFD motif."
Q#24751 - 	CGI_10014149	superfamily	218883	148	310	0.00113315	40.196	cl09398	DUF936 superfamily	NC	 - 	Plant protein of unknown function (DUF936); This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Q#24752 - 	CGI_10014150	superfamily	248028	571	755	1.31E-21	95.6517	cl17474	Steroid_dh superfamily	N	 - 	"3-oxo-5-alpha-steroid 4-dehydrogenase; This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development."
Q#24752 - 	CGI_10014150	superfamily	214781	126	224	2.41E-12	64.6708	cl02747	NRF superfamily	 - 	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#24753 - 	CGI_10014151	superfamily	247787	104	476	0	774.089	cl17233	RecA-like_NTPases superfamily	 - 	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#24753 - 	CGI_10014151	superfamily	215848	494	636	8.71E-24	96.9653	cl08258	ATP-synt_ab_C superfamily	 - 	 - 	"ATP synthase alpha/beta chain, C terminal domain; ATP synthase alpha/beta chain, C terminal domain.  "
Q#24753 - 	CGI_10014151	superfamily	217261	40	102	1.03E-12	64.0836	cl18399	ATP-synt_ab_N superfamily	 - 	 - 	"ATP synthase alpha/beta family, beta-barrel domain; This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella."
Q#24754 - 	CGI_10014152	superfamily	241581	354	454	1.03E-08	52.7738	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#24755 - 	CGI_10014153	superfamily	247044	1507	1612	5.72E-32	122.765	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24755 - 	CGI_10014153	superfamily	247044	1196	1289	5.62E-23	96.5376	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24755 - 	CGI_10014153	superfamily	247044	1634	1737	9.05E-15	72.6493	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24755 - 	CGI_10014153	superfamily	247044	1316	1389	4.95E-08	52.7554	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#24759 - 	CGI_10014157	superfamily	243267	31	395	1.79E-130	382.732	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#24760 - 	CGI_10014158	superfamily	216212	722	1226	0	675.547	cl03037	HCO3_cotransp superfamily	 - 	 - 	HCO3- transporter family; This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-.
Q#24760 - 	CGI_10014158	superfamily	192379	1381	1695	8.98E-57	201.906	cl10764	Hyccin superfamily	 - 	 - 	"Hyccin; Members of this family of proteins may have a role in the beta-catenin-Tcf/Lef signaling pathway, as well as in the process of myelination of the central and peripheral nervous system. Defects in Hyccin are the cause of hypomyelination with congenital cataracts. This disorder is characterized by congenital cataracts, progressive neurologic impairment, and diffuse myelin deficiency. Affected individuals experience progressive pyramidal and cerebellar dysfunction, muscle weakness and wasting prevailing in the lower limbs."
Q#24760 - 	CGI_10014158	superfamily	241651	597	697	0.00015517	42.236	cl00163	PTS_IIA_fru superfamily	N	 - 	"PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation."
Q#24761 - 	CGI_10014159	superfamily	241640	5	130	7.44E-23	97.7322	cl00149	Tryp_SPc superfamily	C	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#24762 - 	CGI_10014160	superfamily	220695	44	168	3.83E-05	43.7215	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#24763 - 	CGI_10014161	superfamily	241640	42	275	1.45E-75	232.552	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#24764 - 	CGI_10014162	superfamily	245864	55	523	6.74E-86	275.311	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#24765 - 	CGI_10014163	superfamily	241567	106	159	5.78E-12	60.0214	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#24767 - 	CGI_10019601	superfamily	248097	318	448	3.64E-16	74.609	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24771 - 	CGI_10019605	superfamily	247725	140	250	2.60E-49	168.623	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24771 - 	CGI_10019605	superfamily	219977	12	88	7.65E-13	65.384	cl18539	Vps51 superfamily	 - 	 - 	"Vps51/Vps67; This family includes a presumed domain found in a number of components of vesicular transport. The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1. Cog1_N is the N-terminus of the Cog1 subunit of the eight-unit Conserved Oligomeric Golgi (COG) complex that participates in retrograde vesicular transport and is required to maintain normal Golgi structure and function. The subunits are located in two lobes and Cog1 serves to bind the two lobes together probably via the highly conserved N-terminal domain of approximately 85 residues."
Q#24772 - 	CGI_10019606	superfamily	241607	45	79	1.69E-06	42.257	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24772 - 	CGI_10019606	superfamily	241607	86	120	1.93E-06	41.8718	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24775 - 	CGI_10019609	superfamily	247723	119	195	2.62E-47	159.089	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24775 - 	CGI_10019609	superfamily	247723	204	273	8.24E-45	152.036	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#24777 - 	CGI_10019611	superfamily	218077	381	429	8.40E-09	52.3362	cl04505	DUF543 superfamily	 - 	 - 	Domain of unknown function (DUF543); This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. The presumed domain contains a conserved amino terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.
Q#24778 - 	CGI_10019612	superfamily	221898	2993	3091	1.65E-19	87.2658	cl16030	DUF3883 superfamily	 - 	 - 	Domain of unknown function (DUF3883); This is a domain is uncharacterized. It is found on restriction endonucleases.
Q#24780 - 	CGI_10019614	superfamily	241596	21	46	0.000835082	36.8083	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#24780 - 	CGI_10019614	superfamily	243123	60	98	1.07E-13	64.8869	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#24782 - 	CGI_10019616	superfamily	241596	50	107	2.52E-10	56.0683	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#24782 - 	CGI_10019616	superfamily	243123	125	159	6.03E-11	57.5681	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#24783 - 	CGI_10019617	superfamily	192535	21	213	0.00355704	37.1902	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#24785 - 	CGI_10019619	superfamily	201806	122	595	5.88E-92	296.703	cl18220	Peptidase_M8 superfamily	N	 - 	Leishmanolysin; Leishmanolysin.  
Q#24789 - 	CGI_10019623	superfamily	222150	643	666	1.10E-05	43.5345	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24789 - 	CGI_10019623	superfamily	222150	560	584	1.84E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24789 - 	CGI_10019623	superfamily	222150	671	696	0.00014493	40.4529	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24789 - 	CGI_10019623	superfamily	222150	588	613	0.00249598	36.6009	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24789 - 	CGI_10019623	superfamily	222150	535	557	0.0053565	35.8305	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24790 - 	CGI_10019624	superfamily	222150	363	387	1.19E-05	43.1493	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24790 - 	CGI_10019624	superfamily	222150	446	469	1.33E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24790 - 	CGI_10019624	superfamily	222150	474	498	0.00471542	35.4453	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#24791 - 	CGI_10019625	superfamily	218364	383	733	8.29E-61	212.542	cl04875	PigN superfamily	 - 	 - 	Phosphatidylinositolglycan class N (PIG-N); Phosphatidylinositolglycan class N (PIG-N) is a mammalian homologue of the yeast protein MCD4P and is expressed in the endoplasmic reticulum. PIG-N is essential for glycosylphosphatidylinositol anchor synthesis. Glycosylphosphatidylinositol (GPI)-anchored proteins are cell surface-localised proteins that serve many important cellular functions.
Q#24791 - 	CGI_10019625	superfamily	248020	143	308	0.000129862	43.6072	cl17466	Sulfatase superfamily	N	 - 	Sulfatase; Sulfatase.  
Q#24793 - 	CGI_10019627	superfamily	152053	423	436	0.00398407	35.5839	cl13123	Cu-binding_MopE superfamily	N	 - 	"Protein metal binding site; This family of proteins represents a unique protein copper binding site that involves a tryptophan metabolite, kynurenine in the protein MopE. The production of kyneurenin by modification of tryptophan and its involvement in copper binding is an innate property of MopE."
Q#24797 - 	CGI_10004029	superfamily	243072	1141	1263	1.47E-34	130.581	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24797 - 	CGI_10004029	superfamily	243072	945	1054	3.83E-19	85.8982	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24797 - 	CGI_10004029	superfamily	243072	995	1164	2.03E-16	78.1942	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24797 - 	CGI_10004029	superfamily	243072	1238	1323	4.67E-07	50.0746	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24798 - 	CGI_10004030	superfamily	247684	13	435	1.37E-103	321.149	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24799 - 	CGI_10002337	superfamily	216686	3	123	9.50E-20	82.3709	cl18377	Galactosyl_T superfamily	N	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#24802 - 	CGI_10007972	superfamily	218753	85	149	8.04E-20	88.1092	cl05390	Tcp11 superfamily	C	 - 	T-complex protein 11; This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the yeast Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants.
Q#24803 - 	CGI_10007973	superfamily	246723	13	369	1.27E-157	457.796	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#24804 - 	CGI_10007974	superfamily	246723	13	369	1.25E-152	449.707	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#24806 - 	CGI_10007976	superfamily	241593	27	145	7.18E-12	63.4601	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#24808 - 	CGI_10002521	superfamily	241613	101	133	1.67E-08	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24808 - 	CGI_10002521	superfamily	241613	226	260	1.72E-08	52.5942	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24808 - 	CGI_10002521	superfamily	241613	187	218	7.11E-08	50.6682	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24808 - 	CGI_10002521	superfamily	241613	268	300	2.88E-05	42.9642	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24808 - 	CGI_10002521	superfamily	241613	141	174	0.00108546	38.3418	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24808 - 	CGI_10002521	superfamily	214531	647	689	2.43E-12	63.7748	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24808 - 	CGI_10002521	superfamily	215683	623	664	2.79E-12	63.3431	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#24808 - 	CGI_10002521	superfamily	214531	560	599	4.86E-09	54.1449	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#24808 - 	CGI_10002521	superfamily	215683	581	620	8.03E-05	41.7719	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#24808 - 	CGI_10002521	superfamily	241613	345	379	0.0082257	35.7346	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#24810 - 	CGI_10002523	superfamily	244906	413	480	5.16E-18	78.7212	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#24811 - 	CGI_10002524	superfamily	217685	234	386	3.36E-18	81.6116	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#24811 - 	CGI_10002524	superfamily	216290	96	213	1.75E-09	55.3722	cl03089	Cu2_monooxygen superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#24818 - 	CGI_10007573	superfamily	241574	136	304	3.89E-58	198.194	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#24818 - 	CGI_10007573	superfamily	241574	306	433	4.71E-06	47.1953	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#24818 - 	CGI_10007573	superfamily	238012	677	718	0.00290467	36.5634	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#24821 - 	CGI_10000563	superfamily	243061	76	176	9.04E-34	117.058	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#24821 - 	CGI_10000563	superfamily	243061	25	73	0.000125486	38.0918	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#24822 - 	CGI_10008482	superfamily	242889	221	289	6.46E-09	53.3999	cl02111	PCI superfamily	C	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#24826 - 	CGI_10008486	superfamily	241563	68	109	3.09E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24826 - 	CGI_10008486	superfamily	241563	28	59	0.00187435	36.6884	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24827 - 	CGI_10008487	superfamily	245208	1	371	0	693.718	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#24829 - 	CGI_10008489	superfamily	241642	181	236	3.59E-09	51.7274	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#24830 - 	CGI_10008490	superfamily	190308	36	172	2.25E-53	184.83	cl18163	Fringe superfamily	N	 - 	"Fringe-like; The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions."
Q#24830 - 	CGI_10008490	superfamily	241563	200	241	0.0058701	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24836 - 	CGI_10001059	superfamily	220679	15	133	2.59E-09	52.3293	cl18567	Methyltransf_16 superfamily	N	 - 	Putative methyltransferase; Putative methyltransferase.  
Q#24844 - 	CGI_10001533	superfamily	241566	213	258	2.07E-11	58.6576	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#24844 - 	CGI_10001533	superfamily	241645	130	196	2.11E-12	62.0314	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#24845 - 	CGI_10001534	superfamily	248097	3	122	4.82E-13	61.127	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24848 - 	CGI_10024616	superfamily	246936	786	864	4.65E-14	70.7441	cl15354	CBS_pair superfamily	N	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#24848 - 	CGI_10024616	superfamily	246936	697	752	0.000176894	41.8541	cl15354	CBS_pair superfamily	C	 - 	"The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase)."
Q#24848 - 	CGI_10024616	superfamily	243238	109	460	7.54E-63	223.684	cl02915	Voltage_gated_ClC superfamily	C	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#24848 - 	CGI_10024616	superfamily	243238	540	672	3.31E-41	159.741	cl02915	Voltage_gated_ClC superfamily	N	 - 	"CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family.  The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria.  They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating.  Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry.  Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge.  In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function."
Q#24851 - 	CGI_10024619	superfamily	217293	1	157	7.83E-32	119.66	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#24851 - 	CGI_10024619	superfamily	202474	166	250	1.25E-21	90.7908	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#24851 - 	CGI_10024619	superfamily	202474	295	326	3.10E-05	43.4113	cl08379	Neur_chan_memb superfamily	N	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#24852 - 	CGI_10024620	superfamily	247684	76	499	2.16E-95	301.889	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24854 - 	CGI_10024622	superfamily	215648	140	366	9.02E-23	96.8959	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#24855 - 	CGI_10024623	superfamily	241733	10	85	1.87E-49	152.784	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#24856 - 	CGI_10024624	superfamily	247725	1459	1581	7.35E-64	216.047	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24856 - 	CGI_10024624	superfamily	247725	2128	2265	2.89E-45	163.171	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24856 - 	CGI_10024624	superfamily	243096	1950	2123	6.15E-42	155.148	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#24856 - 	CGI_10024624	superfamily	243096	1258	1427	1.63E-39	148.215	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#24856 - 	CGI_10024624	superfamily	243054	543	761	1.02E-19	90.9679	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#24856 - 	CGI_10024624	superfamily	241584	2622	2714	1.47E-15	75.6107	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#24856 - 	CGI_10024624	superfamily	243054	657	874	1.17E-12	69.3967	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#24856 - 	CGI_10024624	superfamily	243054	877	1107	2.26E-12	68.2411	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#24856 - 	CGI_10024624	superfamily	247069	49	178	4.47E-10	60.8618	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#24856 - 	CGI_10024624	superfamily	243054	320	541	1.53E-08	56.3	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#24856 - 	CGI_10024624	superfamily	243054	1064	1215	3.56E-08	55.1444	cl02488	SPEC superfamily	N	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#24856 - 	CGI_10024624	superfamily	243054	194	415	5.36E-08	54.7592	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#24856 - 	CGI_10024624	superfamily	245201	2739	2993	3.94E-52	188.171	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24856 - 	CGI_10024624	superfamily	247683	2410	2465	5.84E-24	99.0515	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#24856 - 	CGI_10024624	superfamily	247683	1661	1723	2.98E-19	85.5253	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#24856 - 	CGI_10024624	superfamily	245814	2535	2618	7.19E-15	73.6936	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24857 - 	CGI_10024625	superfamily	218703	4	215	6.19E-85	253.923	cl05325	BCAS2 superfamily	 - 	 - 	Breast carcinoma amplified sequence 2 (BCAS2); This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins. BCAS2 is a putative spliceosome associated protein.
Q#24860 - 	CGI_10024628	superfamily	248458	158	291	5.22E-19	87.3693	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24860 - 	CGI_10024628	superfamily	248458	387	525	6.90E-06	46.9233	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24861 - 	CGI_10024629	superfamily	246723	97	515	1.81E-110	350.065	cl14813	GluZincin superfamily	C	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#24861 - 	CGI_10024629	superfamily	246723	529	711	3.57E-88	290.744	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#24862 - 	CGI_10024630	superfamily	220692	5	282	2.14E-17	81.0965	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#24864 - 	CGI_10024632	superfamily	241624	72	349	1.14E-76	238.765	cl00120	PP2Cc superfamily	 - 	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#24865 - 	CGI_10024633	superfamily	243555	18	207	3.87E-16	77.0462	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#24866 - 	CGI_10024634	superfamily	243035	31	136	0.00160833	35.6734	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#24867 - 	CGI_10024635	superfamily	247769	247	420	1.06E-13	68.5201	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#24868 - 	CGI_10024636	superfamily	243066	39	129	7.56E-21	88.7641	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24868 - 	CGI_10024636	superfamily	219619	366	430	2.58E-08	51.8247	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#24870 - 	CGI_10024638	superfamily	247916	104	211	9.12E-05	42.0026	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#24872 - 	CGI_10024640	superfamily	245201	12	318	0	587.545	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24873 - 	CGI_10024641	superfamily	248318	980	1033	2.53E-18	80.9429	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#24873 - 	CGI_10024641	superfamily	247725	5	147	8.04E-46	162.84	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#24873 - 	CGI_10024641	superfamily	219103	190	338	1.86E-41	149.059	cl05893	Myotub-related superfamily	 - 	 - 	"Myotubularin-related; This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease."
Q#24873 - 	CGI_10024641	superfamily	206020	398	452	7.21E-34	125.313	cl18286	Y_phosphatase_m superfamily	 - 	 - 	"Myotubularin Y_phosphatase-like; This short region is highly conserved and seems to be common to many myotubularin proteins with protein tyrosine pyrophosphate activity. As the family has a number of highly conserved residues such as histidine, cysteine, glutamine and aspartate, it is possible that this represents a catalytic core of the active enzymatic part of the proteins."
Q#24876 - 	CGI_10024644	superfamily	241611	121	234	0.00188384	36.5976	cl00102	PTX superfamily	 - 	 - 	"Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers."
Q#24877 - 	CGI_10024645	superfamily	242849	58	110	1.72E-06	45.2725	cl02041	Cyt-b5 superfamily	C	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#24877 - 	CGI_10024645	superfamily	242849	283	331	0.00769479	34.4869	cl02041	Cyt-b5 superfamily	C	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#24878 - 	CGI_10024646	superfamily	241574	472	726	1.55E-104	324.154	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#24878 - 	CGI_10024646	superfamily	246908	209	307	6.00E-56	187.221	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#24878 - 	CGI_10024646	superfamily	246908	315	414	1.06E-54	184.02	cl15255	SH2 superfamily	 - 	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#24882 - 	CGI_10024651	superfamily	248458	292	425	4.44E-11	64.2573	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24882 - 	CGI_10024651	superfamily	248458	10	121	3.76E-09	58.0941	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24883 - 	CGI_10024652	superfamily	243078	3	119	1.86E-33	121.55	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#24884 - 	CGI_10024653	superfamily	245605	7	265	1.51E-149	422.012	cl11409	RNAP_RPB11_RPB3 superfamily	 - 	 - 	"RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts."
Q#24885 - 	CGI_10024654	superfamily	243073	20	54	9.84E-07	44.7685	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#24885 - 	CGI_10024654	superfamily	245201	116	298	1.81E-20	87.5538	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24886 - 	CGI_10024655	superfamily	243092	56	307	8.82E-68	226.447	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#24886 - 	CGI_10024655	superfamily	222456	570	729	1.21E-55	188.226	cl16480	Katanin_con80 superfamily	 - 	 - 	"con80 domain of Katanin; The con80 domain of katanin is the C-terminal region of the protein that binds to the N-terminal domain of katanin-p60, the catalytic ATPase. The complex associates with a specific subregion of the mitotic spindle leading to increased microtubule disassembly and targeting of p60 to the spindle poles. The assembly and function of the mitotic spindle requires the activity of a number of microtubule-binding proteins. Katanin, a heterodimeric microtubule-severing ATPase, is found localized at mitotic spindle poles. A proposed model is that katanin is targeted to spindle poles through a combination of direct microtubule binding by the p60 subunit and through interactions between the WD40 domain and an unknown protein."
Q#24889 - 	CGI_10024658	superfamily	243073	102	144	3.40E-06	40.9165	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#24890 - 	CGI_10024659	superfamily	243072	49	174	2.85E-35	122.877	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24892 - 	CGI_10024661	superfamily	227778	46	196	1.76E-09	53.6587	cl17122	VPS24 superfamily	 - 	 - 	Conserved protein implicated in secretion [Cell motility and secretion]
Q#24894 - 	CGI_10024663	superfamily	241600	1	179	7.54E-77	231.36	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#24895 - 	CGI_10001824	superfamily	146263	43	162	1.52E-44	152.844	cl04138	SK_channel superfamily	 - 	 - 	Calcium-activated SK potassium channel; Calcium-activated SK potassium channel.  
Q#24895 - 	CGI_10001824	superfamily	198825	337	410	2.52E-15	70.9056	cl03763	CaMBD superfamily	 - 	 - 	"Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other."
Q#24895 - 	CGI_10001824	superfamily	219619	241	319	1.57E-11	60.2991	cl18518	Ion_trans_2 superfamily	 - 	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#24895 - 	CGI_10001824	superfamily	191182	387	445	0.00779299	34.9694	cl04917	Nsp1_C superfamily	N	 - 	Nsp1-like C-terminal region; This family probably forms a coiled-coil. This important region of Nsp1 is involved in binding Nup82.
Q#24896 - 	CGI_10001825	superfamily	244837	67	342	1.34E-63	215.631	cl07971	Glyco_hydro_3 superfamily	 - 	 - 	Glycosyl hydrolase family 3 N terminal domain; Glycosyl hydrolase family 3 N terminal domain.  
Q#24896 - 	CGI_10001825	superfamily	222669	651	718	7.85E-16	73.582	cl17048	Fn3-like superfamily	 - 	 - 	Fibronectin type III-like domain; This domain has a fibronectin type III-like structure. It is often found in association with pfam00933 and pfam01915. Its function is unknown.
Q#24897 - 	CGI_10001826	superfamily	241607	64	88	1.36E-05	38.0198	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24897 - 	CGI_10001826	superfamily	241607	22	56	7.14E-06	38.8043	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24898 - 	CGI_10001827	superfamily	241607	191	214	0.000127747	38.0198	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24898 - 	CGI_10001827	superfamily	241607	16	40	0.000150091	37.6346	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24898 - 	CGI_10001827	superfamily	241607	58	92	0.000259775	36.8642	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24898 - 	CGI_10001827	superfamily	241607	149	183	0.000458642	36.479	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24898 - 	CGI_10001827	superfamily	241607	97	134	0.00325163	33.807	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#24899 - 	CGI_10001526	superfamily	217598	3	107	1.15E-48	163.409	cl04130	KCNQ_channel superfamily	N	 - 	KCNQ voltage-gated potassium channel; This family matches to the C-terminal tail of KCNQ type potassium channels.
Q#24901 - 	CGI_10001528	superfamily	243072	294	423	1.61E-31	117.485	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24901 - 	CGI_10001528	superfamily	243072	373	481	3.99E-27	105.543	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24901 - 	CGI_10001528	superfamily	243072	178	353	3.51E-09	54.3118	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24902 - 	CGI_10001529	superfamily	219789	28	128	1.88E-30	108.122	cl07070	cwf18 superfamily	 - 	 - 	cwf18 pre-mRNA splicing factor; The cwf18 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe.
Q#24903 - 	CGI_10001981	superfamily	245206	1166	1397	2.67E-50	185.566	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#24903 - 	CGI_10001981	superfamily	244888	16	310	1.01E-68	236.145	cl08282	Acyl_transf_1 superfamily	 - 	 - 	Acyl transferase domain; Acyl transferase domain.  
Q#24903 - 	CGI_10001981	superfamily	245209	1442	1514	2.79E-06	47.6301	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#24910 - 	CGI_10002946	superfamily	243072	798	915	1.02E-32	124.418	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24910 - 	CGI_10002946	superfamily	243072	692	852	3.53E-14	70.8754	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24910 - 	CGI_10002946	superfamily	243072	613	747	2.89E-09	56.2378	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24916 - 	CGI_10013230	superfamily	241578	903	1064	4.15E-39	144.357	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24916 - 	CGI_10013230	superfamily	241578	79	238	9.42E-08	51.9086	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24916 - 	CGI_10013230	superfamily	241578	715	885	6.34E-22	95.1476	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24916 - 	CGI_10013230	superfamily	241578	497	672	2.17E-09	57.0129	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24916 - 	CGI_10013230	superfamily	241578	298	440	0.000360612	41.123	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24919 - 	CGI_10013233	superfamily	241584	915	1011	2.56E-09	56.3507	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#24919 - 	CGI_10013233	superfamily	241584	832	907	2.49E-08	53.2691	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#24919 - 	CGI_10013233	superfamily	245814	519	594	1.58E-14	71.3824	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24919 - 	CGI_10013233	superfamily	245814	431	495	1.17E-11	62.4243	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24919 - 	CGI_10013233	superfamily	245814	319	413	3.86E-11	61.6421	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24919 - 	CGI_10013233	superfamily	245814	228	309	5.91E-11	61.405	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24919 - 	CGI_10013233	superfamily	245814	664	753	1.42E-10	60.331	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24919 - 	CGI_10013233	superfamily	245814	110	196	4.43E-06	46.6089	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24919 - 	CGI_10013233	superfamily	245814	617	661	5.63E-06	45.8605	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24919 - 	CGI_10013233	superfamily	245814	29	93	7.35E-05	42.394	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24920 - 	CGI_10013234	superfamily	238012	241	285	6.16E-06	43.1118	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#24920 - 	CGI_10013234	superfamily	241584	42	96	0.000734441	37.4035	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#24921 - 	CGI_10013235	superfamily	243072	25	102	2.40E-11	58.549	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24922 - 	CGI_10013236	superfamily	241583	291	408	4.13E-23	98.8499	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#24922 - 	CGI_10013236	superfamily	216572	10	137	1.75E-05	44.1879	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#24923 - 	CGI_10013237	superfamily	241782	112	437	2.23E-112	340.127	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#24924 - 	CGI_10013238	superfamily	247724	444	563	1.01E-14	73.1391	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24926 - 	CGI_10013240	superfamily	246680	147	228	2.59E-09	51.9526	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#24926 - 	CGI_10013240	superfamily	246680	47	106	5.96E-09	50.8366	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#24927 - 	CGI_10013241	superfamily	243175	136	204	2.45E-16	71.1179	cl02776	GST_C_family superfamily	N	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#24927 - 	CGI_10013241	superfamily	241832	2	58	3.57E-18	76.1234	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#24928 - 	CGI_10013242	superfamily	243175	65	168	3.30E-13	61.8732	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#24928 - 	CGI_10013242	superfamily	241832	6	45	1.58E-11	56.8634	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#24932 - 	CGI_10013248	superfamily	245201	52	299	2.08E-69	230.869	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24933 - 	CGI_10013249	superfamily	241565	43	118	0.000457919	40.3827	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#24933 - 	CGI_10013249	superfamily	241752	307	609	1.77E-47	175.536	cl00283	ADP_ribosyl superfamily	 - 	 - 	"ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active."
Q#24933 - 	CGI_10013249	superfamily	241578	916	1086	3.59E-30	119.627	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#24933 - 	CGI_10013249	superfamily	207701	662	779	2.37E-29	115.469	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#24933 - 	CGI_10013249	superfamily	247684	1262	1321	9.02E-18	85.9071	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#24941 - 	CGI_10008906	superfamily	248097	287	412	1.73E-31	116.596	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24941 - 	CGI_10008906	superfamily	248097	144	269	5.12E-27	104.269	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24941 - 	CGI_10008906	superfamily	248097	38	105	2.10E-07	48.8006	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24943 - 	CGI_10008908	superfamily	248097	26	110	4.27E-17	71.9126	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24948 - 	CGI_10008913	superfamily	247736	1	49	0.000577056	34.1217	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#24949 - 	CGI_10008914	superfamily	248264	194	361	8.87E-16	74.9661	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#24952 - 	CGI_10002301	superfamily	243035	89	201	7.84E-05	39.5254	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#24953 - 	CGI_10003409	superfamily	241563	104	139	0.000196434	39.6279	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24953 - 	CGI_10003409	superfamily	110440	569	596	0.00461656	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#24956 - 	CGI_10010217	superfamily	247792	20	67	6.72E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24956 - 	CGI_10010217	superfamily	241563	157	199	0.00891025	34.7624	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24957 - 	CGI_10010218	superfamily	243072	546	604	2.71E-06	48.1486	cl02529	ANK superfamily	C	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#24957 - 	CGI_10010218	superfamily	247724	1283	1459	1.47E-38	144.401	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24957 - 	CGI_10010218	superfamily	245201	1897	2052	1.68E-26	111.821	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#24957 - 	CGI_10010218	superfamily	246925	1095	1231	0.000241586	44.2686	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#24958 - 	CGI_10010219	superfamily	246679	27	150	2.10E-49	159.23	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#24959 - 	CGI_10010220	superfamily	186642	3	72	1.53E-21	80.4142	cl05017	UPF0203 superfamily	 - 	 - 	Uncharacterized protein family (UPF0203); This family of proteins is functionally uncharacterized.
Q#24960 - 	CGI_10010221	superfamily	241563	81	123	0.00042611	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24961 - 	CGI_10010222	superfamily	241563	61	99	0.00130414	37.0736	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24962 - 	CGI_10010223	superfamily	245226	245	375	3.15E-19	83.1188	cl10012	DnaQ_like_exo superfamily	C	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#24966 - 	CGI_10013610	superfamily	197504	146	261	1.37E-07	48.0545	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#24967 - 	CGI_10013611	superfamily	248458	112	462	9.18E-35	133.208	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#24968 - 	CGI_10013612	superfamily	241622	4	82	1.11E-17	79.1478	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#24968 - 	CGI_10013612	superfamily	128974	394	416	0.000677574	37.9676	cl00302	ZM superfamily	 - 	 - 	"ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules."
Q#24969 - 	CGI_10013614	superfamily	239148	61	209	3.04E-73	221.345	cl02780	MIT_C superfamily	 - 	 - 	"MIT_C; domain found C-terminal to MIT (contained within Microtubule Interacting and Trafficking molecules) domains, as well as in some bacterial proteins. The function of this domain is unknown."
Q#24969 - 	CGI_10013614	superfamily	241764	18	50	2.28E-05	40.4853	cl00299	MIT superfamily	N	 - 	"MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear."
Q#24971 - 	CGI_10013616	superfamily	227412	54	238	4.47E-22	90.9909	cl18811	YIP1 superfamily	N	 - 	"Rab GTPase interacting factor, Golgi membrane protein [Intracellular trafficking and secretion]"
Q#24973 - 	CGI_10013618	superfamily	217414	231	614	1.94E-61	211.419	cl03927	Otopetrin superfamily	 - 	 - 	"Protein of unknown function, DUF270; Protein of unknown function, DUF270.  "
Q#24975 - 	CGI_10013620	superfamily	243066	86	188	1.01E-16	73.4205	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#24976 - 	CGI_10013621	superfamily	247065	1012	1106	1.92E-07	50.421	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#24978 - 	CGI_10013623	superfamily	243058	12	133	2.74E-09	51.1611	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#24980 - 	CGI_10003623	superfamily	219740	45	121	0.0064787	34.7022	cl06992	Peptidase_S64 superfamily	N	 - 	"Peptidase family S64; This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1. The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS:S1) and to have a typical trypsin-like catalytic triad."
Q#24981 - 	CGI_10019010	superfamily	245596	68	240	2.26E-93	276.77	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#24982 - 	CGI_10019011	superfamily	245814	481	555	4.98E-07	49.7951	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	78	155	1.54E-06	48.6395	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	1738	1815	2.13E-06	47.8691	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	180	255	6.96E-06	46.3283	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	1289	1364	6.31E-05	43.6319	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	1591	1659	0.000406241	40.9355	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	683	758	0.00076627	40.1651	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	380	441	0.00183736	39.0095	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	584	654	0.0058035	37.4687	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	273	358	1.83E-10	60.2116	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	1479	1569	1.24E-07	51.7373	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	1380	1468	7.20E-07	49.4261	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	2137	2191	1.71E-05	45.0904	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	880	948	3.23E-05	44.4185	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	2041	2117	6.43E-05	43.6481	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	1936	2026	8.02E-05	43.2629	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	771	861	0.000346177	41.3369	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24982 - 	CGI_10019011	superfamily	245814	1039	1065	0.0053484	37.3861	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24983 - 	CGI_10019012	superfamily	245814	117	178	4.37E-08	47.8184	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24983 - 	CGI_10019012	superfamily	245814	22	103	4.96E-07	45.122	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#24984 - 	CGI_10019013	superfamily	247912	45	405	2.49E-29	119.143	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#24985 - 	CGI_10019014	superfamily	247724	282	442	8.92E-24	99.0674	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#24985 - 	CGI_10019014	superfamily	247912	18	215	6.18E-11	63.2892	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#24988 - 	CGI_10019017	superfamily	241564	533	601	6.69E-28	108.507	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#24988 - 	CGI_10019017	superfamily	241564	649	698	3.35E-22	92.3287	cl00035	BIR superfamily	N	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#24988 - 	CGI_10019017	superfamily	241564	266	336	4.80E-09	54.2123	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#24988 - 	CGI_10019017	superfamily	247792	839	869	1.35E-05	43.9076	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#24990 - 	CGI_10019019	superfamily	245248	44	505	2.12E-72	239.437	cl10080	RPE65 superfamily	 - 	 - 	"Retinal pigment epithelial membrane protein; This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria."
Q#24991 - 	CGI_10019020	superfamily	220249	105	173	6.93E-15	66.0896	cl09695	H_lectin superfamily	 - 	 - 	"H-type lectin domain; The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754."
Q#24993 - 	CGI_10019023	superfamily	248097	197	324	1.07E-19	82.6982	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#24994 - 	CGI_10019024	superfamily	128778	73	169	1.43E-05	43.4075	cl17972	BBC superfamily	C	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#24994 - 	CGI_10019024	superfamily	241563	27	65	4.21E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#24996 - 	CGI_10019026	superfamily	207685	14	65	1.02E-21	82.2218	cl02642	PABP superfamily	C	 - 	"Poly-adenylate binding protein, unique domain; The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family."
Q#24997 - 	CGI_10019027	superfamily	241571	40	153	7.19E-27	104.802	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24997 - 	CGI_10019027	superfamily	241571	168	291	6.09E-14	68.593	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#24999 - 	CGI_10019029	superfamily	248306	94	394	0	539.408	cl17752	Coprogen_oxidas superfamily	 - 	 - 	Coproporphyrinogen III oxidase; Coproporphyrinogen III oxidase.  
Q#25000 - 	CGI_10019030	superfamily	248013	14	30	0.000309576	36.3972	cl17459	CHROMO superfamily	NC	 - 	"Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain."
Q#25001 - 	CGI_10019031	superfamily	149431	278	371	1.04E-34	130.511	cl07111	LLGL superfamily	 - 	 - 	LLGL2; This domain is found in lethal giant larvae homolog 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn. It has been identified in eukaryotes and tends to be found together with WD repeats (pfam00400).
Q#25001 - 	CGI_10019031	superfamily	243092	49	258	2.97E-11	64.6636	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25002 - 	CGI_10019032	superfamily	217474	55	388	7.35E-76	246.88	cl03979	PAE superfamily	 - 	 - 	Pectinacetylesterase; Pectinacetylesterase.  
Q#25004 - 	CGI_10019034	superfamily	241563	120	159	4.08E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25004 - 	CGI_10019034	superfamily	245027	217	286	0.00223897	37.3728	cl09176	FlgN superfamily	C	 - 	FlgN protein; This family includes the FlgN protein and export chaperone involved in flagellar synthesis.
Q#25005 - 	CGI_10019035	superfamily	241563	125	164	3.73E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25006 - 	CGI_10019036	superfamily	245849	1	101	5.98E-15	66.497	cl12045	Ubiq_cyt_C_chap superfamily	 - 	 - 	Ubiquinol-cytochrome C chaperone; Ubiquinol-cytochrome C chaperone.  
Q#25009 - 	CGI_10019039	superfamily	246664	171	546	9.33E-176	504.801	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#25009 - 	CGI_10019039	superfamily	246664	12	45	0.0009823	40.3981	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#25010 - 	CGI_10019040	superfamily	246664	181	519	2.18E-148	433.925	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#25010 - 	CGI_10019040	superfamily	246664	21	88	0.00326286	38.8573	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#25011 - 	CGI_10019041	superfamily	111397	9	85	6.68E-07	44.6395	cl03620	HYR superfamily	 - 	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#25012 - 	CGI_10019042	superfamily	241646	128	171	8.24E-05	39.7414	cl00156	WAP superfamily	 - 	 - 	"whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease."
Q#25014 - 	CGI_10005624	superfamily	241900	447	561	0.000301068	41.4336	cl00490	EEP superfamily	N	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#25014 - 	CGI_10005624	superfamily	241900	128	322	0.00251361	38.6165	cl00490	EEP superfamily	N	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#25015 - 	CGI_10005625	superfamily	149752	53	80	1.91E-12	61.0201	cl07411	zf-LYAR superfamily	 - 	 - 	"LYAR-type C2HC zinc finger; This C2HC zinc finger is found in LYAR proteins, which are involved in cell growth regulation."
Q#25017 - 	CGI_10005627	superfamily	246918	145	197	3.07E-14	66.0711	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25017 - 	CGI_10005627	superfamily	246918	202	254	2.32E-12	61.0635	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25017 - 	CGI_10005627	superfamily	246918	86	129	3.51E-06	43.7295	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25023 - 	CGI_10010905	superfamily	243179	64	172	0.000741713	36.3283	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#25024 - 	CGI_10010906	superfamily	198675	1501	1700	1.66E-71	239.855	cl02436	COLFI superfamily	 - 	 - 	"Fibrillar collagen C-terminal domain; Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc."
Q#25024 - 	CGI_10010906	superfamily	214560	36	197	2.12E-18	85.4868	cl18311	TSPN superfamily	 - 	 - 	Thrombospondin N-terminal -like domains; Heparin-binding and cell adhesion domain of thrombospondin
Q#25028 - 	CGI_10010910	superfamily	110440	522	549	0.00319677	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25029 - 	CGI_10009232	superfamily	241600	125	354	1.56E-90	272.962	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25030 - 	CGI_10009233	superfamily	243115	4	129	9.09E-20	82.3917	cl02623	WIF superfamily	 - 	 - 	"WIF domain; The WIF domain is found in the RYK tyrosine kinase receptors and WIF, the Wnt-inhibitory- factor. The domain is extracellular and contains two conserved cysteines that may form a disulphide bridge. This domain is Wnt binding in WIF, and it has been suggested that RYK may also bind to Wnt. The WIF domain is a member of the immunoglobulin superfamily, and it comprises nine beta-strands and two alpha-helices, with two of the beta-strands (6 and 9) interrupted by four and six residues of irregular secondary structure, respectively. Considering that the activity of Wnts depends on the presence of a palmitoylated cysteine residue in their amino-terminal polypeptide segment, Wnt proteins are lipid-modified and can act as stem cell growth factors, it is likely that the WIF domain recognises and binds to Wnts that have been activated by palmitoylation and that the recognition of palmitoylated Wnts by WIF-1 is effected by its WIF domain rather than by its EGF domains. A strong binding affinity for palmitoylated cysteine residues would further explain the remarkably high affinity of human WIF-1 not only for mammalian Wnts, but also for Wnts from Xenopus and Drosophila."
Q#25032 - 	CGI_10009235	superfamily	241888	82	311	8.90E-94	280.258	cl00473	BI-1-like superfamily	 - 	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#25033 - 	CGI_10009236	superfamily	241888	13	217	1.76E-53	173.943	cl00473	BI-1-like superfamily	 - 	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#25034 - 	CGI_10009237	superfamily	110440	311	337	0.00181163	35.8465	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25035 - 	CGI_10009238	superfamily	110440	316	342	0.00122744	36.2317	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25038 - 	CGI_10009241	superfamily	248264	1	56	7.45E-06	43.3798	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#25039 - 	CGI_10009242	superfamily	241600	64	150	1.85E-28	110.059	cl00085	FReD superfamily	NC	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25039 - 	CGI_10009242	superfamily	248097	210	333	3.53E-16	73.0682	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25040 - 	CGI_10009243	superfamily	221377	40	192	3.28E-16	75.583	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#25044 - 	CGI_10007830	superfamily	194336	222	309	7.47E-16	74.2045	cl02517	ZU5 superfamily	 - 	 - 	ZU5 domain; Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
Q#25044 - 	CGI_10007830	superfamily	246680	517	566	4.96E-05	41.9257	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25045 - 	CGI_10007831	superfamily	220639	48	153	3.60E-34	118.375	cl10916	DUF2315 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2315); This is a family of small conserved proteins found from worms to humans. The function is not known.
Q#25046 - 	CGI_10007832	superfamily	241599	3	32	1.40E-07	45.3121	cl00084	homeodomain superfamily	N	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25047 - 	CGI_10007833	superfamily	243555	24	216	2.09E-17	77.0462	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#25049 - 	CGI_10007835	superfamily	241578	201	357	1.62E-28	109.689	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25050 - 	CGI_10007836	superfamily	241584	888	967	0.00132221	38.6315	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25051 - 	CGI_10007837	superfamily	241578	108	262	7.12E-20	88.5026	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25051 - 	CGI_10007837	superfamily	245213	36	72	4.54E-11	59.9578	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25052 - 	CGI_10007838	superfamily	241584	1220	1300	0.000456936	40.5575	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25054 - 	CGI_10007840	superfamily	241578	269	426	2.68E-29	114.311	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25054 - 	CGI_10007840	superfamily	243035	47	119	5.07E-19	83.8233	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25054 - 	CGI_10007840	superfamily	243035	188	229	8.97E-05	41.4514	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25056 - 	CGI_10004361	superfamily	241574	391	619	1.59E-94	299.501	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25056 - 	CGI_10004361	superfamily	241574	685	902	2.55E-16	78.7817	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25058 - 	CGI_10004363	superfamily	243179	108	199	5.89E-24	92.4293	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#25059 - 	CGI_10004364	superfamily	241546	553	671	1.16E-55	186.221	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#25059 - 	CGI_10004364	superfamily	241546	275	396	1.92E-47	163.109	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#25059 - 	CGI_10004364	superfamily	241546	18	132	1.78E-30	116.5	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#25059 - 	CGI_10004364	superfamily	241546	148	265	8.99E-29	111.493	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#25059 - 	CGI_10004364	superfamily	241546	408	518	1.89E-11	61.802	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#25060 - 	CGI_10023443	superfamily	118676	305	509	1.31E-24	101.731	cl10845	SCHIP-1 superfamily	 - 	 - 	Schwannomin-interacting protein 1; Members of this family are coiled coil protein involved in linking membrane proteins to the cytoskeleton.
Q#25060 - 	CGI_10023443	superfamily	210118	64	85	1.45E-05	42.3127	cl15479	IQ superfamily	 - 	 - 	IQ calmodulin-binding motif; Calmodulin-binding motif.
Q#25061 - 	CGI_10023444	superfamily	245201	4	256	1.18E-127	382.231	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25062 - 	CGI_10023445	superfamily	241705	54	134	9.57E-27	99.5838	cl00228	HIT_like superfamily	N	 - 	"HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups."
Q#25064 - 	CGI_10023447	superfamily	247792	350	388	0.00219428	37.04	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#25067 - 	CGI_10023450	superfamily	245205	138	217	3.18E-12	59.5589	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#25071 - 	CGI_10023455	superfamily	247724	6	160	1.56E-33	118.415	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25072 - 	CGI_10023456	superfamily	247724	6	147	4.69E-34	119.956	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25073 - 	CGI_10023457	superfamily	247856	18	67	6.66E-15	64.4913	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25074 - 	CGI_10023458	superfamily	247856	79	139	6.37E-19	76.0473	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25074 - 	CGI_10023458	superfamily	247856	8	104	9.42E-09	47.9277	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25075 - 	CGI_10023459	superfamily	247856	96	152	1.20E-15	67.5729	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25075 - 	CGI_10023459	superfamily	247856	21	80	1.57E-07	44.8461	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25078 - 	CGI_10023462	superfamily	248458	717	1022	8.47E-43	160.557	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#25083 - 	CGI_10023468	superfamily	217062	70	336	8.59E-49	166.676	cl12266	Branch superfamily	 - 	 - 	"Core-2/I-Branching enzyme; This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans."
Q#25088 - 	CGI_10023473	superfamily	248097	49	178	3.01E-16	71.1422	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25089 - 	CGI_10023474	superfamily	241563	121	159	2.43E-05	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25090 - 	CGI_10023475	superfamily	243035	121	232	1.58E-06	44.533	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25091 - 	CGI_10023476	superfamily	217473	568	634	1.98E-11	63.9233	cl03978	Mab-21 superfamily	NC	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25091 - 	CGI_10023476	superfamily	217473	300	461	1.24E-08	55.4489	cl03978	Mab-21 superfamily	C	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25092 - 	CGI_10023477	superfamily	217473	182	463	8.52E-32	122.859	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25093 - 	CGI_10023478	superfamily	217473	155	444	3.82E-23	97.4357	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25094 - 	CGI_10004261	superfamily	241583	280	480	1.51E-81	265.641	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#25094 - 	CGI_10004261	superfamily	216572	32	181	5.42E-15	73.463	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#25094 - 	CGI_10004261	superfamily	246918	578	629	1.78E-13	67.2267	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25094 - 	CGI_10004261	superfamily	246918	921	979	0.00170451	37.9515	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25094 - 	CGI_10004261	superfamily	204025	1173	1204	0.00201515	37.6161	cl07344	PLAC superfamily	 - 	 - 	PLAC (protease and lacunin) domain; The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins. It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin.
Q#25094 - 	CGI_10004261	superfamily	246918	1113	1165	0.00218657	37.5663	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25094 - 	CGI_10004261	superfamily	246918	985	1037	0.0034405	37.1811	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25095 - 	CGI_10004262	superfamily	246722	5	219	2.35E-115	339.095	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#25095 - 	CGI_10004262	superfamily	246724	221	290	5.33E-42	143.071	cl14815	H3TH_StructSpec-5'-nucleases superfamily	 - 	 - 	"H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases."
Q#25095 - 	CGI_10004262	superfamily	246722	292	341	3.77E-20	87.5596	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#25096 - 	CGI_10004263	superfamily	247805	170	374	1.00E-87	276.673	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25096 - 	CGI_10004263	superfamily	247905	389	516	2.39E-30	116.954	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25097 - 	CGI_10004264	superfamily	245201	83	325	2.88E-76	239.344	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25100 - 	CGI_10005040	superfamily	247725	211	301	1.11E-30	116.324	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25100 - 	CGI_10005040	superfamily	220215	19	96	1.85E-24	98.0662	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#25100 - 	CGI_10005040	superfamily	215882	104	180	7.18E-19	83.099	cl09511	FERM_M superfamily	C	 - 	FERM central domain; This domain is the central structural domain of the FERM domain.
Q#25100 - 	CGI_10005040	superfamily	192138	316	353	7.09E-09	52.6211	cl07378	FA superfamily	 - 	 - 	"FERM adjacent (FA); This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates."
Q#25101 - 	CGI_10005041	superfamily	247744	1	120	8.26E-38	127.369	cl17190	NK superfamily	N	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#25102 - 	CGI_10005042	superfamily	207627	546	625	1.45E-07	51.0963	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#25102 - 	CGI_10005042	superfamily	243086	1230	1283	1.54E-06	47.3822	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#25102 - 	CGI_10005042	superfamily	207627	174	265	0.00835173	36.4635	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#25104 - 	CGI_10021189	superfamily	247684	104	345	5.53E-35	132.401	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25104 - 	CGI_10021189	superfamily	247684	5	105	5.48E-22	94.6515	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25106 - 	CGI_10021191	superfamily	245206	2	40	1.68E-10	53.6049	cl09931	NADB_Rossmann superfamily	NC	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#25107 - 	CGI_10021192	superfamily	247068	218	297	9.74E-10	56.553	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25107 - 	CGI_10021192	superfamily	247068	99	192	1.76E-06	46.923	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25107 - 	CGI_10021192	superfamily	245213	709	743	0.000203585	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25107 - 	CGI_10021192	superfamily	245213	671	706	0.000407661	39.157	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25107 - 	CGI_10021192	superfamily	245213	556	591	0.000685012	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25107 - 	CGI_10021192	superfamily	245213	483	515	0.00106711	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25107 - 	CGI_10021192	superfamily	241584	299	390	0.00241082	37.0907	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25107 - 	CGI_10021192	superfamily	245213	407	441	0.00502036	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25108 - 	CGI_10021193	superfamily	189857	30	129	1.99E-30	108.106	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#25110 - 	CGI_10021195	superfamily	203031	94	140	0.00142372	35.7668	cl04548	FLYWCH superfamily	N	 - 	"FLYWCH zinc finger domain; Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in."
Q#25115 - 	CGI_10021201	superfamily	242406	122	207	5.71E-05	40.2673	cl01271	DUF1768 superfamily	C	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#25116 - 	CGI_10021202	superfamily	241584	176	269	0.000121533	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25120 - 	CGI_10021207	superfamily	216897	3	82	2.04E-22	83.4997	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#25124 - 	CGI_10021211	superfamily	245213	146	182	9.28E-10	51.4834	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25124 - 	CGI_10021211	superfamily	245213	108	143	2.39E-08	48.0166	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25125 - 	CGI_10021212	superfamily	247727	103	207	4.54E-08	48.9655	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#25126 - 	CGI_10021213	superfamily	241613	255	296	4.44E-09	53.7498	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#25126 - 	CGI_10021213	superfamily	244394	91	168	3.71E-18	81.6511	cl06508	MANEC superfamily	 - 	 - 	"MANEC domain; This region of similarity, comprising 8 conserved cysteines, is found in the N-terminal region of several membrane-associated and extracellular proteins. Although formerly called MANSC (for motif at N terminus with seven cysteines) it has now been renamed by MANEC (motif at N terminus with eight cysteines) by Richard Mitter and Stephen Fitzgerald after the discovery of an eighth conserved cysteine. It is postulated that this domain may play a role in the formation of protein complexes involving various protease activators and inhibitors."
Q#25127 - 	CGI_10021214	superfamily	218643	205	474	4.17E-99	302.468	cl05243	DUF766 superfamily	 - 	 - 	Protein of unknown function (DUF766); This family consists of several eukaryotic proteins of unknown function.
Q#25127 - 	CGI_10021214	superfamily	218569	22	116	0.0019588	37.544	cl05100	PP1_inhibitor superfamily	C	 - 	"PKC-activated protein phosphatase-1 inhibitor; Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction."
Q#25128 - 	CGI_10021215	superfamily	246597	74	324	4.89E-55	188.716	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#25129 - 	CGI_10021217	superfamily	150002	80	164	1.99E-20	86.6367	cl07690	Tap-RNA_bind superfamily	 - 	 - 	"Tap, RNA-binding; Members of this family adopt a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. They are mainly found in mRNA export factors, and mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element."
Q#25129 - 	CGI_10021217	superfamily	198842	560	600	5.95E-15	70.4088	cl04338	TAP_C superfamily	N	 - 	"TAP C-terminal domain; The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for nuclear export of mRNA. Tap has a modular structure, and its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling. The structure of the C-terminal domain is composed of four helices. The structure is related to the UBA domain."
Q#25129 - 	CGI_10021217	superfamily	245009	354	503	1.76E-07	49.5885	cl09109	NTF2_like superfamily	 - 	 - 	"Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example,  nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and  binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea and eukaryotes."
Q#25131 - 	CGI_10021219	superfamily	243072	15	141	4.70E-32	122.107	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25131 - 	CGI_10021219	superfamily	243072	82	213	4.09E-28	110.936	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25131 - 	CGI_10021219	superfamily	243072	187	365	9.45E-08	51.2302	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25131 - 	CGI_10021219	superfamily	243146	666	707	1.98E-07	49.1474	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25131 - 	CGI_10021219	superfamily	243146	560	608	5.65E-06	45.0528	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25131 - 	CGI_10021219	superfamily	243073	493	537	7.24E-06	44.7825	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#25131 - 	CGI_10021219	superfamily	243146	781	823	1.18E-05	43.8042	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25131 - 	CGI_10021219	superfamily	243146	731	789	0.000350647	39.5799	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25131 - 	CGI_10021219	superfamily	243146	629	678	0.00043828	39.1947	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25133 - 	CGI_10004451	superfamily	218122	125	350	1.30E-63	208.605	cl04558	Choline_transpo superfamily	N	 - 	Plasma-membrane choline transporter; This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals.
Q#25136 - 	CGI_10004454	superfamily	218122	301	625	1.29E-91	289.497	cl04558	Choline_transpo superfamily	 - 	 - 	Plasma-membrane choline transporter; This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals.
Q#25138 - 	CGI_10004456	superfamily	247792	11	62	1.92E-06	45.8996	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#25138 - 	CGI_10004456	superfamily	110440	615	642	1.30E-06	45.8617	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25138 - 	CGI_10004456	superfamily	241563	158	193	3.05E-06	45.0207	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25138 - 	CGI_10004456	superfamily	241563	99	140	0.00197081	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25139 - 	CGI_10004457	superfamily	241567	58	134	0.000124114	40.6846	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#25140 - 	CGI_10004458	superfamily	241832	36	160	1.31E-83	261.758	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25141 - 	CGI_10004459	superfamily	241567	12	247	2.14E-26	105.375	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#25141 - 	CGI_10004459	superfamily	241567	261	328	0.0001711	41.432	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#25143 - 	CGI_10002572	superfamily	243072	60	186	1.95E-31	117.87	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25144 - 	CGI_10002573	superfamily	245847	17	164	5.85E-13	68.5329	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25144 - 	CGI_10002573	superfamily	243065	1168	1348	3.00E-10	60.4933	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#25145 - 	CGI_10002574	superfamily	245847	34	175	1.65E-07	47.7321	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25150 - 	CGI_10003797	superfamily	243100	279	332	4.07E-14	66.0981	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#25151 - 	CGI_10003798	superfamily	247792	23	64	2.53E-12	63.6188	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#25151 - 	CGI_10003798	superfamily	245674	155	200	4.26E-05	43.0466	cl11531	DUF904 superfamily	C	 - 	Protein of unknown function (DUF904); This family consists of several bacterial and archaeal hypothetical proteins of unknown function.
Q#25151 - 	CGI_10003798	superfamily	221533	184	251	0.00595525	36.5208	cl13726	TMF_DNA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#25152 - 	CGI_10003799	superfamily	247725	1	99	1.62E-64	206.447	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25152 - 	CGI_10003799	superfamily	204041	315	460	2.09E-50	170.841	cl07367	GLTP superfamily	 - 	 - 	Glycolipid transfer protein (GLTP); GLTP is a cytosolic protein that catalyzes the intermembrane transfer of glycolipids.
Q#25153 - 	CGI_10003800	superfamily	246751	216	432	9.61E-86	266.802	cl14883	Lipase superfamily	C	 - 	"Lipase.  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site."
Q#25154 - 	CGI_10003801	superfamily	245814	201	266	3.97E-05	40.5503	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25155 - 	CGI_10003802	superfamily	247866	17	136	1.10E-12	61.3144	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#25156 - 	CGI_10006360	superfamily	247856	967	1033	9.10E-26	103.453	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25156 - 	CGI_10006360	superfamily	247856	839	904	3.13E-21	90.3566	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25156 - 	CGI_10006360	superfamily	247856	726	792	4.58E-20	86.8898	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25156 - 	CGI_10006360	superfamily	243095	536	637	7.76E-23	99.712	cl02570	RhoGAP superfamily	N	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#25156 - 	CGI_10006360	superfamily	243038	54	124	1.19E-21	92.2154	cl02442	DEP superfamily	C	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#25156 - 	CGI_10006360	superfamily	243095	164	286	5.21E-21	94.3192	cl02570	RhoGAP superfamily	C	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#25156 - 	CGI_10006360	superfamily	192987	1078	1168	0.00366401	37.5519	cl13724	TMF_TATA_bd superfamily	 - 	 - 	"TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family."
Q#25157 - 	CGI_10006361	superfamily	247725	4	105	2.08E-68	221.165	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25157 - 	CGI_10006361	superfamily	216381	365	693	1.04E-67	227.473	cl03136	Oxysterol_BP superfamily	 - 	 - 	Oxysterol-binding protein; Oxysterol-binding protein.  
Q#25158 - 	CGI_10006362	superfamily	241574	513	740	3.60E-102	322.228	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25158 - 	CGI_10006362	superfamily	241574	803	1032	6.08E-74	244.418	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25158 - 	CGI_10006362	superfamily	241609	65	146	2.59E-07	49.6962	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#25162 - 	CGI_10018981	superfamily	241547	19	70	1.02E-16	70.7613	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#25163 - 	CGI_10018982	superfamily	241547	1	30	7.02E-08	46.1529	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#25165 - 	CGI_10018984	superfamily	247725	529	621	7.11E-17	78.8593	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25165 - 	CGI_10018984	superfamily	150957	1332	1439	5.86E-31	119.643	cl11034	Vps39_2 superfamily	 - 	 - 	"Vacuolar sorting protein 39 domain 2; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11."
Q#25165 - 	CGI_10018984	superfamily	243036	623	876	2.63E-24	104.627	cl02434	CNH superfamily	 - 	 - 	"CNH domain; Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations."
Q#25165 - 	CGI_10018984	superfamily	220718	1042	1143	1.66E-22	94.9984	cl11033	Vps39_1 superfamily	 - 	 - 	"Vacuolar sorting protein 39 domain 1; This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. The precise function of this domain has not been characterized."
Q#25165 - 	CGI_10018984	superfamily	220068	2	49	1.55E-15	73.9218	cl07486	NUP50 superfamily	C	 - 	"NUP50 (Nucleoporin 50 kDa); Nucleoporin 50 kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localisation signals from importin-alpha."
Q#25165 - 	CGI_10018984	superfamily	207690	265	293	1.76E-05	43.8777	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#25165 - 	CGI_10018984	superfamily	207690	325	352	2.96E-05	43.1073	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#25165 - 	CGI_10018984	superfamily	207690	205	233	8.07E-05	41.9517	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#25166 - 	CGI_10018985	superfamily	241622	6	87	3.72E-21	86.8518	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#25166 - 	CGI_10018985	superfamily	241622	211	291	2.91E-19	81.8442	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#25170 - 	CGI_10018989	superfamily	245208	1	367	1.52E-102	310.354	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#25171 - 	CGI_10018990	superfamily	247723	313	401	5.10E-48	162.909	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25171 - 	CGI_10018990	superfamily	247723	466	541	2.17E-44	152.476	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25171 - 	CGI_10018990	superfamily	241888	130	256	7.37E-26	105.316	cl00473	BI-1-like superfamily	N	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#25172 - 	CGI_10018991	superfamily	197840	96	159	2.75E-23	89.9746	cl18196	PUR superfamily	 - 	 - 	DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria; DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.  
Q#25172 - 	CGI_10018991	superfamily	197840	20	81	3.21E-23	89.9746	cl18196	PUR superfamily	 - 	 - 	DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria; DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.  
Q#25172 - 	CGI_10018991	superfamily	197840	169	227	2.39E-19	79.189	cl18196	PUR superfamily	 - 	 - 	DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria; DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.  
Q#25174 - 	CGI_10018993	superfamily	241958	44	432	1.75E-74	242.036	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#25175 - 	CGI_10018994	superfamily	247723	41	139	1.05E-57	188.132	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25175 - 	CGI_10018994	superfamily	241568	446	496	3.80E-06	44.376	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#25176 - 	CGI_10018995	superfamily	243051	17	173	2.09E-48	164.473	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#25178 - 	CGI_10018997	superfamily	214531	783	826	4.66E-10	56.8413	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25178 - 	CGI_10018997	superfamily	214531	198	240	1.14E-08	52.9893	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25178 - 	CGI_10018997	superfamily	215683	174	215	2.18E-08	52.1723	cl18339	Ldl_recept_b superfamily	 - 	 - 	Low-density lipoprotein receptor repeat class B; This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Q#25178 - 	CGI_10018997	superfamily	214531	467	509	7.31E-08	50.6781	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25178 - 	CGI_10018997	superfamily	214531	833	870	3.31E-07	48.7521	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25178 - 	CGI_10018997	superfamily	214531	431	463	5.82E-05	41.8185	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25178 - 	CGI_10018997	superfamily	214531	510	548	0.00120172	37.9665	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25178 - 	CGI_10018997	superfamily	214531	749	779	0.00235795	37.1961	cl18310	LY superfamily	N	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25178 - 	CGI_10018997	superfamily	214531	692	734	0.0049423	36.4257	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#25179 - 	CGI_10018998	superfamily	247683	340	388	0.000427327	39.4437	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#25179 - 	CGI_10018998	superfamily	207632	777	808	0.00150835	37.4617	cl02531	Plectin superfamily	 - 	 - 	"Plectin repeat; This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen."
Q#25180 - 	CGI_10018999	superfamily	218802	136	177	3.14E-06	43.5042	cl05462	DUF862 superfamily	N	 - 	"PPPDE putative peptidase domain; The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)."
Q#25182 - 	CGI_10019001	superfamily	218802	100	129	0.00117096	35.8002	cl05462	DUF862 superfamily	N	 - 	"PPPDE putative peptidase domain; The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)."
Q#25183 - 	CGI_10019002	superfamily	218802	258	346	0.00226453	36.9558	cl05462	DUF862 superfamily	N	 - 	"PPPDE putative peptidase domain; The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)."
Q#25186 - 	CGI_10019005	superfamily	243263	128	240	1.83E-15	74.3666	cl02990	ASC superfamily	NC	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#25186 - 	CGI_10019005	superfamily	243263	243	266	3.56E-07	49.7138	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#25187 - 	CGI_10019006	superfamily	243263	8	123	8.63E-23	94.397	cl02990	ASC superfamily	NC	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#25187 - 	CGI_10019006	superfamily	243263	119	149	2.87E-08	52.025	cl02990	ASC superfamily	N	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#25188 - 	CGI_10019008	superfamily	217316	16	79	0.00977156	34.5244	cl03832	DUF234 superfamily	C	 - 	Archaea bacterial proteins of unknown function; Archaea bacterial proteins of unknown function.  
Q#25191 - 	CGI_10015410	superfamily	247684	16	434	1.10E-97	306.126	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25192 - 	CGI_10015411	superfamily	247068	165	271	3.95E-20	85.8281	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25195 - 	CGI_10015414	superfamily	198896	1646	1672	0.00371454	37.5865	cl07394	Ca_chan_IQ superfamily	 - 	 - 	"Voltage gated calcium channel IQ domain; Voltage gated calcium channels control cellular calcium entry in response to changes in membrane potential. The isoleucine-glutamine (IQ) motif in the voltage gated calcium channel IQ domain interacts with hydrophobic pockets of Ca2+/calmodulin. The interaction regulates two self-regulatory calcium dependent feedback mechanism, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF)."
Q#25197 - 	CGI_10015416	superfamily	243072	98	234	1.60E-25	99.7654	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25197 - 	CGI_10015416	superfamily	243073	350	393	0.000225407	38.5756	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#25201 - 	CGI_10015420	superfamily	241596	283	333	1.66E-09	54.5275	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#25204 - 	CGI_10015423	superfamily	243050	120	178	6.28E-33	118.53	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#25204 - 	CGI_10015423	superfamily	243050	62	115	5.50E-30	110.121	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#25204 - 	CGI_10015423	superfamily	241599	264	328	8.16E-17	74.202	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25205 - 	CGI_10015424	superfamily	245201	112	368	9.85E-45	155.858	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25206 - 	CGI_10015425	superfamily	215731	136	384	6.76E-82	253.675	cl08245	Gln-synt_C superfamily	 - 	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#25206 - 	CGI_10015425	superfamily	217811	50	130	9.82E-16	71.7659	cl08409	Gln-synt_N superfamily	 - 	 - 	"Glutamine synthetase, beta-Grasp domain; Glutamine synthetase, beta-Grasp domain.  "
Q#25207 - 	CGI_10015426	superfamily	215731	109	357	2.69E-84	259.067	cl08245	Gln-synt_C superfamily	 - 	 - 	"Glutamine synthetase, catalytic domain; Glutamine synthetase, catalytic domain.  "
Q#25207 - 	CGI_10015426	superfamily	217811	24	103	6.94E-19	79.8551	cl08409	Gln-synt_N superfamily	 - 	 - 	"Glutamine synthetase, beta-Grasp domain; Glutamine synthetase, beta-Grasp domain.  "
Q#25208 - 	CGI_10015427	superfamily	244906	599	667	2.89E-24	98.7515	cl08315	CAP_GLY superfamily	 - 	 - 	"CAP-Gly domain; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove."
Q#25212 - 	CGI_10015910	superfamily	243134	310	434	2.12E-25	102.342	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#25212 - 	CGI_10015910	superfamily	243134	589	711	2.40E-23	96.5643	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#25212 - 	CGI_10015910	superfamily	243134	449	575	1.27E-18	83.0824	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#25212 - 	CGI_10015910	superfamily	243134	153	297	2.68E-18	81.9268	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#25213 - 	CGI_10015911	superfamily	241833	197	424	7.59E-25	102.601	cl00389	SIS superfamily	 - 	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#25213 - 	CGI_10015911	superfamily	241833	22	162	3.20E-12	65.2365	cl00389	SIS superfamily	C	 - 	SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Q#25216 - 	CGI_10015914	superfamily	221506	192	361	3.93E-26	108.76	cl13686	BSMAP superfamily	 - 	 - 	Brain specific membrane anchored protein; This family of proteins is found in eukaryotes. Proteins in this family are typically between 285 and 331 amino acids in length. BSMAP has a putative transmembrane domain and is predicted to be a type I membrane glycoprotein.
Q#25216 - 	CGI_10015914	superfamily	221506	1	112	1.27E-11	64.8473	cl13686	BSMAP superfamily	N	 - 	Brain specific membrane anchored protein; This family of proteins is found in eukaryotes. Proteins in this family are typically between 285 and 331 amino acids in length. BSMAP has a putative transmembrane domain and is predicted to be a type I membrane glycoprotein.
Q#25216 - 	CGI_10015914	superfamily	220131	987	1249	0.00965798	38.4114	cl11721	DUF1943 superfamily	 - 	 - 	"Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined."
Q#25217 - 	CGI_10015915	superfamily	216112	468	818	3.27E-96	309.997	cl02964	RNB superfamily	 - 	 - 	RNB domain; This domain is the catalytic domain of ribonuclease II.
Q#25217 - 	CGI_10015915	superfamily	246722	21	196	6.08E-32	124.301	cl14812	PIN_SF superfamily	 - 	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#25218 - 	CGI_10015916	superfamily	215825	64	263	1.05E-55	187.124	cl02828	Calreticulin superfamily	N	 - 	Calreticulin family; Calreticulin family.  
Q#25218 - 	CGI_10015916	superfamily	215825	21	64	5.20E-08	52.3042	cl02828	Calreticulin superfamily	C	 - 	Calreticulin family; Calreticulin family.  
Q#25219 - 	CGI_10015917	superfamily	215825	128	423	2.63E-111	338.122	cl02828	Calreticulin superfamily	 - 	 - 	Calreticulin family; Calreticulin family.  
Q#25222 - 	CGI_10015920	superfamily	245814	60	120	1.33E-07	49.4099	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25222 - 	CGI_10015920	superfamily	245814	262	317	0.000159055	40.1651	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25222 - 	CGI_10015920	superfamily	245814	346	432	1.27E-09	55.5893	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25223 - 	CGI_10015921	superfamily	222432	566	659	3.27E-10	58.0882	cl16451	Bravo_FIGEY superfamily	N	 - 	C-terminal domain of Fibronectin type III; This is the very C-terminal region of neural adhesion molecule L1 proteins that are also known as Bravo or NrCAM. It lies upstream of the IG and Fn3 domains and has the highly conserved motif FIGEY. The function is not known.
Q#25223 - 	CGI_10015921	superfamily	245814	333	419	1.34E-08	52.8929	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25223 - 	CGI_10015921	superfamily	245814	39	112	1.24E-06	47.055	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25223 - 	CGI_10015921	superfamily	245814	245	312	2.95E-05	42.8777	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25224 - 	CGI_10015922	superfamily	245814	169	254	6.55E-10	56.3597	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25224 - 	CGI_10015922	superfamily	245814	23	90	3.74E-06	45.083	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25224 - 	CGI_10015922	superfamily	245814	409	486	0.000372316	39.1465	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25229 - 	CGI_10019043	superfamily	241583	121	156	9.82E-07	45.2547	cl00064	ZnMc superfamily	C	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#25232 - 	CGI_10019046	superfamily	238012	960	1004	1.06E-13	68.1498	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	415	461	9.69E-12	62.757	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	746	790	1.66E-11	61.9866	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	462	503	6.65E-10	57.3642	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	907	958	3.23E-09	55.4382	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	1007	1054	2.61E-08	52.7418	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	297	348	2.47E-06	46.9638	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	853	899	5.85E-05	42.7266	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	238012	359	405	0.000903288	39.2598	cl11390	EGF_Lam superfamily	C	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#25232 - 	CGI_10019046	superfamily	243198	56	295	3.37E-105	336.254	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#25232 - 	CGI_10019046	superfamily	243080	579	711	8.70E-28	111.759	cl02548	Laminin_B superfamily	 - 	 - 	Laminin B (Domain IV); Laminin B (Domain IV).  
Q#25232 - 	CGI_10019046	superfamily	225368	1136	1243	0.000340212	40.8626	cl01058	NtpF superfamily	 - 	 - 	Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]
Q#25232 - 	CGI_10019046	superfamily	191136	1217	1301	0.00169609	39.4486	cl04860	Transcrip_act superfamily	NC	 - 	Transcriptional activator; This family of proteins may act as a transcriptional activator. It plays a role in stress response in plants.
Q#25233 - 	CGI_10019047	superfamily	241782	589	828	6.77E-28	116.193	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#25233 - 	CGI_10019047	superfamily	217293	238	376	6.50E-22	95.3923	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25233 - 	CGI_10019047	superfamily	217293	8	131	5.88E-17	80.7547	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25233 - 	CGI_10019047	superfamily	202474	140	239	2.33E-10	60.3601	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#25233 - 	CGI_10019047	superfamily	202474	425	511	5.68E-10	59.2045	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#25234 - 	CGI_10019048	superfamily	222150	1056	1081	2.35E-05	43.1493	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#25234 - 	CGI_10019048	superfamily	222150	965	987	0.00174723	37.7565	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#25235 - 	CGI_10019049	superfamily	245029	17	147	1.93E-16	71.1396	cl09190	MAPEG superfamily	 - 	 - 	"MAPEG family; This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity."
Q#25236 - 	CGI_10019050	superfamily	241678	8	404	0	574.202	cl00198	Phosphoglycerate_kinase superfamily	 - 	 - 	"Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level phosphorylation events in the glycolytic pathway. Substrate-level phosphorylation is defined as production of  ATP by a process, which is catalyzed by water-soluble enzymes in the cytosol; not involving membranes and ion gradients."
Q#25237 - 	CGI_10019051	superfamily	218520	20	185	5.59E-10	54.5918	cl05007	EBP superfamily	 - 	 - 	"Emopamil binding protein; Emopamil binding protein (EBP) is as a gene that encodes a non-glycosylated type I integral membrane protein of endoplasmic reticulum and shows high level expression in epithelial tissues. The EBP protein has emopamil binding domains, including the sterol acceptor site and the catalytic centre, which show Delta8-Delta7 sterol isomerase activity. Human sterol isomerase, a homologue of mouse EBP, is suggested not only to play a role in cholesterol biosynthesis, but also to affect lipoprotein internalisation. In humans, mutations of EBP are known to cause the genetic disorder of X-linked dominant chondrodysplasia punctata (CDPX2). This syndrome of humans is lethal in most males, and affected females display asymmetric hyperkeratotic skin and skeletal abnormalities."
Q#25240 - 	CGI_10019054	superfamily	247684	15	71	1.82E-05	40.5085	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25243 - 	CGI_10019057	superfamily	241832	505	608	1.66E-51	173.511	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25243 - 	CGI_10019057	superfamily	241832	45	144	1.98E-38	136.972	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25243 - 	CGI_10019057	superfamily	241832	160	258	2.48E-37	134.275	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25243 - 	CGI_10019057	superfamily	241832	280	369	1.61E-19	84.8446	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25243 - 	CGI_10019057	superfamily	241832	375	464	1.51E-18	81.9991	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25244 - 	CGI_10019058	superfamily	241600	342	399	1.60E-18	82.6735	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25245 - 	CGI_10019059	superfamily	241600	327	536	7.66E-44	155.476	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25245 - 	CGI_10019059	superfamily	149439	240	306	2.64E-18	79.6766	cl07120	Rpn3_C superfamily	 - 	 - 	Proteasome regulatory subunit C-terminal; This eukaryotic domain is found at the C-terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function. It occurs together with the PCI/PINT domain (pfam01399).
Q#25245 - 	CGI_10019059	superfamily	242889	168	258	7.72E-18	78.823	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#25245 - 	CGI_10019059	superfamily	243034	82	115	0.0060424	34.7975	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#25246 - 	CGI_10019060	superfamily	242889	108	206	1.83E-23	92.2809	cl02111	PCI superfamily	 - 	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#25246 - 	CGI_10019060	superfamily	149439	213	279	2.35E-19	79.6766	cl07120	Rpn3_C superfamily	 - 	 - 	Proteasome regulatory subunit C-terminal; This eukaryotic domain is found at the C-terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function. It occurs together with the PCI/PINT domain (pfam01399).
Q#25247 - 	CGI_10019061	superfamily	217293	27	112	2.89E-25	95.3923	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25248 - 	CGI_10019062	superfamily	217293	9	111	6.47E-32	120.815	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25248 - 	CGI_10019062	superfamily	202474	227	339	2.58E-28	110.821	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#25248 - 	CGI_10019062	superfamily	202474	118	168	2.25E-11	61.9009	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#25248 - 	CGI_10019062	superfamily	217293	176	220	3.54E-07	49.1683	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25249 - 	CGI_10019063	superfamily	217293	15	221	1.79E-70	219.041	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25249 - 	CGI_10019063	superfamily	202474	228	278	8.40E-12	61.9009	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#25250 - 	CGI_10019064	superfamily	218652	19	318	3.26E-128	382.027	cl12311	CLPTM1 superfamily	N	 - 	"Cleft lip and palate transmembrane protein 1 (CLPTM1); This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family. This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis."
Q#25251 - 	CGI_10019065	superfamily	224127	45	164	8.61E-08	51.9627	cl18702	Gid superfamily	C	 - 	"NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]"
Q#25253 - 	CGI_10019067	superfamily	235416	33	114	4.98E-12	66.7076	cl18883	PRK05335 superfamily	N	 - 	tRNA (uracil-5-)-methyltransferase Gid; Reviewed
Q#25253 - 	CGI_10019067	superfamily	243130	416	458	2.32E-09	53.6485	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#25253 - 	CGI_10019067	superfamily	206103	260	328	0.000953087	37.4894	cl16485	GIDA_assoc_3 superfamily	 - 	 - 	"GidA associated domain 3; The GidA associated domain 3 is a motif that has been identified at the C-terminus of protein GidA. It consists of 4 helices, the last three being rather short and forming small bundle at the top end of the first longer one. It is here named helical domain 3 because in GidA it is preceded by two other C-terminal helical domain (based on crystal structures). GidA is an tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA and to be responsible for the interaction with protein MnmE. Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, pfam12631."
Q#25255 - 	CGI_10019069	superfamily	243092	57	334	1.12E-09	58.5004	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25255 - 	CGI_10019069	superfamily	203864	477	504	1.87E-06	45.4951	cl06967	NUC153 superfamily	 - 	 - 	NUC153 domain; This small domain is found in a a novel nucleolar family.
Q#25255 - 	CGI_10019069	superfamily	131316	308	438	0.00273386	39.2153	cl17983	benz_CoA_red_C superfamily	N	 - 	"benzoyl-CoA reductase, subunit C; This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions."
Q#25256 - 	CGI_10019070	superfamily	248097	205	230	0.00214581	36.089	cl17543	C1q superfamily	NC	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25257 - 	CGI_10019071	superfamily	241645	384	460	2.35E-13	67.5997	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#25257 - 	CGI_10019071	superfamily	243092	745	1066	1.21E-15	77.7604	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25257 - 	CGI_10019071	superfamily	190637	661	731	2.13E-13	67.811	cl04081	HELP superfamily	 - 	 - 	"HELP motif; The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family. The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain. In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation. The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons."
Q#25257 - 	CGI_10019071	superfamily	243092	905	1262	2.68E-13	70.8268	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25258 - 	CGI_10019072	superfamily	242141	74	355	2.19E-121	361.765	cl00851	Fumerase superfamily	 - 	 - 	"Fumarate hydratase (Fumerase); This family consists of several bacterial fumarate hydratase proteins FumA and FumB. Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre."
Q#25258 - 	CGI_10019072	superfamily	242096	359	568	3.78E-100	304.445	cl00795	Fumerase_C superfamily	 - 	 - 	"Fumarase C-terminus; This family consists of the C terminal region of several bacterial fumarate hydratase proteins (FumA and FumB). Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth."
Q#25260 - 	CGI_10019074	superfamily	242075	25	218	4.80E-74	225.519	cl00764	EMG1 superfamily	 - 	 - 	EMG1/NEP1 methyltransferase; Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases.
Q#25261 - 	CGI_10019075	superfamily	241571	167	270	5.89E-24	94.0162	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25262 - 	CGI_10019076	superfamily	148158	119	196	5.85E-23	88.7287	cl05731	ICAT superfamily	 - 	 - 	"Beta-catenin-interacting protein ICAT; This family consists of several eukaryotic beta-catenin-interacting (ICAT) proteins. Beta-catenin is a multifunctional protein involved in both cell adhesion and transcriptional activation. Transcription mediated by the beta-catenin/Tcf complex is involved in embryological development and is upregulated in various cancers. ICAT selectively inhibits beta-catenin/Tcf binding in vivo, without disrupting beta-catenin/cadherin interactions."
Q#25263 - 	CGI_10019077	superfamily	247041	55	325	4.19E-95	288.061	cl15692	CE4_SF superfamily	 - 	 - 	"Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins."
Q#25265 - 	CGI_10019079	superfamily	241567	383	617	4.44E-81	258.299	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#25265 - 	CGI_10019079	superfamily	246680	10	65	0.0013872	37.5664	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25266 - 	CGI_10019080	superfamily	243092	49	341	2.18E-89	272.286	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25267 - 	CGI_10019081	superfamily	221564	33	105	8.85E-20	79.1779	cl13797	P5-ATPase superfamily	C	 - 	"P5-type ATPase cation transporter; This domain family is found in eukaryotes, and is typically between 110 and 126 amino acids in length. The family is found in association with pfam00122, pfam00702. P-type ATPases comprise a large superfamily of proteins, present in both prokaryotes and eukaryotes, that transport inorganic cations and other substrates across cell membranes."
Q#25271 - 	CGI_10014273	superfamily	244897	36	214	1.28E-18	83.6894	cl08298	PTZ00007 superfamily	C	 - 	(NAP-L) nucleosome assembly protein -L; Provisional
Q#25272 - 	CGI_10014274	superfamily	247675	45	339	8.24E-131	378.379	cl17011	Arginase_HDAC superfamily	 - 	 - 	"Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs."
Q#25274 - 	CGI_10014276	superfamily	219542	104	204	2.04E-41	147.388	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#25274 - 	CGI_10014276	superfamily	219541	493	634	3.41E-28	110.636	cl18516	Cu-oxidase_2 superfamily	N	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#25274 - 	CGI_10014276	superfamily	215896	264	383	9.11E-24	98.5212	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#25275 - 	CGI_10014277	superfamily	248097	41	160	6.24E-19	78.0758	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25276 - 	CGI_10014278	superfamily	215896	31	125	1.95E-20	81.5724	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#25277 - 	CGI_10014279	superfamily	219542	44	144	1.01E-41	136.603	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#25278 - 	CGI_10014280	superfamily	219541	169	322	2.19E-29	111.021	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#25278 - 	CGI_10014280	superfamily	215896	2	66	5.74E-16	73.8684	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#25279 - 	CGI_10014281	superfamily	219542	133	231	9.19E-41	138.143	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#25280 - 	CGI_10014282	superfamily	219542	161	263	9.85E-40	142.766	cl18517	Cu-oxidase_3 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#25280 - 	CGI_10014282	superfamily	219541	550	698	6.95E-27	107.169	cl18516	Cu-oxidase_2 superfamily	 - 	 - 	Multicopper oxidase; This entry contains many divergent copper oxidase-like domains that are not recognised by the pfam00394 model.
Q#25280 - 	CGI_10014282	superfamily	215896	320	440	5.56E-26	104.684	cl18351	Cu-oxidase superfamily	N	 - 	Multicopper oxidase; Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Q#25281 - 	CGI_10014283	superfamily	247727	134	242	0.000380788	38.5703	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#25283 - 	CGI_10014285	superfamily	241580	291	363	9.37E-36	128.441	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#25284 - 	CGI_10014286	superfamily	243035	70	188	2.54E-30	117.336	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25284 - 	CGI_10014286	superfamily	215827	383	559	7.89E-33	127.585	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#25285 - 	CGI_10014287	superfamily	246676	5	184	1.77E-36	127.791	cl14616	Cyt_b561 superfamily	 - 	 - 	"Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous."
Q#25286 - 	CGI_10014288	superfamily	243066	11	114	3.75E-16	74.5761	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25286 - 	CGI_10014288	superfamily	198867	91	209	3.73E-05	42.3285	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#25286 - 	CGI_10014288	superfamily	243146	304	344	6.18E-05	41.1207	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25286 - 	CGI_10014288	superfamily	243146	337	380	0.000742988	37.641	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25289 - 	CGI_10014291	superfamily	129885	80	252	2.40E-42	146.731	cl17977	nst superfamily	C	 - 	"UDP-galactose transporter; The 10-12 TMS Nucleotide Sugar Transporters (TC 2.A.7.10)Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids."
Q#25290 - 	CGI_10010224	superfamily	202894	71	138	9.81E-26	94.595	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#25291 - 	CGI_10010225	superfamily	247755	1869	2093	3.27E-109	349.111	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#25291 - 	CGI_10010225	superfamily	247755	833	1050	3.29E-105	337.555	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#25292 - 	CGI_10010226	superfamily	248097	6	124	1.05E-17	73.8386	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25293 - 	CGI_10010227	superfamily	248097	125	254	3.66E-18	77.6906	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25294 - 	CGI_10010229	superfamily	248097	74	203	7.50E-18	76.1498	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25295 - 	CGI_10010230	superfamily	247727	79	176	1.09E-10	56.2842	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#25296 - 	CGI_10010231	superfamily	241913	54	165	2.04E-28	103.021	cl00509	hot_dog superfamily	 - 	 - 	"The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold.  These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate.  This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis."
Q#25297 - 	CGI_10010232	superfamily	117316	211	250	2.09E-07	47.0093	cl07385	zf-RING-like superfamily	 - 	 - 	RING-like domain; This is a zinc finger domain that is related to the C3HC4 RING finger domain (pfam00097).
Q#25298 - 	CGI_10010233	superfamily	247805	225	270	5.26E-06	44.783	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25299 - 	CGI_10010234	superfamily	247905	498	615	7.71E-28	110.79	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25299 - 	CGI_10010234	superfamily	247805	225	438	6.87E-53	184.996	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25302 - 	CGI_10010237	superfamily	150797	12	181	9.74E-57	179.11	cl10866	DUF2366 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2366); This is a family of proteins conserved from nematodes to humans. The function is not known.
Q#25303 - 	CGI_10010238	superfamily	241584	169	255	6.69E-05	42.4835	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25303 - 	CGI_10010238	superfamily	241584	463	559	0.000380513	39.7871	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25304 - 	CGI_10007383	superfamily	245235	565	959	0	818.045	cl10023	POLBc superfamily	 - 	 - 	"DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y).  Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis."
Q#25304 - 	CGI_10007383	superfamily	245226	290	519	8.53E-155	462.046	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#25304 - 	CGI_10007383	superfamily	222632	997	1069	5.57E-31	117.892	cl16754	zf-C4pol superfamily	 - 	 - 	"C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1."
Q#25305 - 	CGI_10007384	superfamily	241645	8	94	0.000115435	40.3592	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#25306 - 	CGI_10007385	superfamily	114645	81	201	1.73E-07	50.5275	cl05479	MCLC superfamily	NC	 - 	Mid-1-related chloride channel (MCLC); This family consists of several mid-1-related chloride channels. mid-1-related chloride channel (MCLC) proteins function as a chloride channel when incorporated in the planar lipid bilayer.
Q#25307 - 	CGI_10007386	superfamily	243035	221	325	7.30E-26	100.002	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25316 - 	CGI_10007395	superfamily	246748	107	192	0.00752775	35.531	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#25319 - 	CGI_10002766	superfamily	245595	3	241	1.08E-67	213.152	cl11393	Peptidase_M14_like superfamily	 - 	 - 	"M14 family of metallocarboxypeptidases and related proteins; The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others.  Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism."
Q#25320 - 	CGI_10017177	superfamily	247725	832	1057	2.06E-81	266.81	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25320 - 	CGI_10017177	superfamily	241622	1180	1253	4.00E-15	73.3698	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#25320 - 	CGI_10017177	superfamily	241622	1090	1175	8.85E-13	66.8214	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#25320 - 	CGI_10017177	superfamily	246680	1537	1609	0.0043876	37.4407	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25321 - 	CGI_10017178	superfamily	243187	567	739	2.33E-102	316.819	cl02789	EFG_like_IV superfamily	 - 	 - 	"Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm."
Q#25321 - 	CGI_10017178	superfamily	247724	29	244	1.03E-98	308.777	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25321 - 	CGI_10017178	superfamily	243185	387	480	5.99E-46	160.036	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#25321 - 	CGI_10017178	superfamily	243183	735	814	5.41E-39	139.983	cl02785	Elongation_Factor_C superfamily	 - 	 - 	"Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p.  This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain.  EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown."
Q#25322 - 	CGI_10017179	superfamily	241581	136	234	3.95E-20	86.6714	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#25322 - 	CGI_10017179	superfamily	190615	338	404	2.07E-07	49.5276	cl04028	dsRNA_bind superfamily	 - 	 - 	"Double stranded RNA binding domain; This domain is a divergent double stranded RNA-binding domain. It is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules."
Q#25323 - 	CGI_10017180	superfamily	243066	30	131	1.56E-25	101.54	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25323 - 	CGI_10017180	superfamily	198867	142	240	2.28E-12	63.7167	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#25323 - 	CGI_10017180	superfamily	243146	381	426	3.97E-09	53.4342	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25323 - 	CGI_10017180	superfamily	243146	430	472	1.66E-08	51.5082	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25323 - 	CGI_10017180	superfamily	243146	331	378	3.89E-08	50.3526	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25323 - 	CGI_10017180	superfamily	243146	487	538	3.32E-06	44.8567	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25323 - 	CGI_10017180	superfamily	243146	528	574	9.06E-05	40.5093	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25324 - 	CGI_10017181	superfamily	115560	872	913	0.0026928	38.3196	cl06117	MEA1 superfamily	N	 - 	"Male enhanced antigen 1 (MEA1); This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localised in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis."
Q#25329 - 	CGI_10017186	superfamily	241739	1190	1452	1.19E-159	488.259	cl00268	class_II_aaRS-like_core superfamily	 - 	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#25329 - 	CGI_10017186	superfamily	241738	1458	1680	9.94E-75	248.752	cl00266	HGTP_anticodon superfamily	 - 	 - 	"HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b)."
Q#25329 - 	CGI_10017186	superfamily	241550	368	500	7.99E-73	244.854	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#25329 - 	CGI_10017186	superfamily	243175	72	155	2.30E-26	105.864	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#25329 - 	CGI_10017186	superfamily	241805	815	864	1.37E-18	82.2832	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#25329 - 	CGI_10017186	superfamily	241805	745	794	3.85E-17	78.4312	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#25329 - 	CGI_10017186	superfamily	241805	1022	1071	1.05E-16	76.8904	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#25329 - 	CGI_10017186	superfamily	241805	951	997	1.57E-15	73.8088	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#25329 - 	CGI_10017186	superfamily	241805	1096	1141	2.88E-13	67.2604	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#25329 - 	CGI_10017186	superfamily	241805	881	928	2.11E-09	55.7044	cl00349	S15_NS1_EPRS_RNA-bind superfamily	 - 	 - 	"S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism."
Q#25329 - 	CGI_10017186	superfamily	241550	201	295	8.89E-47	170.125	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#25329 - 	CGI_10017186	superfamily	217810	499	674	2.00E-34	131.993	cl04341	tRNA-synt_1c_C superfamily	 - 	 - 	"tRNA synthetases class I (E and Q), anti-codon binding domain; Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln)."
Q#25330 - 	CGI_10017187	superfamily	241811	5	55	6.35E-25	88.9737	cl00355	Ribosomal_S14 superfamily	 - 	 - 	Ribosomal protein S14p/S29e; This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
Q#25331 - 	CGI_10017188	superfamily	198867	158	253	2.65E-22	92.6067	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#25331 - 	CGI_10017188	superfamily	243066	38	149	7.69E-18	79.9689	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25331 - 	CGI_10017188	superfamily	245847	327	408	6.32E-05	42.1044	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25331 - 	CGI_10017188	superfamily	245847	486	561	0.00528729	36.3264	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25332 - 	CGI_10017189	superfamily	241592	2	35	4.03E-09	52.6571	cl00074	H2A superfamily	C	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#25333 - 	CGI_10017190	superfamily	245319	209	799	1.91E-99	334.317	cl10505	CBF superfamily	 - 	 - 	CBF/Mak21 family; CBF/Mak21 family.  
Q#25334 - 	CGI_10017191	superfamily	242542	26	199	2.72E-08	50.6924	cl01505	YhhN superfamily	 - 	 - 	"YhhN-like protein; The members of this family are similar to the hypothetical protein yhhN expressed by E. coli. Many of the members of this family are annotated as being possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues."
Q#25335 - 	CGI_10017192	superfamily	242542	44	231	4.82E-25	97.6867	cl01505	YhhN superfamily	 - 	 - 	"YhhN-like protein; The members of this family are similar to the hypothetical protein yhhN expressed by E. coli. Many of the members of this family are annotated as being possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues."
Q#25336 - 	CGI_10017193	superfamily	242542	44	231	4.82E-25	97.6867	cl01505	YhhN superfamily	 - 	 - 	"YhhN-like protein; The members of this family are similar to the hypothetical protein yhhN expressed by E. coli. Many of the members of this family are annotated as being possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues."
Q#25337 - 	CGI_10017194	superfamily	247637	77	405	0	551.714	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#25338 - 	CGI_10017195	superfamily	245835	130	242	0.00238179	38.0895	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#25341 - 	CGI_10017198	superfamily	247725	45	153	4.90E-64	203.325	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25342 - 	CGI_10017199	superfamily	219977	1	62	1.53E-10	59.2208	cl18539	Vps51 superfamily	N	 - 	"Vps51/Vps67; This family includes a presumed domain found in a number of components of vesicular transport. The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1. Cog1_N is the N-terminus of the Cog1 subunit of the eight-unit Conserved Oligomeric Golgi (COG) complex that participates in retrograde vesicular transport and is required to maintain normal Golgi structure and function. The subunits are located in two lobes and Cog1 serves to bind the two lobes together probably via the highly conserved N-terminal domain of approximately 85 residues."
Q#25343 - 	CGI_10017200	superfamily	243045	356	452	4.91E-17	77.6735	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#25343 - 	CGI_10017200	superfamily	241596	89	141	2.45E-13	66.0835	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#25343 - 	CGI_10017200	superfamily	243045	170	237	1.66E-09	55.7171	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#25345 - 	CGI_10017202	superfamily	243269	19	420	5.85E-113	344.637	cl03012	Ammonium_transp superfamily	 - 	 - 	Ammonium Transporter Family; Ammonium Transporter Family.  
Q#25348 - 	CGI_10017205	superfamily	243069	25	248	1.14E-88	267.476	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#25352 - 	CGI_10017209	superfamily	247744	8	53	0.00023105	39.5962	cl17190	NK superfamily	C	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#25355 - 	CGI_10017212	superfamily	218109	89	169	6.37E-15	69.2765	cl12292	Gly_transf_sug superfamily	 - 	 - 	"Glycosyltransferase sugar-binding region containing DXD motif; The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases."
Q#25356 - 	CGI_10017213	superfamily	247725	46	145	3.18E-45	155.943	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25356 - 	CGI_10017213	superfamily	243094	292	615	5.39E-147	431.526	cl02569	RasGAP superfamily	 - 	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#25356 - 	CGI_10017213	superfamily	246669	160	294	6.49E-33	122.861	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#25358 - 	CGI_10013584	superfamily	241584	13	101	0.000435696	37.8611	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25358 - 	CGI_10013584	superfamily	241571	104	191	3.65E-06	44.3255	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25360 - 	CGI_10013586	superfamily	248012	2	109	8.97E-18	74.9216	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#25362 - 	CGI_10013588	superfamily	219556	97	179	8.41E-34	123.459	cl06678	AdoMet_MTase superfamily	C	 - 	Predicted AdoMet-dependent methyltransferase; Proteins in this family have been predicted to function as AdoMet-dependent methyltransferases.
Q#25365 - 	CGI_10013591	superfamily	242274	215	339	3.30E-05	42.7846	cl01053	SGNH_hydrolase superfamily	C	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#25367 - 	CGI_10013593	superfamily	198738	69	152	1.44E-41	138.608	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#25368 - 	CGI_10013594	superfamily	241597	758	826	2.93E-16	75.4125	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#25368 - 	CGI_10013594	superfamily	219470	324	364	7.14E-12	63.0888	cl06557	BCNT superfamily	NC	 - 	Bucentaur or craniofacial development; Bucentaur or craniofacial development protein 1 (BCNT) in ruminents has a different domain architecture to that in mouse and human. For this reason it has been used as a model for molecular evolution. Both bovine and human BCNTs are phosphorylated by casein kinase II in vitro.
Q#25368 - 	CGI_10013594	superfamily	219470	233	266	1.26E-11	62.3184	cl06557	BCNT superfamily	NC	 - 	Bucentaur or craniofacial development; Bucentaur or craniofacial development protein 1 (BCNT) in ruminents has a different domain architecture to that in mouse and human. For this reason it has been used as a model for molecular evolution. Both bovine and human BCNTs are phosphorylated by casein kinase II in vitro.
Q#25368 - 	CGI_10013594	superfamily	219431	891	932	1.27E-06	47.0404	cl06504	zf-CW superfamily	 - 	 - 	"CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found."
Q#25369 - 	CGI_10013595	superfamily	243092	369	546	1.78E-07	53.1076	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25369 - 	CGI_10013595	superfamily	243092	249	413	0.00017812	43.8628	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25372 - 	CGI_10013598	superfamily	243035	74	153	4.80E-12	59.5557	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25372 - 	CGI_10013598	superfamily	243035	1	55	0.000285313	37.9846	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25372 - 	CGI_10013598	superfamily	243035	174	213	5.56E-07	46.0538	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25373 - 	CGI_10003340	superfamily	243161	10	96	1.04E-16	72.0417	cl02739	THAP superfamily	 - 	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#25374 - 	CGI_10002823	superfamily	247684	7	382	0	633.996	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25377 - 	CGI_10002826	superfamily	243015	113	193	4.46E-14	65.361	cl02381	Tim17 superfamily	N	 - 	"Tim17/Tim22/Tim23/Pmp24 family; The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane. This family includes Tim17, Tim22 and Tim23. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27 in."
Q#25378 - 	CGI_10002827	superfamily	246597	4	288	0	630.797	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#25379 - 	CGI_10002549	superfamily	243092	299	431	0.00307857	38.47	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25379 - 	CGI_10002549	superfamily	110440	519	546	0.003736	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25379 - 	CGI_10002549	superfamily	241563	60	99	0.00382853	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25383 - 	CGI_10000827	superfamily	243034	29	86	3.22E-05	37.3596	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#25384 - 	CGI_10009280	superfamily	248247	213	269	1.04E-10	60.3106	cl17693	Integrin_beta superfamily	C	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#25384 - 	CGI_10009280	superfamily	248247	25	61	8.05E-09	54.5326	cl17693	Integrin_beta superfamily	NC	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#25385 - 	CGI_10009281	superfamily	248247	7	298	1.50E-166	477.096	cl17693	Integrin_beta superfamily	N	 - 	"Integrin, beta chain; Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF."
Q#25386 - 	CGI_10009282	superfamily	243034	624	711	8.63E-06	44.6784	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#25386 - 	CGI_10009282	superfamily	203444	87	120	9.97E-14	69.2491	cl05761	PRP1_N superfamily	N	 - 	"PRP1 splicing factor, N-terminal; This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1. It is involved in mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression."
Q#25386 - 	CGI_10009282	superfamily	214642	386	418	0.00138057	37.5286	cl02592	HAT superfamily	 - 	 - 	HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Q#25386 - 	CGI_10009282	superfamily	243034	335	398	0.00535964	36.204	cl02429	TPR superfamily	N	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#25388 - 	CGI_10009284	superfamily	243065	1681	1839	1.06E-09	59.3377	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#25388 - 	CGI_10009284	superfamily	219677	2049	2074	0.00807612	36.6468	cl18521	EGF_2 superfamily	 - 	 - 	EGF-like domain; This family contains EGF domains found in a variety of extracellular proteins.
Q#25389 - 	CGI_10009285	superfamily	215647	601	830	9.34E-41	150.452	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#25390 - 	CGI_10009286	superfamily	243142	30	141	3.98E-09	54.9399	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#25391 - 	CGI_10009287	superfamily	149667	1	94	7.61E-08	46.9799	cl07343	GON superfamily	N	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#25392 - 	CGI_10009288	superfamily	149667	2	52	0.000216418	37.7351	cl07343	GON superfamily	N	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#25393 - 	CGI_10009289	superfamily	246680	12	89	0.000166549	39.8776	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25394 - 	CGI_10009290	superfamily	243035	40	169	6.54E-18	75.3489	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25399 - 	CGI_10009586	superfamily	197448	50	108	2.32E-17	72.9061	cl15240	Reelin_subrepeat_like superfamily	N	 - 	"Tandem repeat subunit of reelin and related proteins; Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns."
Q#25400 - 	CGI_10009587	superfamily	243267	57	423	7.64E-127	373.872	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#25401 - 	CGI_10009588	superfamily	243267	26	394	2.45E-98	300.685	cl03000	Innexin superfamily	 - 	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#25404 - 	CGI_10009591	superfamily	241578	26	110	4.88E-11	56.2425	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25405 - 	CGI_10009592	superfamily	248054	33	247	3.40E-14	70.7943	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#25406 - 	CGI_10009593	superfamily	243069	551	706	1.11E-05	45.4364	cl02525	Band_7 superfamily	N	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#25407 - 	CGI_10009594	superfamily	221582	475	621	2.05E-11	63.0451	cl13834	Milton superfamily	 - 	 - 	"Kinesin associated protein; This domain family is found in eukaryotes, and is typically between 143 and 173 amino acids in length. The family is found in association with pfam04849. This family is a region of the protein milton. Milton recruits the heavy chain of kinesin to mitochondria to allow the motor movement function of kinesin."
Q#25408 - 	CGI_10009595	superfamily	245323	2046	2289	2.51E-132	418.57	cl10511	Beach superfamily	 - 	 - 	"BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins."
Q#25408 - 	CGI_10009595	superfamily	245323	2322	2467	1.58E-64	224.044	cl10511	Beach superfamily	N	 - 	"BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking,  are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins."
Q#25408 - 	CGI_10009595	superfamily	247725	1928	2027	3.31E-34	130.493	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25408 - 	CGI_10009595	superfamily	243092	2591	2844	6.68E-17	83.1532	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25409 - 	CGI_10001544	superfamily	247723	79	122	5.82E-20	78.4692	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25410 - 	CGI_10001545	superfamily	243152	59	189	1.57E-41	138.576	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#25411 - 	CGI_10007036	superfamily	151906	82	172	1.00E-16	72.0085	cl12990	LEDGF superfamily	 - 	 - 	Lens epithelium-derived growth factor (LEDGF); LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure.
Q#25413 - 	CGI_10007038	superfamily	245353	235	253	0.00879225	36.1478	cl10644	APO_RNA-bind superfamily	NC	 - 	"APO RNA-binding; This domain contains conserved cysteine and histidine residues. It resembles zinc fingers, and binds to zinc. This domain functions as an RNA-binding domain."
Q#25414 - 	CGI_10007039	superfamily	241884	8	220	5.08E-149	416.635	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#25415 - 	CGI_10007040	superfamily	217390	275	415	1.07E-05	43.7025	cl18407	TPT superfamily	 - 	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#25416 - 	CGI_10007041	superfamily	246597	79	156	9.15E-30	110.441	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#25417 - 	CGI_10007042	superfamily	241600	67	278	7.46E-102	299.156	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25418 - 	CGI_10007043	superfamily	241600	72	267	1.64E-95	282.592	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25419 - 	CGI_10007044	superfamily	243035	27	64	3.78E-05	38.3698	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25422 - 	CGI_10001643	superfamily	243092	31	289	3.41E-13	68.1304	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25425 - 	CGI_10025748	superfamily	222608	26	126	9.47E-15	65.7386	cl18680	DIOX_N superfamily	 - 	 - 	non-haem dioxygenase in morphine synthesis N-terminal; This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.
Q#25426 - 	CGI_10025749	superfamily	245847	15	87	6.86E-06	40.2326	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25428 - 	CGI_10025753	superfamily	241574	190	382	7.82E-80	256.359	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25428 - 	CGI_10025753	superfamily	241574	444	672	2.55E-56	192.416	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25428 - 	CGI_10025753	superfamily	241568	9	45	0.0088027	35.1312	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#25429 - 	CGI_10025754	superfamily	191444	96	179	3.88E-13	61.5713	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#25430 - 	CGI_10025755	superfamily	247724	1	158	2.67E-69	217.747	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25430 - 	CGI_10025755	superfamily	181730	217	320	4.69E-12	62.4767	cl18118	PRK09256 superfamily	N	 - 	hypothetical protein; Provisional
Q#25432 - 	CGI_10025757	superfamily	241640	326	583	2.64E-82	260.286	cl00149	Tryp_SPc superfamily	 - 	 - 	Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Q#25432 - 	CGI_10025757	superfamily	245847	46	185	1.48E-17	80.0889	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25434 - 	CGI_10025759	superfamily	204299	464	597	1.53E-48	166.799	cl10718	VEFS-Box superfamily	 - 	 - 	"VEFS-Box of polycomb protein; The VEFS-Box (VRN2-EMF2-FIS2-Su(z)12) box is the C-terminal region of these proteins, characterized by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain. Some of these sequences are associated with a zinc-finger domain about 100 residues towards the N-terminus. This protein is one of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression."
Q#25435 - 	CGI_10025760	superfamily	245882	21	402	1.05E-174	498.354	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#25436 - 	CGI_10025761	superfamily	245882	22	405	1.62E-165	474.857	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#25437 - 	CGI_10025762	superfamily	245882	22	405	6.94E-162	465.612	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#25439 - 	CGI_10025764	superfamily	248022	10	393	3.58E-51	185.174	cl17468	Aa_trans superfamily	 - 	 - 	"Transmembrane amino acid transporter protein; This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases."
Q#25440 - 	CGI_10025765	superfamily	247725	16	67	6.19E-05	42.8394	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25440 - 	CGI_10025765	superfamily	247724	377	438	0.000299116	41.0746	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25441 - 	CGI_10025766	superfamily	150822	10	33	0.000267047	36.6469	cl10896	WRW superfamily	C	 - 	"Mitochondrial F1F0-ATP synthase, subunit f; This is a family of small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some members of the family have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known."
Q#25443 - 	CGI_10025768	superfamily	247723	115	188	1.47E-47	155.875	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25444 - 	CGI_10025769	superfamily	241587	208	261	5.17E-09	53.0618	cl00069	GGL superfamily	 - 	 - 	"G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors"
Q#25444 - 	CGI_10025769	superfamily	243090	279	403	1.42E-46	160.096	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#25444 - 	CGI_10025769	superfamily	243038	19	106	1.06E-10	58.4557	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#25445 - 	CGI_10025770	superfamily	247986	666	820	6.00E-10	58.9238	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#25445 - 	CGI_10025770	superfamily	247986	483	565	7.74E-07	49.679	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#25445 - 	CGI_10025770	superfamily	245225	67	413	6.09E-31	125.875	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#25446 - 	CGI_10025771	superfamily	149077	638	748	1.38E-42	152.008	cl06719	TMC superfamily	 - 	 - 	"TMC domain; These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters."
Q#25447 - 	CGI_10025772	superfamily	245882	24	407	0	527.629	cl12119	Alpha_L_fucos superfamily	 - 	 - 	Alpha-L-fucosidase; Alpha-L-fucosidase.  
Q#25448 - 	CGI_10025773	superfamily	241578	105	261	1.54E-43	156.298	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25448 - 	CGI_10025773	superfamily	243061	1	97	3.54E-31	118.984	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25448 - 	CGI_10025773	superfamily	246918	346	398	2.06E-12	63.7599	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	803	854	2.88E-12	63.3747	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	746	797	1.14E-11	61.8339	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	860	911	2.14E-11	60.6783	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	575	626	8.33E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	632	683	9.58E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	518	569	9.70E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	461	512	5.63E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	404	455	6.17E-10	56.4411	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	689	740	8.52E-10	56.0559	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25448 - 	CGI_10025773	superfamily	246918	290	341	1.43E-09	55.6707	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25449 - 	CGI_10025774	superfamily	245814	181	203	0.00488523	33.6167	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25449 - 	CGI_10025774	superfamily	245814	115	170	0.000440639	36.9893	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25450 - 	CGI_10025775	superfamily	248264	13	106	1.64E-08	51.469	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#25454 - 	CGI_10025779	superfamily	215724	1	279	1.53E-112	330.735	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#25456 - 	CGI_10025781	superfamily	198867	20	127	1.95E-05	42.3285	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#25457 - 	CGI_10025782	superfamily	243092	1561	1679	2.19E-20	93.5536	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25457 - 	CGI_10025782	superfamily	247743	456	566	0.00376699	38.72	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#25458 - 	CGI_10025783	superfamily	243066	18	122	3.55E-21	89.2137	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25458 - 	CGI_10025783	superfamily	198867	132	228	9.70E-16	73.5296	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#25458 - 	CGI_10025783	superfamily	243146	361	406	1.45E-10	57.2862	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25458 - 	CGI_10025783	superfamily	243146	456	503	0.000895489	37.641	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25463 - 	CGI_10025788	superfamily	243072	359	468	2.13E-07	50.0746	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25464 - 	CGI_10025789	superfamily	241750	8	264	1.43E-68	215.13	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#25465 - 	CGI_10025790	superfamily	241750	56	300	2.50E-60	195.1	cl00281	metallo-dependent_hydrolases superfamily	 - 	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#25466 - 	CGI_10025791	superfamily	241832	89	170	3.16E-37	126.479	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25467 - 	CGI_10025792	superfamily	110440	84	110	0.0018744	33.5353	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25467 - 	CGI_10025792	superfamily	110440	125	152	0.00603037	32.3797	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25470 - 	CGI_10025795	superfamily	247723	1200	1283	2.23E-51	178.611	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25470 - 	CGI_10025795	superfamily	248011	600	666	1.75E-09	57.5065	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#25470 - 	CGI_10025795	superfamily	243078	1482	1616	6.68E-27	109.674	cl02544	VHS_ENTH_ANTH superfamily	 - 	 - 	"VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding."
Q#25470 - 	CGI_10025795	superfamily	243154	1362	1413	1.46E-17	80.3392	cl02715	Surp superfamily	 - 	 - 	Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.
Q#25470 - 	CGI_10025795	superfamily	203903	1784	1827	5.93E-08	52.1645	cl07067	cwf21 superfamily	 - 	 - 	cwf21 domain; The cwf21 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe. The function of the cwf21 domain is to bind directly to the spliceosomal protein Prp8. Mutations in the cwf21 domain prevent Prp8 from binding. The structure of this domain has recently been solved which shows this domain to be composed of two alpha helices.
Q#25470 - 	CGI_10025795	superfamily	248011	688	765	4.68E-07	50.1422	cl17457	PKD superfamily	 - 	 - 	"polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases."
Q#25472 - 	CGI_10025798	superfamily	154924	239	349	6.58E-46	154.085	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#25472 - 	CGI_10025798	superfamily	154924	167	235	2.03E-31	115.472	cl02467	C4 superfamily	N	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#25472 - 	CGI_10025798	superfamily	154924	1	46	1.01E-13	66.166	cl02467	C4 superfamily	N	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#25472 - 	CGI_10025798	superfamily	154924	64	86	1.36E-05	42.6688	cl02467	C4 superfamily	C	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#25475 - 	CGI_10025801	superfamily	154924	135	201	5.04E-29	105.842	cl02467	C4 superfamily	N	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#25477 - 	CGI_10025803	superfamily	154924	72	169	1.57E-48	158.999	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#25477 - 	CGI_10025803	superfamily	154924	183	289	8.61E-39	133.669	cl02467	C4 superfamily	 - 	 - 	C-terminal tandem repeated domain in type 4 procollagen; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Q#25478 - 	CGI_10025804	superfamily	241626	129	248	4.96E-56	178.952	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#25481 - 	CGI_10008988	superfamily	245598	83	279	6.02E-76	241.029	cl11396	Patatin_and_cPLA2 superfamily	 - 	 - 	"Patatins and Phospholipases; Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms."
Q#25481 - 	CGI_10008988	superfamily	247856	397	422	0.00758481	34.6617	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25482 - 	CGI_10008989	superfamily	241563	62	98	0.000324078	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25482 - 	CGI_10008989	superfamily	241563	8	52	0.00362434	35.5328	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25484 - 	CGI_10008991	superfamily	199156	90	105	0.001918	32.8004	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#25485 - 	CGI_10008992	superfamily	243119	359	403	3.85E-06	43.9717	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#25486 - 	CGI_10008993	superfamily	243119	61	107	7.18E-06	39.7346	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#25488 - 	CGI_10008995	superfamily	241958	72	504	3.17E-100	310.601	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#25489 - 	CGI_10008996	superfamily	217293	1	151	1.10E-46	160.491	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25489 - 	CGI_10008996	superfamily	202474	158	354	8.03E-30	115.058	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#25491 - 	CGI_10006490	superfamily	241600	200	335	3.24E-57	186.677	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25492 - 	CGI_10006493	superfamily	243035	103	189	2.53E-19	79.9713	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25493 - 	CGI_10006494	superfamily	243066	3	87	1.44E-19	82.6653	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25493 - 	CGI_10006494	superfamily	198867	97	207	7.65E-15	69.6776	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#25494 - 	CGI_10006495	superfamily	243035	324	439	6.03E-20	84.9789	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25494 - 	CGI_10006495	superfamily	243066	22	123	7.71E-26	100.384	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25494 - 	CGI_10006495	superfamily	198867	135	241	4.15E-08	50.8028	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#25496 - 	CGI_10009011	superfamily	217473	2935	3021	6.08E-07	52.7525	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25498 - 	CGI_10009013	superfamily	243100	649	694	0.0041261	36.148	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#25499 - 	CGI_10009014	superfamily	241623	246	495	1.35E-33	127.461	cl00119	PI3Kc_like superfamily	 - 	 - 	"Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRRAP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control."
Q#25500 - 	CGI_10009015	superfamily	241647	102	128	6.16E-05	41.7446	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#25500 - 	CGI_10009015	superfamily	241647	222	249	0.000125087	40.589	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#25500 - 	CGI_10009015	superfamily	241647	332	361	0.000295811	39.4334	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#25500 - 	CGI_10009015	superfamily	207669	575	620	1.10E-10	58.6098	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#25500 - 	CGI_10009015	superfamily	207669	506	552	5.61E-10	56.6838	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#25500 - 	CGI_10009015	superfamily	207669	439	485	4.19E-09	53.9874	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#25500 - 	CGI_10009015	superfamily	207669	820	880	4.90E-06	45.1278	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#25500 - 	CGI_10009015	superfamily	207669	763	813	9.61E-06	44.3574	cl02610	FF superfamily	 - 	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#25500 - 	CGI_10009015	superfamily	207669	705	739	0.00991833	35.1126	cl02610	FF superfamily	C	 - 	"FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions."
Q#25501 - 	CGI_10009016	superfamily	247684	10	441	9.32E-79	257.206	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25502 - 	CGI_10009017	superfamily	247684	10	519	8.86E-91	290.718	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25505 - 	CGI_10009020	superfamily	247684	10	383	4.18E-66	221.767	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25513 - 	CGI_10009934	superfamily	243035	50	123	4.83E-09	50.311	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25515 - 	CGI_10009936	superfamily	246723	116	771	0	684.418	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#25516 - 	CGI_10009937	superfamily	245864	23	233	3.99E-79	247.192	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#25517 - 	CGI_10009938	superfamily	217473	113	386	1.83E-36	139.037	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25518 - 	CGI_10009939	superfamily	247984	109	312	1.52E-26	107.311	cl17430	FtsJ superfamily	 - 	 - 	"FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping."
Q#25519 - 	CGI_10009940	superfamily	242897	7	110	2.63E-22	85.5103	cl02129	ParBc superfamily	 - 	 - 	ParB-like nuclease domain; ParB-like nuclease domain.  
Q#25520 - 	CGI_10009941	superfamily	241599	6	63	1.67E-19	77.6688	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25521 - 	CGI_10009942	superfamily	241599	67	117	1.75E-17	71.8908	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25522 - 	CGI_10009943	superfamily	241599	624	681	4.69E-21	88.4544	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25522 - 	CGI_10009943	superfamily	241599	745	802	2.23E-20	86.5284	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25522 - 	CGI_10009943	superfamily	241578	261	414	2.97E-38	141.198	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25522 - 	CGI_10009943	superfamily	207701	9	126	2.16E-15	74.3167	cl02699	VIT superfamily	 - 	 - 	Vault protein inter-alpha-trypsin domain; Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors.
Q#25525 - 	CGI_10020721	superfamily	198827	1	84	2.30E-22	85.9439	cl03803	BAF superfamily	 - 	 - 	Barrier to autointegration factor; The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.
Q#25526 - 	CGI_10020722	superfamily	198827	81	169	1.35E-49	156.821	cl03803	BAF superfamily	 - 	 - 	Barrier to autointegration factor; The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.
Q#25528 - 	CGI_10020724	superfamily	198827	1	74	3.57E-43	136.79	cl03803	BAF superfamily	 - 	 - 	Barrier to autointegration factor; The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.
Q#25530 - 	CGI_10020726	superfamily	241571	58	164	2.06E-25	101.72	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25530 - 	CGI_10020726	superfamily	241571	172	273	9.40E-20	85.5418	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25530 - 	CGI_10020726	superfamily	241571	411	514	1.13E-19	85.5418	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25530 - 	CGI_10020726	superfamily	241571	290	396	4.99E-17	77.8378	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25530 - 	CGI_10020726	superfamily	241600	533	606	6.12E-16	76.5103	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#25531 - 	CGI_10020727	superfamily	247805	48	246	7.75E-88	269.74	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25531 - 	CGI_10020727	superfamily	247905	270	391	4.18E-21	88.834	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25532 - 	CGI_10020728	superfamily	245836	182	396	1.14E-91	281.825	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#25532 - 	CGI_10020728	superfamily	217793	399	495	3.20E-29	111.018	cl04328	mRNA_cap_C superfamily	 - 	 - 	"mRNA capping enzyme, C-terminal domain; mRNA capping enzyme, C-terminal domain.  "
Q#25532 - 	CGI_10020728	superfamily	241574	41	106	8.99E-07	47.2788	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25534 - 	CGI_10020730	superfamily	248312	117	259	1.74E-07	48.5037	cl17758	PMP22_Claudin superfamily	 - 	 - 	PMP-22/EMP/MP20/Claudin family; PMP-22/EMP/MP20/Claudin family.  
Q#25535 - 	CGI_10020731	superfamily	238191	11	513	5.46E-119	365.502	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#25536 - 	CGI_10020732	superfamily	219673	105	289	6.54E-58	189.046	cl06835	COPIIcoated_ERV superfamily	 - 	 - 	"Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localisation. All proteins identified biochemically as Erv41p-Erv46p interactors are localised to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi."
Q#25537 - 	CGI_10020733	superfamily	243077	334	386	1.70E-20	85.2897	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#25538 - 	CGI_10020734	superfamily	191444	100	170	9.85E-09	49.2449	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#25539 - 	CGI_10020735	superfamily	242274	14	210	7.51E-72	220.202	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#25540 - 	CGI_10020736	superfamily	241568	43	98	6.78E-05	39.3684	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#25541 - 	CGI_10020737	superfamily	241571	394	506	1.17E-19	86.3122	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25542 - 	CGI_10020738	superfamily	241571	725	840	5.52E-26	104.802	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25542 - 	CGI_10020738	superfamily	241571	255	367	6.71E-23	95.9422	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25542 - 	CGI_10020738	superfamily	241571	614	724	2.25E-20	88.6234	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25542 - 	CGI_10020738	superfamily	241571	146	254	2.95E-17	79.7638	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25542 - 	CGI_10020738	superfamily	241571	373	499	4.82E-16	76.297	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25542 - 	CGI_10020738	superfamily	241571	57	120	2.86E-06	47.0219	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25543 - 	CGI_10020739	superfamily	242323	113	221	2.51E-20	86.0231	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#25545 - 	CGI_10020741	superfamily	243035	46	124	6.01E-05	42.2218	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25545 - 	CGI_10020741	superfamily	241578	215	399	1.47E-21	93.6129	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25546 - 	CGI_10020742	superfamily	243035	180	250	3.34E-06	45.3034	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25546 - 	CGI_10020742	superfamily	243035	378	454	0.000414782	38.755	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25546 - 	CGI_10020742	superfamily	241619	257	329	0.000327049	39.0992	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#25547 - 	CGI_10020743	superfamily	241737	123	290	1.04E-87	262.143	cl00264	Ferritin_like superfamily	 - 	 - 	"Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF)."
Q#25550 - 	CGI_10020746	superfamily	241748	17	197	5.73E-89	270.742	cl00279	APP_MetAP superfamily	C	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#25550 - 	CGI_10020746	superfamily	241748	284	333	1.94E-14	70.823	cl00279	APP_MetAP superfamily	N	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#25552 - 	CGI_10020748	superfamily	247724	5	172	3.67E-41	138.446	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25554 - 	CGI_10020750	superfamily	241574	9	88	0.000689559	34.5065	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25555 - 	CGI_10020751	superfamily	241574	127	258	1.12E-31	117.324	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25555 - 	CGI_10020751	superfamily	241574	301	383	4.55E-07	47.6033	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25556 - 	CGI_10020752	superfamily	247905	418	485	4.01E-12	63.4108	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25556 - 	CGI_10020752	superfamily	247805	3	144	6.79E-06	44.6356	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25557 - 	CGI_10020753	superfamily	241563	61	100	0.000228004	40.1552	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25558 - 	CGI_10020754	superfamily	247856	2	35	6.43E-05	41.7645	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25558 - 	CGI_10020754	superfamily	241620	89	105	0.000968744	37.8033	cl00113	CRIB superfamily	C	 - 	"PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules."
Q#25559 - 	CGI_10020755	superfamily	241832	90	192	9.52E-10	54.1537	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25560 - 	CGI_10020756	superfamily	241610	684	736	8.74E-22	90.0018	cl00101	KU superfamily	 - 	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#25561 - 	CGI_10020757	superfamily	241874	11	495	0	634.905	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#25562 - 	CGI_10020758	superfamily	216301	22	199	1.24E-51	166.671	cl03099	EMP24_GP25L superfamily	 - 	 - 	emp24/gp25L/p24 family/GOLD; Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains.
Q#25565 - 	CGI_10010772	superfamily	217473	99	333	1.82E-24	102.828	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25566 - 	CGI_10010773	superfamily	242902	64	126	2.13E-14	69.9682	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#25566 - 	CGI_10010773	superfamily	247724	366	425	0.00762412	36.0152	cl17170	Ras_like_GTPase superfamily	NC	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25567 - 	CGI_10010774	superfamily	242902	38	130	3.57E-11	59.9531	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#25571 - 	CGI_10010778	superfamily	243034	101	178	5.74E-07	47.3748	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#25571 - 	CGI_10010778	superfamily	242223	279	375	5.73E-26	100.925	cl00960	Fic superfamily	 - 	 - 	"Fic/DOC family; This family consists of the Fic (filamentation induced by cAMP) protein and doc (death on curing). The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism. This family contains a central conserved motif HPFXXGNG in most members. The exact molecular function of these proteins is uncertain. P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation. A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family. Doc induces a reversible growth arrest of E. coli cells by targetting the protein synthesis machinery. Doc hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation, a domain that is intrinsically disordered in solution but that folds into an alpha-helix on binding to Doc.This domain forms complexes with Phd antitoxins containing pfam02604."
Q#25572 - 	CGI_10010779	superfamily	207662	816	896	2.13E-54	185.066	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#25572 - 	CGI_10010779	superfamily	247905	527	640	8.03E-24	99.2344	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25572 - 	CGI_10010779	superfamily	245599	977	1171	3.21E-77	253.084	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#25572 - 	CGI_10010779	superfamily	247805	258	466	7.05E-40	147.021	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25574 - 	CGI_10010781	superfamily	246918	44	93	2.22E-09	50.2779	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25574 - 	CGI_10010781	superfamily	243119	101	144	0.00039136	36.2577	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#25576 - 	CGI_10006341	superfamily	247805	39	147	3.77E-11	56.1916	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25577 - 	CGI_10006343	superfamily	241756	19	332	7.89E-172	483.208	cl00289	FIG superfamily	 - 	 - 	"FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule Inositol-1,4,5-triphosphate. Many of these enzymes are inhibited by Li+."
Q#25578 - 	CGI_10006344	superfamily	243106	1895	2034	7.20E-50	175.08	cl02608	BAH superfamily	 - 	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#25578 - 	CGI_10006344	superfamily	243091	1402	1521	3.26E-37	139.007	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#25578 - 	CGI_10006344	superfamily	243084	1677	1781	2.38E-27	109.787	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#25578 - 	CGI_10006344	superfamily	197795	1351	1398	9.19E-13	65.8838	cl02673	AWS superfamily	 - 	 - 	associated with SET domains; subdomain of PRESET
Q#25578 - 	CGI_10006344	superfamily	247999	1822	1862	2.12E-05	44.5102	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#25579 - 	CGI_10006345	superfamily	220642	4	93	4.59E-13	69.2021	cl10921	DAP3 superfamily	C	 - 	"Mitochondrial ribosomal death-associated protein 3; This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29)."
Q#25580 - 	CGI_10006346	superfamily	241571	20	135	3.61E-08	50.8739	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25580 - 	CGI_10006346	superfamily	245213	144	174	0.000239551	38.7718	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25580 - 	CGI_10006346	superfamily	245213	185	213	0.000348003	38.3866	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25581 - 	CGI_10006347	superfamily	245847	9	110	3.43E-08	49.038	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25582 - 	CGI_10001173	superfamily	243051	205	361	5.82E-42	148.295	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#25582 - 	CGI_10001173	superfamily	243051	22	184	8.26E-40	142.132	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#25582 - 	CGI_10001173	superfamily	243051	367	498	7.95E-34	125.183	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#25584 - 	CGI_10022939	superfamily	241589	11	141	8.18E-47	156.64	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#25584 - 	CGI_10022939	superfamily	241589	204	338	2.66E-40	139.691	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#25585 - 	CGI_10022940	superfamily	241589	63	197	1.83E-41	138.536	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#25586 - 	CGI_10022941	superfamily	241589	64	198	1.09E-42	141.617	cl00071	GLECT superfamily	 - 	 - 	"Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation."
Q#25588 - 	CGI_10022943	superfamily	242201	204	284	3.71E-13	67.4998	cl00933	ClpS superfamily	 - 	 - 	"ATP-dependent Clp protease adaptor protein ClpS; In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins."
Q#25589 - 	CGI_10022944	superfamily	241868	40	206	1.34E-26	100.257	cl00447	Nudix_Hydrolase superfamily	 - 	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#25590 - 	CGI_10022945	superfamily	241599	198	252	4.48E-16	71.5056	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25593 - 	CGI_10022948	superfamily	247724	122	235	3.99E-65	203.788	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25593 - 	CGI_10022948	superfamily	218609	71	124	3.31E-20	83.5771	cl05189	Destabilase superfamily	C	 - 	"Destabilase; Destabilase is an endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves isopeptide bonds formed by transglutaminase (Factor XIIIa) between glutamine gamma-carboxamide and the epsilon-amino group of lysine."
Q#25596 - 	CGI_10022951	superfamily	247042	16	449	2.68E-148	451.928	cl15693	Sema superfamily	 - 	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#25596 - 	CGI_10022951	superfamily	246918	754	805	4.72E-13	65.6859	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25596 - 	CGI_10022951	superfamily	246918	634	681	2.58E-12	63.7599	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25596 - 	CGI_10022951	superfamily	246918	566	610	1.17E-11	61.8339	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25596 - 	CGI_10022951	superfamily	246918	809	863	5.81E-09	54.1299	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25596 - 	CGI_10022951	superfamily	243104	452	500	2.28E-06	46.3924	cl02601	PSI superfamily	 - 	 - 	"Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman)."
Q#25596 - 	CGI_10022951	superfamily	246918	510	561	5.02E-05	42.1887	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25596 - 	CGI_10022951	superfamily	246918	869	909	0.00283037	37.1811	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25597 - 	CGI_10022952	superfamily	247725	92	235	3.85E-90	272.61	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25597 - 	CGI_10022952	superfamily	243100	241	270	0.000192122	39.4696	cl02576	B_zip1 superfamily	N	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#25600 - 	CGI_10022955	superfamily	241584	779	888	1.46E-14	71.3735	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25600 - 	CGI_10022955	superfamily	241584	1010	1098	3.85E-08	52.4987	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25600 - 	CGI_10022955	superfamily	241584	909	1000	0.00242382	37.8611	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25600 - 	CGI_10022955	superfamily	243035	27	156	3.18E-12	65.4037	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25600 - 	CGI_10022955	superfamily	245814	599	670	4.75E-11	60.5358	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25600 - 	CGI_10022955	superfamily	245814	696	779	7.85E-11	60.397	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25600 - 	CGI_10022955	superfamily	245814	187	281	7.97E-11	60.3567	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25600 - 	CGI_10022955	superfamily	245814	405	469	1.76E-10	59.413	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25600 - 	CGI_10022955	superfamily	245814	302	361	9.99E-09	54.0984	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25600 - 	CGI_10022955	superfamily	245814	497	577	1.51E-08	53.6633	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25601 - 	CGI_10022956	superfamily	222150	583	610	0.000206749	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#25601 - 	CGI_10022956	superfamily	222150	553	580	0.000250026	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#25604 - 	CGI_10022959	superfamily	245847	195	337	6.23E-17	76.0561	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25604 - 	CGI_10022959	superfamily	241619	101	147	0.000216778	38.7173	cl00112	PAN_APPLE superfamily	C	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#25605 - 	CGI_10022960	superfamily	245226	211	378	4.81E-20	85.8152	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#25606 - 	CGI_10022961	superfamily	247805	185	399	1.58E-78	249.709	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25606 - 	CGI_10022961	superfamily	247905	409	537	6.58E-35	128.51	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25608 - 	CGI_10022963	superfamily	216686	84	266	3.11E-43	149.01	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#25611 - 	CGI_10004058	superfamily	247856	16	69	5.38E-10	51.7797	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25612 - 	CGI_10004059	superfamily	247723	113	186	2.81E-26	97.8049	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25613 - 	CGI_10004060	superfamily	241832	388	484	1.75E-40	145.153	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25613 - 	CGI_10004060	superfamily	241832	141	244	1.48E-39	142.457	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25613 - 	CGI_10004060	superfamily	241832	515	616	1.13E-35	131.671	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25613 - 	CGI_10004060	superfamily	241832	265	366	3.34E-35	130.13	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25613 - 	CGI_10004060	superfamily	241832	23	128	1.10E-31	120.656	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25613 - 	CGI_10004060	superfamily	241832	639	731	6.36E-24	98.1588	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25616 - 	CGI_10001334	superfamily	219917	38	293	9.18E-42	147.908	cl07264	Ribonuc_P_40 superfamily	 - 	 - 	"Ribonuclease P 40kDa (Rpp40) subunit; The tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule and at least eight protein subunits. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 (this entry) are involved in extensive, but weak, protein-protein interactions in the holoenzyme complex."
Q#25619 - 	CGI_10001617	superfamily	241563	63	94	0.000255408	36.4964	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25620 - 	CGI_10001711	superfamily	246680	169	247	1.18E-12	61.1974	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25620 - 	CGI_10001711	superfamily	245874	28	119	0.00135184	35.865	cl12111	TNFR superfamily	C	 - 	"Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers."
Q#25621 - 	CGI_10001712	superfamily	246680	425	499	3.86E-12	62.353	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25622 - 	CGI_10001852	superfamily	240441	1153	1242	2.90E-20	87.6203	cl18913	Na_channel_gate superfamily	 - 	 - 	Inactivation gate of the voltage-gated sodium channel alpha subunits; This region is part of the intracellular linker between domains III and IV of the alpha subunits of voltage-gated sodium channels. It is responsible for fast inactivation of the channel and essential for proper physiological function.
Q#25622 - 	CGI_10001852	superfamily	219069	703	903	2.63E-14	73.5654	cl05828	Na_trans_assoc superfamily	 - 	 - 	"Sodium ion transport-associated; Members of this family contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of pfam00520 and, less often, one copy of pfam00612."
Q#25624 - 	CGI_10001854	superfamily	248012	108	196	2.65E-10	56.4321	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#25627 - 	CGI_10001881	superfamily	247805	43	149	5.98E-09	50.0284	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25636 - 	CGI_10008799	superfamily	247866	16	211	2.00E-12	64.0108	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#25637 - 	CGI_10008800	superfamily	220634	24	580	7.63E-118	385.368	cl12379	DUF2146 superfamily	C	 - 	Uncharacterized conserved protein (DUF2146); This is a family of proteins conserved from plants to humans. In Dictyostelium it is annotated as Mss11p but this could not be confirmed. Mss11p is required for the activation of pseudo-hyphal and invasive growth by Ste12p in yeast.
Q#25637 - 	CGI_10008800	superfamily	220634	707	997	2.27E-62	227.436	cl12379	DUF2146 superfamily	N	 - 	Uncharacterized conserved protein (DUF2146); This is a family of proteins conserved from plants to humans. In Dictyostelium it is annotated as Mss11p but this could not be confirmed. Mss11p is required for the activation of pseudo-hyphal and invasive growth by Ste12p in yeast.
Q#25638 - 	CGI_10008801	superfamily	245819	493	669	3.11E-33	126.54	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#25638 - 	CGI_10008801	superfamily	219812	154	401	1.81E-15	75.8056	cl07121	NIT superfamily	 - 	 - 	"Nitrate and nitrite sensing; The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure."
Q#25638 - 	CGI_10008801	superfamily	219526	453	479	0.000173052	42.2211	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#25639 - 	CGI_10008802	superfamily	247792	17	76	0.00157565	36.9872	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#25640 - 	CGI_10008803	superfamily	217390	170	318	8.55E-18	78.7557	cl18407	TPT superfamily	 - 	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#25641 - 	CGI_10001928	superfamily	221349	128	192	4.92E-08	48.504	cl13416	Git3_C superfamily	 - 	 - 	"G protein-coupled glucose receptor regulating Gpa2 C-term; Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This family is the conserved C-terminal domain of the member proteins."
Q#25642 - 	CGI_10001929	superfamily	217617	81	274	3.38E-30	116.362	cl15988	Sulfotransfer_2 superfamily	 - 	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#25643 - 	CGI_10001930	superfamily	247723	1	80	9.93E-31	115.842	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25646 - 	CGI_10024930	superfamily	243096	796	984	6.40E-36	135.888	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#25647 - 	CGI_10024931	superfamily	243069	27	199	6.17E-103	297.971	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#25648 - 	CGI_10024932	superfamily	243035	47	163	4.06E-24	91.9125	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25649 - 	CGI_10024933	superfamily	243035	157	272	8.02E-24	93.4533	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25649 - 	CGI_10024933	superfamily	243035	41	123	1.26E-14	67.6449	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25650 - 	CGI_10024934	superfamily	243035	6	50	0.0060132	31.4362	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25652 - 	CGI_10024936	superfamily	245226	216	383	4.95E-20	86.9708	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#25653 - 	CGI_10024937	superfamily	247684	1	272	3.94E-43	155.527	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25658 - 	CGI_10024943	superfamily	245612	333	501	6.64E-75	245.797	cl11426	Amidase superfamily	C	 - 	Amidase; Amidase.  
Q#25662 - 	CGI_10024948	superfamily	193253	9	168	5.36E-19	82.7773	cl15084	MT superfamily	N	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#25663 - 	CGI_10024949	superfamily	245226	18	48	0.00356857	32.2122	cl10012	DnaQ_like_exo superfamily	NC	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#25665 - 	CGI_10024951	superfamily	217473	78	333	8.26E-25	104.369	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25666 - 	CGI_10024952	superfamily	245847	149	272	0.00592723	34.7856	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#25668 - 	CGI_10024955	superfamily	241867	47	240	6.24E-55	180.104	cl00446	Lactamase_B superfamily	C	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#25670 - 	CGI_10024957	superfamily	248458	31	204	3.11E-05	44.6121	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#25670 - 	CGI_10024957	superfamily	248458	282	408	0.000706861	40.3749	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#25673 - 	CGI_10024961	superfamily	247724	72	312	2.14E-52	174.879	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25675 - 	CGI_10024963	superfamily	217836	12	93	0.00496026	34.1786	cl09556	Sas10_Utp3 superfamily	 - 	 - 	"Sas10/Utp3/C1D family; This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex. It also includes the human C1D protein and Saccharomyces cerevisiae YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs, and Sas10 which has been identified as a regulator of chromatin silencing. This family also includes the human protein Neuroguidin an initiation factor 4E (eIF4E) binding protein."
Q#25677 - 	CGI_10024965	superfamily	201479	2	105	1.05E-29	114.263	cl02994	Transglut_N superfamily	 - 	 - 	Transglutaminase family; Transglutaminase family.  
Q#25677 - 	CGI_10024965	superfamily	247916	254	344	6.53E-16	73.5711	cl17362	Transglut_core superfamily	 - 	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#25677 - 	CGI_10024965	superfamily	216198	574	659	1.00E-12	65.4128	cl08295	Transglut_C superfamily	 - 	 - 	"Transglutaminase family, C-terminal ig like domain; Transglutaminase family, C-terminal ig like domain.  "
Q#25681 - 	CGI_10024969	superfamily	247792	20	61	2.74E-07	45.1292	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#25682 - 	CGI_10024970	superfamily	245531	411	484	1.30E-15	72.7817	cl11158	BEN superfamily	 - 	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#25683 - 	CGI_10024971	superfamily	214773	222	425	3.42E-54	184.933	cl18315	CAP10 superfamily	 - 	 - 	Putative lipopolysaccharide-modifying enzyme; Putative lipopolysaccharide-modifying enzyme.  
Q#25683 - 	CGI_10024971	superfamily	216033	23	119	2.62E-13	66.2032	cl16959	Filamin superfamily	 - 	 - 	Filamin/ABP280 repeat; Filamin/ABP280 repeat.  
Q#25684 - 	CGI_10024972	superfamily	206083	1209	1233	0.00578003	36.432	cl16471	zf-C2H2_6 superfamily	 - 	 - 	C2H2-type zinc finger; C2H2-type zinc finger.  
Q#25685 - 	CGI_10024973	superfamily	241862	51	296	4.15E-05	43.1438	cl00437	COG0428 superfamily	 - 	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#25686 - 	CGI_10024974	superfamily	248469	295	414	1.10E-09	56.6095	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#25686 - 	CGI_10024974	superfamily	241581	6	91	0.00275383	36.5954	cl00062	FHA superfamily	 - 	 - 	"Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation)."
Q#25687 - 	CGI_10024975	superfamily	241677	2	119	1.82E-71	213.273	cl00197	cyclophilin superfamily	N	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#25688 - 	CGI_10024976	superfamily	241591	25	100	2.04E-26	97.6919	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#25689 - 	CGI_10000359	superfamily	243035	58	156	5.05E-24	91.5273	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25690 - 	CGI_10002240	superfamily	216686	87	273	7.61E-40	147.855	cl18377	Galactosyl_T superfamily	 - 	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#25690 - 	CGI_10002240	superfamily	245814	706	777	2.21E-13	67.6368	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25691 - 	CGI_10002241	superfamily	247856	158	208	6.42E-06	41.7645	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25691 - 	CGI_10002241	superfamily	242164	100	152	0.0096658	33.3122	cl00878	Ribosomal_S24e superfamily	C	 - 	Ribosomal protein S24e; Ribosomal protein S24e.  
Q#25692 - 	CGI_10002242	superfamily	243074	97	141	9.50E-18	78.7025	cl02535	F-box-like superfamily	 - 	 - 	F-box-like; This is an F-box-like family.
Q#25693 - 	CGI_10002243	superfamily	243092	21	137	0.000465467	38.0848	cl02567	WD40 superfamily	C	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25694 - 	CGI_10002101	superfamily	248097	2	105	1.31E-18	75.7646	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25695 - 	CGI_10002102	superfamily	248097	82	188	1.70E-19	80.387	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25696 - 	CGI_10002103	superfamily	243072	30	118	2.34E-08	52.771	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25696 - 	CGI_10002103	superfamily	149414	196	258	1.36E-17	78.4674	cl07091	TRP_2 superfamily	 - 	 - 	Transient receptor ion channel II; This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023).
Q#25697 - 	CGI_10003039	superfamily	222429	8	85	1.21E-19	82.6736	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#25699 - 	CGI_10003041	superfamily	222429	6	71	7.09E-10	54.1688	cl18676	Myb_DNA-bind_5 superfamily	 - 	 - 	Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes.
Q#25700 - 	CGI_10003042	superfamily	222150	596	621	1.76E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#25703 - 	CGI_10007224	superfamily	247725	732	911	4.84E-74	244.555	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25703 - 	CGI_10007224	superfamily	243096	592	724	1.95E-21	93.9016	cl02571	RhoGEF superfamily	N	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#25703 - 	CGI_10007224	superfamily	243095	1091	1266	2.85E-48	172.42	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#25703 - 	CGI_10007224	superfamily	246669	957	1065	1.97E-32	124.157	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#25704 - 	CGI_10007225	superfamily	215648	553	726	3.89E-19	87.6511	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#25704 - 	CGI_10007225	superfamily	245225	51	345	1.27E-14	76.1275	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#25705 - 	CGI_10007226	superfamily	241900	46	334	6.09E-89	275.787	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#25707 - 	CGI_10007228	superfamily	241618	45	79	2.12E-07	43.0267	cl00111	PAH superfamily	 - 	 - 	"Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers"
Q#25708 - 	CGI_10007229	superfamily	246748	351	566	3.14E-25	106.138	cl14876	Zinc_peptidase_like superfamily	 - 	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#25708 - 	CGI_10007229	superfamily	244870	206	270	9.59E-10	57.4098	cl08238	PA superfamily	C	 - 	"PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated  protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2."
Q#25709 - 	CGI_10007230	superfamily	214545	791	931	8.28E-50	174.045	cl10551	CULLIN superfamily	 - 	 - 	Cullin; Cullin.  
Q#25709 - 	CGI_10007230	superfamily	245539	1038	1103	9.07E-27	105.714	cl11186	Cullin_Nedd8 superfamily	 - 	 - 	"Cullin protein neddylation domain; This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue."
Q#25710 - 	CGI_10007231	superfamily	247727	42	152	6.99E-18	76.6998	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#25714 - 	CGI_10015997	superfamily	247923	12	153	6.15E-25	95.4754	cl17369	Glyco_tran_28_C superfamily	 - 	 - 	Glycosyltransferase family 28 C-terminal domain; The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase (EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (EC 2.4.1.-). Structural analysis suggests the C-terminal domain contains the UDP-GlcNAc binding site.
Q#25716 - 	CGI_10015999	superfamily	241563	68	109	3.84E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25717 - 	CGI_10016000	superfamily	245864	43	398	4.88E-44	160.136	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#25718 - 	CGI_10016001	superfamily	245864	120	354	4.16E-50	175.544	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#25721 - 	CGI_10016005	superfamily	248097	2	77	2.77E-12	59.201	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25722 - 	CGI_10016006	superfamily	246918	150	209	4.31E-09	50.6631	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25722 - 	CGI_10016006	superfamily	246918	20	69	1.46E-06	43.7295	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25722 - 	CGI_10016006	superfamily	246918	85	144	0.00370273	34.0995	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25724 - 	CGI_10016008	superfamily	243091	317	430	1.08E-07	50.4107	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#25724 - 	CGI_10016008	superfamily	243091	153	205	1.80E-05	43.6348	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#25724 - 	CGI_10016008	superfamily	243091	484	599	0.000137295	40.7807	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#25725 - 	CGI_10016009	superfamily	243072	478	617	1.33E-14	71.6458	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25725 - 	CGI_10016009	superfamily	243072	369	520	4.07E-13	67.4086	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25725 - 	CGI_10016009	superfamily	243073	736	774	1.01E-07	49.7761	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#25725 - 	CGI_10016009	superfamily	243091	132	243	1.85E-10	59.2703	cl02566	SET superfamily	 - 	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#25726 - 	CGI_10016010	superfamily	220532	16	196	2.41E-31	119.798	cl12374	ATG13 superfamily	 - 	 - 	"Autophagy-related protein 13; Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage."
Q#25734 - 	CGI_10014823	superfamily	241874	31	593	0	586.068	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#25737 - 	CGI_10014826	superfamily	241729	320	732	0	836.573	cl00254	NOS_oxygenase superfamily	 - 	 - 	"Nitric oxide synthase (NOS) produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . Nitric oxide synthases are homodimers. In eukaryotes, each monomer has an N-terminal oxygenase domain which binds to the substrate L-Arg,  zinc, and to the cofactors heme and 5.6.7.8-(6R)-tetrahydrobiopterin (BH4) . Eukaryotic NOSs also have a C-terminal electron supplying reductase region, which is homologous to cytochrome P450 reductase and binds NADH, FAD and FMN.  While prokaryotes can produce NO as a byproduct of denitrification, using a completely different set of enzymes than NOS, a few prokaryotes also have a NOS which consists solely of the NOS oxygenase domain. Prokaryotic NOS binds to the substrate L-Arg, zinc, and to the cofactors heme and tetrahydrofolate."
Q#25737 - 	CGI_10014826	superfamily	244539	1021	1430	0	648.237	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#25737 - 	CGI_10014826	superfamily	241622	6	89	3.63E-12	64.5102	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#25737 - 	CGI_10014826	superfamily	241863	782	955	1.69E-30	119.419	cl00438	Flavodoxin_2 superfamily	 - 	 - 	Flavodoxin-like fold; This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
Q#25739 - 	CGI_10014828	superfamily	191444	67	131	0.000172218	36.9185	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#25741 - 	CGI_10014830	superfamily	243035	41	165	7.52E-32	111.943	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25742 - 	CGI_10014831	superfamily	207794	83	128	4.91E-15	76.4822	cl02948	GH20_hexosaminidase superfamily	C	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#25742 - 	CGI_10014831	superfamily	111707	47	75	2.22E-08	53.5728	cl03741	Glyco_hydro_20b superfamily	N	 - 	"Glycosyl hydrolase family 20, domain 2; This domain has a zincin-like fold."
Q#25743 - 	CGI_10014832	superfamily	243077	107	148	0.000473195	38.6805	cl02542	DnaJ superfamily	C	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#25743 - 	CGI_10014832	superfamily	247999	543	579	0.000204857	39.8878	cl17445	PHD superfamily	C	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#25744 - 	CGI_10014833	superfamily	241733	6	73	3.99E-43	136.112	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#25745 - 	CGI_10014834	superfamily	240523	1	165	1.86E-55	176.659	cl18941	DAXX_histone_binding superfamily	 - 	 - 	"Histone binding domain of the death-domain associated protein (DAXX); DAXX is a nuclear protein that modulates transcription of various genes and is involved in cell death and/or the suppression of growth. DAXX is also a histone chaperone conserved in Metazoa that acts specifically on histone H3.3. This alignment models a functional domain of DAXX that interacts with the histone H3.3-H4 dimer, and in doing so competes with DNA binding and interactions between the histone chaperone ASF1/CIA and the H3-H4 dimer."
Q#25746 - 	CGI_10004608	superfamily	243062	187	298	5.21E-14	66.1453	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#25747 - 	CGI_10004609	superfamily	243062	219	327	1.87E-13	64.9897	cl02510	TGF_beta superfamily	 - 	 - 	Transforming growth factor beta like domain; Transforming growth factor beta like domain.  
Q#25748 - 	CGI_10004610	superfamily	152135	1437	1513	3.00E-18	82.3635	cl18049	Mif2 superfamily	 - 	 - 	"Mif2/CENP-C like; Mif2 is a yeast DNA-binding kinetochore protein which is orthologous to mammalian CENP-C, the inner-kinetochore centromere (CEN) binding protein. Mif2 binds in the CDEIII region of the budding-yeast centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins. Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerisation domain of a bacterial transcription factor. The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast."
Q#25750 - 	CGI_10004612	superfamily	243100	135	188	4.95E-12	61.8609	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#25752 - 	CGI_10002640	superfamily	247787	8	171	6.01E-32	116.529	cl17233	RecA-like_NTPases superfamily	N	 - 	"RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion."
Q#25753 - 	CGI_10002641	superfamily	218215	140	255	2.81E-17	78.2947	cl04683	Pinin_SDK_memA superfamily	 - 	 - 	pinin/SDK/memA/ protein conserved region; Members of this family have very varied localisations within the eukaryotic cell. pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque. SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing. memA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions.
Q#25753 - 	CGI_10002641	superfamily	147050	6	139	7.41E-13	65.4672	cl04684	Pinin_SDK_N superfamily	 - 	 - 	pinin/SDK conserved region; SDK2/3 is localised in nuclear speckles where as pinin is known to localise at the desmosomes where it is thought to be involved in anchoring intermediate filaments to the desmosomal plaque. The role of SDK2/3 in the nucleus is thought to be concerned with modulation of alternative pre-mRNA splicing. pinin has also been implicated as a tumour suppressor. The conserved region is found at the N-terminus of the member proteins.
Q#25754 - 	CGI_10002642	superfamily	242899	7	156	3.18E-51	162.345	cl02135	TRAPP superfamily	 - 	 - 	"Transport protein particle (TRAPP) component; TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterized TRAPP proteins and has a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi."
Q#25756 - 	CGI_10022967	superfamily	245612	1	114	2.55E-45	154.007	cl11426	Amidase superfamily	N	 - 	Amidase; Amidase.  
Q#25757 - 	CGI_10022968	superfamily	243072	36	166	2.05E-23	90.9058	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25758 - 	CGI_10022969	superfamily	243072	17	117	1.93E-13	62.401	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25759 - 	CGI_10022970	superfamily	213389	171	311	2.87E-14	71.1663	cl17092	STING_C superfamily	C	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#25759 - 	CGI_10022970	superfamily	213389	498	640	1.59E-08	53.4471	cl17092	STING_C superfamily	C	 - 	"C-terminal domain of STING; STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain."
Q#25759 - 	CGI_10022970	superfamily	248012	60	115	0.00321805	36.8677	cl17458	TIR_2 superfamily	NC	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#25759 - 	CGI_10022970	superfamily	248012	360	467	0.00490399	36.0165	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#25760 - 	CGI_10022971	superfamily	216363	115	214	2.16E-16	71.7326	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#25761 - 	CGI_10022972	superfamily	247805	300	453	5.68E-19	85.0816	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25761 - 	CGI_10022972	superfamily	247905	616	750	4.97E-13	67.2628	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25761 - 	CGI_10022972	superfamily	213148	501	614	1.55E-11	62.7146	cl17041	helicase_insert_domain superfamily	 - 	 - 	"helical domain inserted in SF2-type helicase domain in Hef-, MDA5- and FancM-like proteins; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex."
Q#25761 - 	CGI_10022972	superfamily	221155	823	931	2.31E-08	53.1404	cl13152	RIG-I_C-RD superfamily	 - 	 - 	"C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity."
Q#25761 - 	CGI_10022972	superfamily	246680	112	185	3.84E-05	42.9436	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25762 - 	CGI_10022973	superfamily	247805	508	653	3.66E-18	83.5408	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#25762 - 	CGI_10022973	superfamily	247905	927	1062	8.58E-16	76.1224	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#25762 - 	CGI_10022973	superfamily	221155	1134	1250	2.58E-13	68.5484	cl13152	RIG-I_C-RD superfamily	 - 	 - 	"C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity."
Q#25762 - 	CGI_10022973	superfamily	213148	712	846	4.20E-12	65.0258	cl17041	helicase_insert_domain superfamily	 - 	 - 	"helical domain inserted in SF2-type helicase domain in Hef-, MDA5- and FancM-like proteins; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex."
Q#25762 - 	CGI_10022973	superfamily	246680	208	281	0.00628998	36.3952	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25764 - 	CGI_10022975	superfamily	243066	69	158	1.61E-22	89.5345	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25764 - 	CGI_10022975	superfamily	109845	279	318	1.48E-10	55.8527	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#25764 - 	CGI_10022975	superfamily	109845	194	238	1.70E-06	44.2967	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#25764 - 	CGI_10022975	superfamily	109845	170	208	7.92E-06	42.3707	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#25764 - 	CGI_10022975	superfamily	109845	249	293	0.000296305	37.7483	cl02971	Pentapeptide superfamily	 - 	 - 	"Pentapeptide repeats (8 copies); These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid."
Q#25767 - 	CGI_10022978	superfamily	222150	479	504	2.08E-06	45.0753	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#25767 - 	CGI_10022978	superfamily	222150	451	476	3.42E-06	44.3049	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#25768 - 	CGI_10022979	superfamily	222370	4	76	4.27E-18	75.2521	cl16386	Longin superfamily	 - 	 - 	"Regulated-SNARE-like domain; Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain."
Q#25768 - 	CGI_10022979	superfamily	201526	96	152	2.62E-15	67.9485	cl09522	Synaptobrevin superfamily	C	 - 	Synaptobrevin; Synaptobrevin.  
Q#25769 - 	CGI_10022980	superfamily	242186	28	200	9.69E-56	177.364	cl00911	AMMECR1 superfamily	 - 	 - 	"AMMECR1; This family consists of several AMMECR1 as well as several uncharacterized proteins. The contiguous gene deletion syndrome AMME is characterized by Alport syndrome, midface hypoplasia, mental retardation and elliptocytosis and is caused by a deletion in Xq22.3, comprising several genes including COL4A5, FACL4 and AMMECR1. This family contains sequences from several eukaryotic species as well as archaebacteria and it has been suggested that the AMMECR1 protein may have a basic cellular function, potentially in either the transcription, replication, repair or translation machinery."
Q#25771 - 	CGI_10022982	superfamily	241559	876	961	1.56E-09	56.5503	cl00030	CH superfamily	N	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#25772 - 	CGI_10022983	superfamily	243092	10	265	1.29E-22	94.7092	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25773 - 	CGI_10022984	superfamily	247725	1	160	1.81E-66	215.199	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25773 - 	CGI_10022984	superfamily	219103	155	268	7.00E-45	155.222	cl05893	Myotub-related superfamily	 - 	 - 	"Myotubularin-related; This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease."
Q#25773 - 	CGI_10022984	superfamily	206020	330	384	3.45E-24	96.0378	cl18286	Y_phosphatase_m superfamily	 - 	 - 	"Myotubularin Y_phosphatase-like; This short region is highly conserved and seems to be common to many myotubularin proteins with protein tyrosine pyrophosphate activity. As the family has a number of highly conserved residues such as histidine, cysteine, glutamine and aspartate, it is possible that this represents a catalytic core of the active enzymatic part of the proteins."
Q#25774 - 	CGI_10022985	superfamily	206084	108	132	0.0016907	35.6544	cl16472	zf-C2HC_2 superfamily	 - 	 - 	zinc-finger of a C2HC-type; This family contains a number of divergent C2H2 type zinc fingers.
Q#25778 - 	CGI_10022989	superfamily	241574	77	247	1.13E-64	211.29	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25778 - 	CGI_10022989	superfamily	241574	267	490	9.14E-15	72.6185	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#25779 - 	CGI_10022990	superfamily	241874	48	489	2.24E-93	301.733	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#25779 - 	CGI_10022990	superfamily	241874	635	786	5.29E-61	216.546	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#25782 - 	CGI_10022993	superfamily	245206	289	558	1.80E-126	374.881	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#25782 - 	CGI_10022993	superfamily	241578	25	255	8.24E-90	279.642	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25783 - 	CGI_10022994	superfamily	243092	102	426	1.08E-53	182.535	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25784 - 	CGI_10022995	superfamily	241572	181	269	3.71E-05	41.0701	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#25785 - 	CGI_10022996	superfamily	245201	875	1102	1.80E-36	139.679	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25785 - 	CGI_10022996	superfamily	245201	1495	1736	2.40E-33	130.434	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25785 - 	CGI_10022996	superfamily	241584	1339	1430	2.52E-13	68.6771	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25785 - 	CGI_10022996	superfamily	241584	510	590	5.09E-13	67.5215	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25785 - 	CGI_10022996	superfamily	241584	38	128	7.28E-12	64.4399	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25785 - 	CGI_10022996	superfamily	245814	763	832	1.93E-09	56.7287	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25785 - 	CGI_10022996	superfamily	245814	1264	1332	4.05E-09	55.9583	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25785 - 	CGI_10022996	superfamily	241584	183	279	6.82E-07	49.4171	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25785 - 	CGI_10022996	superfamily	245814	674	738	1.69E-05	44.7875	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25785 - 	CGI_10022996	superfamily	241584	290	343	3.23E-05	44.4095	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25785 - 	CGI_10022996	superfamily	241584	385	435	0.000147441	42.0983	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25786 - 	CGI_10022997	superfamily	241584	13	106	4.28E-08	54.0395	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25787 - 	CGI_10022998	superfamily	241584	8	87	3.25E-09	55.5803	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25787 - 	CGI_10022998	superfamily	241584	407	499	5.14E-08	52.1135	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25787 - 	CGI_10022998	superfamily	241584	115	193	1.09E-07	51.3431	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25787 - 	CGI_10022998	superfamily	241584	305	396	9.79E-07	48.2615	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25787 - 	CGI_10022998	superfamily	241584	204	295	2.81E-06	46.7207	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25788 - 	CGI_10022999	superfamily	241584	497	587	2.18E-12	64.0547	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25788 - 	CGI_10022999	superfamily	241584	90	184	2.97E-11	60.9731	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25788 - 	CGI_10022999	superfamily	241584	195	288	2.55E-10	57.8915	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25788 - 	CGI_10022999	superfamily	241584	599	685	1.06E-09	56.3507	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25788 - 	CGI_10022999	superfamily	241584	399	486	2.48E-09	55.1951	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25788 - 	CGI_10022999	superfamily	241584	311	389	1.54E-08	52.8839	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25788 - 	CGI_10022999	superfamily	241584	25	80	1.79E-06	46.7207	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#25790 - 	CGI_10023001	superfamily	243096	1296	1468	4.21E-18	84.6568	cl02571	RhoGEF superfamily	 - 	 - 	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Q#25790 - 	CGI_10023001	superfamily	245814	1093	1162	1.23E-08	54.4175	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25790 - 	CGI_10023001	superfamily	245814	1672	1754	2.01E-10	59.8264	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25790 - 	CGI_10023001	superfamily	245814	971	1054	9.14E-07	49.0409	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25790 - 	CGI_10023001	superfamily	245814	1785	1825	0.000274288	41.5724	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25791 - 	CGI_10023002	superfamily	245814	14	76	1.39E-13	61.3511	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25792 - 	CGI_10023003	superfamily	241599	177	234	7.96E-21	83.832	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25793 - 	CGI_10023005	superfamily	243072	43	165	1.11E-36	131.737	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25794 - 	CGI_10023006	superfamily	243072	18	148	3.63E-32	113.633	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25796 - 	CGI_10028051	superfamily	148902	38	106	0.000796804	37.4327	cl06535	EMI superfamily	 - 	 - 	EMI domain; The Pfam alignment is truncated at the C-terminus and does not include the final cysteine defined in Callebaut et al. This is to stop the family overlapping with other domains.
Q#25797 - 	CGI_10028052	superfamily	241583	244	475	1.74E-81	264.621	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#25797 - 	CGI_10028052	superfamily	189857	704	826	4.33E-21	91.5426	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#25797 - 	CGI_10028052	superfamily	216572	89	182	4.39E-06	46.1139	cl03265	Pep_M12B_propep superfamily	N	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#25798 - 	CGI_10028053	superfamily	246613	10	70	2.30E-31	111.648	cl14058	lectin_L-type superfamily	NC	 - 	"legume lectins; The L-type (legume-type) lectins are a highly diverse family of carbohydrate binding proteins that generally display no enzymatic activity toward the sugars they bind.  This family includes arcelin, concanavalinA, the lectin-like receptor kinases, the ERGIC-53/VIP36/EMP46 type1 transmembrane proteins, and an alpha-amylase inhibitor.  L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face".  This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers.  Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely."
Q#25801 - 	CGI_10028056	superfamily	241594	13	158	1.38E-62	198.173	cl00077	HECTc superfamily	N	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#25802 - 	CGI_10028057	superfamily	217473	96	320	8.39E-24	101.673	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#25803 - 	CGI_10028058	superfamily	245201	92	379	0	552.372	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25803 - 	CGI_10028058	superfamily	116877	471	559	2.90E-15	71.9435	cl07051	MRP-S33 superfamily	 - 	 - 	"Mitochondrial ribosomal subunit S27; This family of proteins corresponds to mitochondrial ribosomal subunit S27 in prokaryotes and to subunit S33 in humans. It is a small 106 residue protein.The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome."
Q#25804 - 	CGI_10028059	superfamily	219448	215	304	2.21E-16	75.8145	cl06523	DRMBL superfamily	 - 	 - 	DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.
Q#25804 - 	CGI_10028059	superfamily	241867	28	129	1.04E-11	63.3414	cl00446	Lactamase_B superfamily	N	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#25808 - 	CGI_10028063	superfamily	217390	224	278	0.00011852	40.2357	cl18407	TPT superfamily	N	 - 	Triose-phosphate Transporter family; This family includes transporters with a specificity for triose phosphate.
Q#25809 - 	CGI_10028064	superfamily	248097	68	184	1.04E-15	71.9126	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25810 - 	CGI_10028065	superfamily	248097	51	82	5.10E-08	46.1042	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25811 - 	CGI_10028066	superfamily	243035	95	205	2.44E-19	80.8117	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25812 - 	CGI_10028067	superfamily	248097	74	190	2.17E-16	75.7646	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25812 - 	CGI_10028067	superfamily	248097	368	466	1.17E-10	59.201	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25813 - 	CGI_10028068	superfamily	241563	61	96	0.000506209	38.6144	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25814 - 	CGI_10028069	superfamily	220215	78	174	0.00272488	37.5898	cl09630	FERM_N superfamily	 - 	 - 	FERM N-terminal domain; This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
Q#25814 - 	CGI_10028069	superfamily	246925	583	689	0.00812472	38.4906	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#25816 - 	CGI_10028071	superfamily	247725	782	872	3.26E-47	165.213	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25816 - 	CGI_10028071	superfamily	247057	14	79	1.27E-28	111.229	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#25816 - 	CGI_10028071	superfamily	241622	228	304	1.95E-10	59.1174	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#25816 - 	CGI_10028071	superfamily	247725	1017	1091	1.60E-20	89.3652	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25816 - 	CGI_10028071	superfamily	151082	87	187	1.04E-09	57.1667	cl11167	CRIC_ras_sig superfamily	 - 	 - 	"Connector enhancer of kinase suppressor of ras; The CRIC - Connector enhancer of kinase suppressor of ras - domain functions as a scaffold in several signal cascades and acts on proliferation, differentiation and apoptosis."
Q#25817 - 	CGI_10028072	superfamily	215827	57	228	6.05E-39	142.222	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#25819 - 	CGI_10028074	superfamily	245596	55	272	7.85E-113	328.387	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#25822 - 	CGI_10028077	superfamily	243555	73	130	3.82E-05	43.1486	cl03871	Chitin_bind_3 superfamily	N	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#25823 - 	CGI_10028078	superfamily	245206	8	254	6.06E-118	340.542	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#25824 - 	CGI_10028079	superfamily	215827	312	489	2.81E-41	151.082	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#25826 - 	CGI_10028081	superfamily	243072	180	281	4.66E-13	67.0234	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25826 - 	CGI_10028081	superfamily	243072	238	383	6.91E-08	51.2302	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25826 - 	CGI_10028081	superfamily	243073	685	724	1.01E-06	46.7199	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#25826 - 	CGI_10028081	superfamily	243072	83	230	0.000123867	41.2151	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25827 - 	CGI_10028082	superfamily	216839	16	123	1.34E-23	93.5551	cl12260	TFIIE_alpha superfamily	 - 	 - 	"TFIIE alpha subunit; The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta, and joins the pre-initiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also Archaeoglobus fulgidus tfe."
Q#25828 - 	CGI_10028083	superfamily	217293	117	322	3.84E-53	181.292	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#25828 - 	CGI_10028083	superfamily	202474	329	540	5.53E-20	88.4797	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#25836 - 	CGI_10028091	superfamily	245814	333	395	1.64E-05	43.2467	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25837 - 	CGI_10028092	superfamily	243152	29	156	5.99E-35	120.471	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#25849 - 	CGI_10028104	superfamily	245201	33	290	1.88E-82	255.907	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25850 - 	CGI_10028105	superfamily	246918	148	207	6.29E-12	59.5227	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25850 - 	CGI_10028105	superfamily	246918	84	143	8.78E-06	42.1887	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25851 - 	CGI_10028107	superfamily	248097	83	174	5.09E-14	64.979	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25852 - 	CGI_10028108	superfamily	248097	52	123	7.56E-11	55.7342	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25853 - 	CGI_10028109	superfamily	248097	22	70	9.08E-08	46.1042	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25854 - 	CGI_10028110	superfamily	248097	217	342	3.93E-16	73.4534	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#25855 - 	CGI_10028111	superfamily	243066	6	91	1.36E-10	54.0961	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25856 - 	CGI_10028112	superfamily	244886	7	94	4.90E-21	80.7733	cl08278	Rotamase_2 superfamily	 - 	 - 	PPIC-type PPIASE domain; PPIC-type PPIASE domain.  
Q#25857 - 	CGI_10028113	superfamily	243035	22	126	2.85E-15	67.3297	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#25858 - 	CGI_10028114	superfamily	246918	746	798	2.98E-15	72.2343	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25858 - 	CGI_10028114	superfamily	246918	917	969	8.73E-14	67.9971	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25858 - 	CGI_10028114	superfamily	246918	575	627	3.55E-13	66.0711	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25858 - 	CGI_10028114	superfamily	246918	632	684	4.87E-12	62.9895	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25858 - 	CGI_10028114	superfamily	246918	803	855	6.59E-10	56.8263	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25860 - 	CGI_10028116	superfamily	241835	89	148	1.01E-11	56.899	cl00392	Ribosomal_L35p superfamily	 - 	 - 	Ribosomal protein L35; Ribosomal protein L35.  
Q#25862 - 	CGI_10028118	superfamily	246918	193	243	2.75E-12	61.4487	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25862 - 	CGI_10028118	superfamily	246918	249	306	1.44E-11	59.1375	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25862 - 	CGI_10028118	superfamily	246918	78	130	3.12E-10	55.6707	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25862 - 	CGI_10028118	superfamily	246918	135	187	1.36E-06	45.2703	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25862 - 	CGI_10028118	superfamily	246918	14	68	4.28E-05	40.6479	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#25863 - 	CGI_10028119	superfamily	241874	67	268	1.75E-88	284.183	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#25865 - 	CGI_10028121	superfamily	243049	56	82	0.000317032	38.113	cl02472	IGFBP superfamily	NC	 - 	Insulin-like growth factor binding protein; Insulin-like growth factor binding protein.  
Q#25866 - 	CGI_10028122	superfamily	203013	5	33	4.80E-07	46.0798	cl04519	zf-HIT superfamily	 - 	 - 	HIT zinc finger; This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) that specifically interacts with the ligand binding domain of the thyroid receptor.
Q#25868 - 	CGI_10028124	superfamily	247063	58	122	2.42E-12	59.823	cl15768	TGS superfamily	 - 	 - 	"The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role."
Q#25869 - 	CGI_10028125	superfamily	247725	1268	1383	3.26E-58	199.469	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25869 - 	CGI_10028125	superfamily	247725	1908	2022	3.12E-56	193.691	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25869 - 	CGI_10028125	superfamily	247725	2253	2368	1.87E-53	185.602	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25869 - 	CGI_10028125	superfamily	247725	2436	2525	1.91E-11	63.6498	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#25869 - 	CGI_10028125	superfamily	207690	1486	1514	0.000528203	40.4109	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#25870 - 	CGI_10028126	superfamily	242274	4	213	5.55E-97	284.952	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#25874 - 	CGI_10028130	superfamily	110440	486	510	0.000428477	38.1577	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#25874 - 	CGI_10028130	superfamily	241563	59	95	0.000496662	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25875 - 	CGI_10005875	superfamily	244824	110	602	0	680.888	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#25875 - 	CGI_10005875	superfamily	114894	1088	1128	6.29E-11	64.2684	cl17945	GDE_C superfamily	C	 - 	"Amylo-alpha-1,6-glucosidase; This family includes human glycogen branching enzyme. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homologue that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33)."
Q#25876 - 	CGI_10005876	superfamily	241677	1	154	3.28E-104	297.811	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#25878 - 	CGI_10005878	superfamily	242903	222	307	2.55E-32	124.248	cl02148	APC10-like superfamily	C	 - 	"APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An  APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here."
Q#25878 - 	CGI_10005878	superfamily	241760	1345	1393	3.07E-17	78.1258	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#25878 - 	CGI_10005878	superfamily	241571	848	938	0.0019144	38.5475	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#25879 - 	CGI_10005879	superfamily	243054	9373	9588	3.29E-32	129.873	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	9485	9695	7.21E-30	122.939	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	8831	9045	1.55E-24	107.146	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	9050	9250	1.28E-22	101.368	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	8720	8936	4.50E-21	96.7459	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	8178	8394	7.35E-21	96.3607	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	6800	7021	3.70E-20	94.0495	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	7307	7518	4.83E-20	93.6643	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	241559	49	153	5.44E-19	87.7515	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#25879 - 	CGI_10005879	superfamily	243054	7636	7850	4.84E-17	84.8047	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	424	610	8.07E-16	80.9527	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	8608	8827	3.14E-15	79.0267	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	8396	8606	2.70E-14	76.3303	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	7527	7742	8.78E-14	74.4043	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	7852	8065	3.70E-11	66.3152	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	6669	6914	1.70E-10	64.004	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	6559	6719	1.40E-08	58.226	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	288	516	1.02E-06	52.448	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	141488	9945	10014	4.28E-34	130.646	cl02524	GAS2 superfamily	 - 	 - 	Growth-Arrest-Specific Protein 2 Domain; Growth-Arrest-Specific Protein 2 Domain.  
Q#25879 - 	CGI_10005879	superfamily	243054	9268	9368	8.51E-10	60.8065	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	9707	9762	1.20E-05	48.0949	cl02488	SPEC superfamily	C	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	864	1072	2.75E-05	48.2108	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	243054	8091	8173	5.63E-05	45.7837	cl02488	SPEC superfamily	N	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#25879 - 	CGI_10005879	superfamily	207632	4263	4295	0.00900486	38.5857	cl02531	Plectin superfamily	 - 	 - 	"Plectin repeat; This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen."
Q#25880 - 	CGI_10005880	superfamily	241559	17	102	1.40E-19	78.8919	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#25881 - 	CGI_10003120	superfamily	247727	374	445	0.000322746	39.7207	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#25882 - 	CGI_10003121	superfamily	198738	520	602	5.49E-52	174.817	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#25882 - 	CGI_10003121	superfamily	247057	382	454	3.18E-24	97.4809	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#25883 - 	CGI_10002464	superfamily	245201	38	245	6.57E-100	295.764	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25885 - 	CGI_10003376	superfamily	217309	142	553	5.83E-140	418.254	cl09289	EMP70 superfamily	 - 	 - 	Endomembrane protein 70; Endomembrane protein 70.  
Q#25888 - 	CGI_10001426	superfamily	221377	231	375	1.15E-09	55.9378	cl13449	DUF3504 superfamily	 - 	 - 	Domain of unknown function (DUF3504); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.
Q#25889 - 	CGI_10009492	superfamily	247723	356	427	6.38E-31	117.262	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25889 - 	CGI_10009492	superfamily	247792	798	831	3.19E-06	45.5144	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#25889 - 	CGI_10009492	superfamily	247723	659	730	3.22E-19	83.8589	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#25889 - 	CGI_10009492	superfamily	245674	922	967	0.000319947	39.965	cl11531	DUF904 superfamily	C	 - 	Protein of unknown function (DUF904); This family consists of several bacterial and archaeal hypothetical proteins of unknown function.
Q#25889 - 	CGI_10009492	superfamily	245716	126	147	0.00354632	36.4533	cl11592	zf-CCCH superfamily	N	 - 	Zinc finger C-x8-C-x5-C-x3-H type (and similar); Zinc finger C-x8-C-x5-C-x3-H type (and similar).  
Q#25890 - 	CGI_10009493	superfamily	248024	11	324	1.88E-69	221.638	cl17470	SBF superfamily	 - 	 - 	"Sodium Bile acid symporter family; This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae, this is a putative transmembrane protein involved in resistance to arsenic compounds."
Q#25891 - 	CGI_10009494	superfamily	241578	320	464	1.78E-20	89.273	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25891 - 	CGI_10009494	superfamily	241578	509	670	1.04E-12	66.5462	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25891 - 	CGI_10009494	superfamily	245213	195	231	1.18E-10	58.0318	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25891 - 	CGI_10009494	superfamily	245213	273	309	2.15E-08	51.4834	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25891 - 	CGI_10009494	superfamily	245213	155	192	2.20E-07	48.4018	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25891 - 	CGI_10009494	superfamily	245213	234	270	1.15E-06	46.4758	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#25892 - 	CGI_10009495	superfamily	243362	177	336	4.35E-50	166.447	cl03262	DnaJ_C superfamily	 - 	 - 	C-terminal substrate binding domain of DnaJ and HSP40; The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70.
Q#25892 - 	CGI_10009495	superfamily	243077	4	57	1.33E-25	97.6161	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#25893 - 	CGI_10009496	superfamily	243072	402	523	7.26E-36	133.663	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25893 - 	CGI_10009496	superfamily	243072	201	326	2.66E-31	120.566	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25893 - 	CGI_10009496	superfamily	243072	65	227	5.42E-25	102.462	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#25894 - 	CGI_10009497	superfamily	246680	12	92	3.15E-17	71.3594	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25895 - 	CGI_10009498	superfamily	247637	11	330	9.62E-130	394.643	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#25895 - 	CGI_10009498	superfamily	243179	716	794	3.45E-05	43.2903	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#25897 - 	CGI_10009500	superfamily	241563	18	50	0.00119894	36.9315	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25897 - 	CGI_10009500	superfamily	241717	54	130	0.00742698	36.4017	cl00240	RRF superfamily	N	 - 	"Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation.  Thus ribosomes are "recycled" and ready for another round of protein synthesis.  RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear.  RRF is essential for bacterial growth.  It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species."
Q#25898 - 	CGI_10009501	superfamily	242116	27	561	0	1081.23	cl00817	MM_CoA_mutase superfamily	 - 	 - 	"Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In higher animals, MCM is involved in the breakdown of odd-chain fatty acids, several amino acids, and cholesterol. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversible inactivation. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Examples include Propionbacterium shermanni MCM during propionic acid fermentation, E.coli MCM in a pathway for the conversion of succinate to propionate and Streptomyces MCM in polyketide biosynthesis. P. shermanni and Streptomyces cinnamonensis MCMs are alpha/beta heterodimers, with both subunits being homologous members of this family. It has been shown for P. shermanni MCM that only the alpha subunit binds coenzyme B12 and substrates. Human MCM is a homodimer with two active sites. Mouse and E.coli MCMs are also homodimers. ICM from S. cinnamonensis is comprised of a large and a small subunit. The holoenzyme appears to be an alpha2beta2 heterotetramer with up to 2 molecules of coenzyme B12 bound. The small subunit binds coenzyme B12. ICM catalyzes the reversible rearrangement of n-butyryl-CoA to isobutyryl-CoA (intermediates in fatty acid and valine catabolism, which in S. cinnamonensis can be converted to methylmalonyl-CoA and used in polyketide synthesis). In humans, impaired activity of MCM results in methylmalonic aciduria, a disorder of propionic acid metabolism."
Q#25898 - 	CGI_10009501	superfamily	241759	603	724	1.33E-53	181.251	cl00293	B12-binding_like superfamily	 - 	 - 	"B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif."
Q#25900 - 	CGI_10002367	superfamily	247724	19	179	1.98E-95	278.666	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25902 - 	CGI_10004759	superfamily	243100	5	27	0.000809067	32.9212	cl02576	B_zip1 superfamily	NC	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#25903 - 	CGI_10004760	superfamily	243058	574	686	1.43E-15	76.9695	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#25903 - 	CGI_10004760	superfamily	243058	834	946	1.43E-15	76.9695	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#25903 - 	CGI_10004760	superfamily	243058	461	594	3.39E-10	60.7911	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#25903 - 	CGI_10004760	superfamily	243058	651	727	2.03E-07	52.3167	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#25903 - 	CGI_10004760	superfamily	243058	911	987	2.03E-07	52.3167	cl02500	ARM superfamily	C	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#25903 - 	CGI_10004760	superfamily	243058	310	416	7.26E-06	47.6943	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#25903 - 	CGI_10004760	superfamily	151853	97	165	7.51E-07	50.0858	cl12943	Suppressor_APC superfamily	 - 	 - 	"Adenomatous polyposis coli tumour suppressor protein; The tumour suppressor protein, APC, has a nuclear export activity as well as many different intracellular functions. The structure consists of three alpha-helices forming two separate antiparallel coiled coils."
Q#25903 - 	CGI_10004760	superfamily	147850	2151	2176	0.000667382	40.4728	cl05471	APC_crr superfamily	 - 	 - 	APC cysteine-rich region; This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). In the human protein many cancer-linked SNPs are found near the first three occurrences of the motif. These repeats bind beta-catenin.
Q#25904 - 	CGI_10004761	superfamily	243146	260	306	3.23E-10	54.975	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25904 - 	CGI_10004761	superfamily	243146	226	271	8.32E-07	45.6271	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#25905 - 	CGI_10004762	superfamily	242179	23	100	2.81E-46	145.583	cl00897	Ribosomal_S27e superfamily	 - 	 - 	Ribosomal protein S27; Ribosomal protein S27.  
Q#25906 - 	CGI_10004763	superfamily	147555	1	243	6.31E-65	207.005	cl05148	CRF-BP superfamily	 - 	 - 	"Corticotropin-releasing factor binding protein (CRF-BP); This family consists of several eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development."
Q#25907 - 	CGI_10004764	superfamily	245008	1617	1681	1.71E-12	65.2872	cl09101	E_set superfamily	 - 	 - 	"Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; The E or "early" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase."
Q#25907 - 	CGI_10004764	superfamily	207794	328	757	1.47E-153	479.866	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#25907 - 	CGI_10004764	superfamily	207794	1189	1598	5.92E-153	478.325	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#25907 - 	CGI_10004764	superfamily	243574	35	190	2.03E-24	102.793	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#25907 - 	CGI_10004764	superfamily	243574	903	1051	3.74E-21	93.1631	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#25907 - 	CGI_10004764	superfamily	111707	1130	1191	0.000395492	40.8612	cl03741	Glyco_hydro_20b superfamily	N	 - 	"Glycosyl hydrolase family 20, domain 2; This domain has a zincin-like fold."
Q#25908 - 	CGI_10008695	superfamily	241994	4	113	9.48E-49	169.239	cl00632	ATP-synt_F superfamily	 - 	 - 	"ATP synthase (F/14-kDa) subunit; This family includes 14-kDa subunit from vATPases, which is in the peripheral catalytic part of the complex. The family also includes archaebacterial ATP synthase subunit F."
Q#25908 - 	CGI_10008695	superfamily	246680	256	340	0.0012204	38.3368	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#25909 - 	CGI_10008696	superfamily	241645	229	296	0.0015872	36.091	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#25910 - 	CGI_10008697	superfamily	243084	2196	2292	4.28E-51	177.952	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#25910 - 	CGI_10008697	superfamily	241617	661	733	5.85E-20	87.4601	cl00110	MBD superfamily	 - 	 - 	"MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin.  MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family."
Q#25910 - 	CGI_10008697	superfamily	247999	2034	2081	2.64E-13	67.9008	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#25910 - 	CGI_10008697	superfamily	247999	2088	2131	8.89E-10	57.5004	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#25910 - 	CGI_10008697	superfamily	243137	1004	1029	0.00596248	37.1827	cl02674	DDT superfamily	C	 - 	"DDT domain; This domain is approximately 60 residues in length, and is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is exclusively associated with nuclear domains, and is thought to be arranged into three alpha helices."
Q#25913 - 	CGI_10008700	superfamily	243100	491	555	2.97E-10	56.8035	cl02576	B_zip1 superfamily	 - 	 - 	"basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins; Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region."
Q#25913 - 	CGI_10008700	superfamily	197676	90	114	0.0022606	36.2897	cl18194	ZnF_C2H2 superfamily	 - 	 - 	zinc finger; zinc finger.  
Q#25916 - 	CGI_10008703	superfamily	247068	841	938	6.70E-19	84.6725	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	458	549	4.23E-17	79.2797	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	1064	1159	1.75E-15	74.6573	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	263	352	2.03E-13	68.8793	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	1167	1267	3.70E-13	68.1089	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	1275	1381	1.27E-09	57.3234	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	361	450	1.62E-08	54.2418	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	551	610	2.00E-08	53.8566	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	635	712	3.94E-07	50.0046	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	1406	1446	5.96E-07	49.6194	cl15786	CA_like superfamily	C	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	946	1053	4.01E-06	46.923	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	795	830	0.000532012	40.3746	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25916 - 	CGI_10008703	superfamily	247068	121	166	0.00497101	37.3291	cl15786	CA_like superfamily	N	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#25917 - 	CGI_10008704	superfamily	242323	406	515	3.17E-19	83.7119	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#25918 - 	CGI_10008705	superfamily	244824	90	531	1.06E-135	408.157	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#25919 - 	CGI_10008706	superfamily	241563	101	137	3.47E-06	44.7776	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25920 - 	CGI_10008707	superfamily	241782	36	459	0	628.078	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#25921 - 	CGI_10008708	superfamily	241648	8	35	0.000152378	38.5531	cl00158	ZnF_GATA superfamily	C	 - 	Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Q#25922 - 	CGI_10008709	superfamily	221997	11	102	3.94E-05	37.8018	cl18631	Complex1_LYR_2 superfamily	 - 	 - 	"Complex1_LYR-like; This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria."
Q#25923 - 	CGI_10008710	superfamily	217940	9	74	4.52E-09	50.3709	cl18433	TAP42 superfamily	C	 - 	TAP42-like family; The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 (pfam04176) interacts with TAP42 and negatively regulates the TOR signaling pathway.
Q#25924 - 	CGI_10007951	superfamily	243061	38	94	1.87E-05	39.3723	cl02509	SRCR superfamily	NC	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25925 - 	CGI_10007952	superfamily	221913	683	864	2.46E-40	150.383	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#25925 - 	CGI_10007952	superfamily	247743	241	281	0.00487696	38.2811	cl17189	AAA superfamily	C	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#25926 - 	CGI_10007953	superfamily	243061	2627	2727	4.51E-37	138.244	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1852	1953	1.87E-21	93.1754	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1532	1629	2.76E-21	92.7902	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	2185	2289	1.03E-20	90.8642	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	907	1008	1.49E-20	90.479	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1633	1733	1.33E-19	87.7826	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	2419	2507	2.06E-19	87.3974	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1749	1843	9.25E-19	85.4714	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	580	678	1.38E-18	84.701	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	2074	2171	8.49E-18	82.3898	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1207	1309	1.81E-16	78.5378	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	233	299	1.18E-15	76.2266	cl02509	SRCR superfamily	C	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	819	900	1.77E-15	75.8414	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1433	1521	7.65E-15	73.9154	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	116	206	9.99E-14	70.4486	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	425	526	4.61E-13	68.5226	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	335	422	1.63E-12	66.9818	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	696	791	2.52E-12	66.3362	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1	61	2.77E-12	66.2114	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1956	2055	5.00E-12	65.441	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	2304	2395	5.44E-12	65.441	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1312	1412	6.03E-12	65.441	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	2516	2618	1.99E-11	63.9002	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1105	1197	3.99E-07	50.8034	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25926 - 	CGI_10007953	superfamily	243061	1017	1099	8.26E-06	46.9514	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#25927 - 	CGI_10007954	superfamily	243040	277	375	7.84E-19	82.9398	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#25927 - 	CGI_10007954	superfamily	245814	192	265	8.80E-07	47.0987	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25927 - 	CGI_10007954	superfamily	245814	100	160	1.59E-06	46.3283	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25927 - 	CGI_10007954	superfamily	245814	512	580	1.17E-08	52.8929	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25927 - 	CGI_10007954	superfamily	245814	407	490	1.11E-07	49.8113	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25927 - 	CGI_10007954	superfamily	245814	41	65	0.00500649	35.4357	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#25928 - 	CGI_10007955	superfamily	241758	5	147	8.63E-20	80.4918	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#25929 - 	CGI_10007956	superfamily	241758	150	248	1.02E-15	70.8618	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#25929 - 	CGI_10007956	superfamily	241758	48	117	2.71E-08	50.061	cl00292	AANH_like superfamily	N	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#25932 - 	CGI_10007959	superfamily	241659	10	87	1.06E-26	101.579	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#25932 - 	CGI_10007959	superfamily	243034	272	377	3.03E-16	73.5683	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#25933 - 	CGI_10007960	superfamily	247684	1	427	1.44E-106	328.468	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25934 - 	CGI_10007961	superfamily	241563	44	81	5.99E-08	49.7852	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#25936 - 	CGI_10027339	superfamily	248264	163	202	0.000566725	37.987	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#25938 - 	CGI_10027341	superfamily	244843	81	613	1.44E-122	376.571	cl08040	Ggt superfamily	 - 	 - 	Gamma-glutamyltransferase [Amino acid transport and metabolism]
Q#25939 - 	CGI_10027342	superfamily	243066	28	121	1.50E-35	128.44	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#25939 - 	CGI_10027342	superfamily	219619	375	427	2.19E-07	48.7432	cl18518	Ion_trans_2 superfamily	N	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#25940 - 	CGI_10027343	superfamily	245225	93	418	3.21E-16	79.4749	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#25940 - 	CGI_10027343	superfamily	247986	445	551	5.38E-08	53.1458	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#25940 - 	CGI_10027343	superfamily	197504	658	788	5.11E-21	90.8116	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#25941 - 	CGI_10027344	superfamily	247986	334	411	2.46E-07	50.8346	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#25941 - 	CGI_10027344	superfamily	197504	540	677	3.17E-31	119.316	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#25943 - 	CGI_10027346	superfamily	204985	4	95	1.65E-28	114.576	cl14987	Chorein_N superfamily	C	 - 	"N-terminal region of Chorein, a TM vesicle-mediated sorter; Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport."
Q#25943 - 	CGI_10027346	superfamily	219122	2504	2585	4.63E-09	59.2303	cl05933	DUF1162 superfamily	NC	 - 	Protein of unknown function (DUF1162); This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins.
Q#25944 - 	CGI_10027347	superfamily	243092	9	320	3.31E-69	234.922	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#25944 - 	CGI_10027347	superfamily	219240	816	1229	0	552.935	cl18502	COPI_C superfamily	 - 	 - 	Coatomer (COPI) alpha subunit C-terminus; This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport. Note that many family members also contain the pfam04053 domain.
Q#25945 - 	CGI_10027348	superfamily	241762	200	253	8.68E-23	89.9693	cl00297	R3H superfamily	 - 	 - 	"R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner."
Q#25947 - 	CGI_10027350	superfamily	245201	271	566	6.59E-70	231.654	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#25949 - 	CGI_10027352	superfamily	215821	55	152	1.00E-25	96.5406	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#25952 - 	CGI_10027355	superfamily	247856	125	182	4.11E-12	62.9505	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#25955 - 	CGI_10027358	superfamily	243660	57	113	0.0012898	37.2841	cl04176	TDT superfamily	N	 - 	"The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump (SSU1) of Saccharomyces cerevisiae. In plants, the plasma membrane protein SLAC1 (Slow Anion Channel-Associated 1), which is preferentially expressed in guard cells, encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. SLAC1 is essential  in mediating stomatal responses to physiological and stress stimuli. Members of the TDT family exhibit 10 putative transmembrane alpha-helical spanners (TMSs)."
Q#25957 - 	CGI_10027360	superfamily	244539	51	304	1.23E-116	338.387	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#25959 - 	CGI_10027362	superfamily	241659	38	119	0.00283733	33.3907	cl00175	alpha-crystallin-Hsps_p23-like superfamily	N	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#25960 - 	CGI_10027363	superfamily	241782	63	319	4.40E-25	103.7	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#25961 - 	CGI_10027364	superfamily	241782	6	139	3.76E-12	63.6389	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#25962 - 	CGI_10027365	superfamily	241782	70	279	6.70E-13	67.8761	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#25964 - 	CGI_10027367	superfamily	247057	506	551	6.12E-05	41.1336	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#25965 - 	CGI_10027368	superfamily	221744	92	176	0.00228637	36.2599	cl18614	CABIT superfamily	N	 - 	"Cell-cycle sustaining, positive selection,; The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2."
Q#25966 - 	CGI_10027369	superfamily	217160	44	346	6.03E-66	220.168	cl18393	DUF187 superfamily	 - 	 - 	"Uncharacterized BCR, COG1649; Uncharacterized BCR, COG1649.  "
Q#25972 - 	CGI_10027375	superfamily	217915	1144	1380	4.03E-43	166.528	cl14957	Spc97_Spc98 superfamily	N	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#25972 - 	CGI_10027375	superfamily	217915	299	594	3.03E-38	151.505	cl14957	Spc97_Spc98 superfamily	C	 - 	Spc97 / Spc98 family; The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2.
Q#25972 - 	CGI_10027375	superfamily	247746	585	627	0.00490008	37.8332	cl17192	ATP-synt_B superfamily	NC	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#25975 - 	CGI_10027378	superfamily	241578	7	146	1.29E-14	67.7018	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#25976 - 	CGI_10027379	superfamily	241626	66	126	1.45E-06	43.057	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#25977 - 	CGI_10027380	superfamily	241832	4	121	2.93E-48	152.5	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#25978 - 	CGI_10027381	superfamily	220692	1	275	1.08E-11	63.3773	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#25980 - 	CGI_10027383	superfamily	247804	603	645	4.06E-07	48.3406	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#25980 - 	CGI_10027383	superfamily	203011	429	513	2.46E-38	138.879	cl04515	SWIRM superfamily	 - 	 - 	SWIRM domain; This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
Q#25981 - 	CGI_10027384	superfamily	242876	13	152	8.03E-33	115.914	cl02092	Clat_adaptor_s superfamily	 - 	 - 	Clathrin adaptor complex small chain; Clathrin adaptor complex small chain.  
Q#25982 - 	CGI_10027385	superfamily	241599	48	104	2.57E-16	68.424	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25985 - 	CGI_10027388	superfamily	241599	175	231	5.37E-21	83.832	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#25986 - 	CGI_10027390	superfamily	241750	120	178	3.15E-15	69.9804	cl00281	metallo-dependent_hydrolases superfamily	NC	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#25986 - 	CGI_10027390	superfamily	241750	63	108	1.16E-09	54.5261	cl00281	metallo-dependent_hydrolases superfamily	NC	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#25987 - 	CGI_10027391	superfamily	247724	16	172	4.86E-17	76.4948	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25989 - 	CGI_10027393	superfamily	247755	11	92	5.62E-27	101.568	cl17201	ABC_ATPase superfamily	C	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#25990 - 	CGI_10027394	superfamily	247743	351	493	0.000585778	40.2071	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#25991 - 	CGI_10027395	superfamily	247684	37	389	0	703.685	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#25992 - 	CGI_10027396	superfamily	247724	20	179	3.25E-68	209.055	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#25993 - 	CGI_10027397	superfamily	243033	8	84	1.08E-06	42.6906	cl02428	Ependymin superfamily	N	 - 	Ependymin; Ependymin.  
Q#25995 - 	CGI_10027399	superfamily	177822	249	472	1.42E-15	76.4973	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#25996 - 	CGI_10027400	superfamily	177822	389	612	1.20E-15	77.2677	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#25996 - 	CGI_10027400	superfamily	177822	62	285	4.21E-15	75.7269	cl18088	PLN02164 superfamily	N	 - 	sulfotransferase
Q#25997 - 	CGI_10027401	superfamily	243074	215	251	1.91E-05	41.3381	cl02535	F-box-like superfamily	C	 - 	F-box-like; This is an F-box-like family.
Q#25998 - 	CGI_10027402	superfamily	218900	2	251	5.90E-99	291.879	cl05572	Aph-1 superfamily	 - 	 - 	"Aph-1 protein; This family consists of several eukaryotic Aph-1 proteins.Gamma-secretase catalyzes the intramembrane proteolysis of Notch, beta-amyloid precursor protein, and other substrates as part of a new signaling paradigm and as a key step in the pathogenesis of Alzheimer's disease. It is thought that the presenilin heterodimer comprises the catalytic site and that a highly glycosylated form of nicastrin associates with it. Aph-1 and Pen-2, two membrane proteins genetically linked to gamma-secretase, associate directly with presenilin and nicastrin in the active protease complex. Co-expression of all four proteins leads to marked increases in presenilin heterodimers, full glycosylation of nicastrin, and enhanced gamma-secretase activity."
Q#25999 - 	CGI_10027403	superfamily	245202	27	98	5.32E-32	114.5	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#26001 - 	CGI_10027405	superfamily	243169	169	256	1.47E-40	145.366	cl02766	NGN superfamily	 - 	 - 	"N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization Substance G (NusG) and its eukaryotic homolog Spt5 are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms a Spt4-Spt5 complex that is an essential RNA Polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria."
Q#26001 - 	CGI_10027405	superfamily	241810	463	513	6.88E-26	102.604	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#26001 - 	CGI_10027405	superfamily	241810	695	746	2.72E-24	97.9405	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#26001 - 	CGI_10027405	superfamily	241810	414	462	9.61E-22	90.639	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#26001 - 	CGI_10027405	superfamily	241810	989	1043	9.65E-22	91.0386	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#26001 - 	CGI_10027405	superfamily	241810	589	631	4.77E-19	82.9529	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#26001 - 	CGI_10027405	superfamily	241810	268	304	1.55E-15	72.5014	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#26001 - 	CGI_10027405	superfamily	248304	767	860	3.15E-16	76.7257	cl17750	CTD superfamily	 - 	 - 	"Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif."
Q#26001 - 	CGI_10027405	superfamily	221333	104	163	0.000372099	40.1181	cl13391	Spt5_N superfamily	N	 - 	"Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4."
Q#26003 - 	CGI_10027407	superfamily	245201	89	338	1.70E-56	188.861	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26006 - 	CGI_10027410	superfamily	202085	54	94	6.87E-09	52.7478	cl03401	zf-CXXC superfamily	 - 	 - 	"CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR."
Q#26007 - 	CGI_10027411	superfamily	219165	125	313	2.96E-66	223.331	cl06019	LMF1 superfamily	C	 - 	"Lipase maturation factor; This family of transmembrane proteins includes the lipase maturation factor, LMF1. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states. The precise role of LMF1 in lipase folding has yet to be determined."
Q#26007 - 	CGI_10027411	superfamily	219165	353	580	3.12E-59	204.457	cl06019	LMF1 superfamily	N	 - 	"Lipase maturation factor; This family of transmembrane proteins includes the lipase maturation factor, LMF1. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states. The precise role of LMF1 in lipase folding has yet to be determined."
Q#26008 - 	CGI_10027412	superfamily	247724	613	711	1.77E-07	51.1828	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26008 - 	CGI_10027412	superfamily	246925	333	438	0.00597282	38.8758	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#26009 - 	CGI_10027413	superfamily	218970	52	560	1.43E-78	259.882	cl09405	DUF1032 superfamily	 - 	 - 	Protein of unknown function (DUF1032); This family consists of several conserved eukaryotic proteins of unknown function.
Q#26010 - 	CGI_10027414	superfamily	248012	187	320	7.93E-21	86.2232	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#26011 - 	CGI_10027415	superfamily	248012	113	238	1.70E-17	75.8228	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#26012 - 	CGI_10027416	superfamily	247057	698	769	2.84E-39	141.055	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#26012 - 	CGI_10027416	superfamily	247057	610	672	5.33E-35	128.581	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#26012 - 	CGI_10027416	superfamily	247057	536	598	5.73E-31	117.329	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#26014 - 	CGI_10027418	superfamily	241763	8	209	4.03E-83	248.308	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#26018 - 	CGI_10027423	superfamily	243066	24	122	5.97E-11	59.9385	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#26020 - 	CGI_10003966	superfamily	243051	449	603	9.79E-34	125.953	cl02479	MAM superfamily	 - 	 - 	"Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region."
Q#26020 - 	CGI_10003966	superfamily	245213	179	211	6.89E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26021 - 	CGI_10003967	superfamily	246976	1	371	4.50E-68	229.22	cl15483	Dymeclin superfamily	C	 - 	"Dyggve-Melchior-Clausen syndrome protein; Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 residues long and present in plants and animals. Mutations in the gene coding for this protein in humans give rise to the disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM 223800) which is an autosomal-recessive disorder characterized by the association of a spondylo-epi-metaphyseal dysplasia and mental retardation. DYM transcripts are widely expressed throughout human development and Dymeclin is not an integral membrane protein of the ER, but rather a peripheral membrane protein dynamically associated with the Golgi apparatus."
Q#26022 - 	CGI_10003968	superfamily	246976	33	265	2.84E-72	236.154	cl15483	Dymeclin superfamily	N	 - 	"Dyggve-Melchior-Clausen syndrome protein; Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 residues long and present in plants and animals. Mutations in the gene coding for this protein in humans give rise to the disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM 223800) which is an autosomal-recessive disorder characterized by the association of a spondylo-epi-metaphyseal dysplasia and mental retardation. DYM transcripts are widely expressed throughout human development and Dymeclin is not an integral membrane protein of the ER, but rather a peripheral membrane protein dynamically associated with the Golgi apparatus."
Q#26023 - 	CGI_10003969	superfamily	247097	5	39	0.00769078	31.2674	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#26024 - 	CGI_10003970	superfamily	219653	105	366	7.40E-124	360.868	cl06813	N2227 superfamily	 - 	 - 	N2227-like protein; This family features sequences that are similar to a region of hypothetical yeast gene product N2227. This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions.
Q#26025 - 	CGI_10003971	superfamily	241574	34	123	1.55E-06	47.1953	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#26025 - 	CGI_10003971	superfamily	241574	240	308	4.45E-05	42.9582	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#26027 - 	CGI_10003973	superfamily	110440	128	154	0.000697326	35.0761	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26029 - 	CGI_10006607	superfamily	215724	7	321	2.31E-170	478.652	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#26031 - 	CGI_10006609	superfamily	247986	44	269	6.11E-13	65.4722	cl17432	PBPb superfamily	 - 	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#26033 - 	CGI_10006611	superfamily	149105	191	272	0.00798519	36.6441	cl12353	TMPIT superfamily	C	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#26035 - 	CGI_10003936	superfamily	247856	608	666	7.20E-06	44.8461	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#26036 - 	CGI_10003937	superfamily	247724	15	175	1.16E-57	180.85	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26037 - 	CGI_10003938	superfamily	247724	1	107	5.95E-31	109.974	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26038 - 	CGI_10003939	superfamily	247724	15	176	7.04E-66	202.421	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26039 - 	CGI_10003940	superfamily	247724	7	76	1.34E-24	91.0988	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26040 - 	CGI_10003941	superfamily	241874	21	566	0	689.603	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#26041 - 	CGI_10003942	superfamily	148169	60	263	5.88E-30	112.515	cl05744	Alpha-2-MRAP_C superfamily	 - 	 - 	"Alpha-2-macroglobulin RAP, C-terminal domain; The alpha-2-macroglobulin receptor-associated protein (RAP) is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of all currently known ligands of these receptors. Two different studies have provided conflicted domain boundaries."
Q#26042 - 	CGI_10003943	superfamily	246680	6	88	1.65E-22	86.5303	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#26044 - 	CGI_10000002	superfamily	247684	18	110	6.39E-54	174.503	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#26045 - 	CGI_10000003	superfamily	241600	1	74	4.47E-20	79.9771	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26051 - 	CGI_10000012	superfamily	245839	12	130	9.13E-53	167.782	cl12020	Anticodon_Ia_like superfamily	 - 	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#26051 - 	CGI_10000012	superfamily	245839	106	156	1.54E-05	42.5385	cl12020	Anticodon_Ia_like superfamily	N	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#26052 - 	CGI_10000013	superfamily	243184	52	145	4.29E-31	109.741	cl02786	Translation_factor_III superfamily	 - 	 - 	"Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the same fold (although they are not completely superimposable), the double split beta-alpha-beta fold. This fold is observed in a large number of ribonucleotide binding proteins and is also referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.  This domain III is found in several elongation factors, as well as in peptide chain release factors and in GT-1 family of GTPase (GTPBP1)."
Q#26052 - 	CGI_10000013	superfamily	243185	3	47	4.95E-15	66.7623	cl02787	Translation_Factor_II_like superfamily	N	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#26053 - 	CGI_10000015	superfamily	149349	2	90	1.23E-17	71.8922	cl07026	SRI superfamily	 - 	 - 	"SRI (Set2 Rpb1 interacting) domain; The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation."
Q#26054 - 	CGI_10000016	superfamily	243035	1	77	9.64E-15	64.1781	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26055 - 	CGI_10000017	superfamily	242113	1	117	2.22E-26	99.7086	cl00814	Cyclase superfamily	N	 - 	Putative cyclase; Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.
Q#26058 - 	CGI_10000019	superfamily	222090	50	141	9.79E-08	48.423	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#26059 - 	CGI_10000021	superfamily	245864	50	105	1.57E-10	56.1326	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#26064 - 	CGI_10000029	superfamily	220672	5	63	3.37E-09	50.323	cl10957	Frag1 superfamily	C	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#26065 - 	CGI_10000030	superfamily	246722	1	83	2.61E-58	177.816	cl14812	PIN_SF superfamily	N	 - 	"PIN (PilT N terminus) domain: Superfamily; PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain.  The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+).  The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins.  Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly."
Q#26067 - 	CGI_10000032	superfamily	247724	11	158	2.00E-41	139.216	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26068 - 	CGI_10000033	superfamily	215779	1	61	1.03E-19	77.5511	cl02819	Ribosomal_S3_C superfamily	N	 - 	"Ribosomal protein S3, C-terminal domain; This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer."
Q#26070 - 	CGI_10000035	superfamily	241599	177	227	1.42E-10	55.7125	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#26073 - 	CGI_10000038	superfamily	241782	1	147	1.09E-52	175.647	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#26075 - 	CGI_10000041	superfamily	241552	3	47	8.73E-11	52.3756	cl00017	Cyt_c_Oxidase_VIa superfamily	N	 - 	"Cytochrome c oxidase subunit VIa.   Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes.  It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome.  Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform.  Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip in CcO, depending on the presence of cardiolipin and palmitate."
Q#26076 - 	CGI_10000040	superfamily	245864	3	35	3.65E-10	53.8214	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#26078 - 	CGI_10000044	superfamily	110440	85	111	0.00619405	32.3797	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26080 - 	CGI_10000045	superfamily	241832	15	103	2.48E-32	109.937	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26082 - 	CGI_10000047	superfamily	192703	1	133	1.41E-60	185.552	cl12637	YbhQ superfamily	 - 	 - 	Putative inner membrane protein YbhQ; This family is conserved in Proteobacteria. The function is not known but most members are annotated as being inner membrane protein YbhQ.
Q#26083 - 	CGI_10000049	superfamily	242042	1	67	2.24E-41	131.032	cl00712	RNA_pol_N superfamily	 - 	 - 	RNA polymerases N / 8 kDa subunit; RNA polymerases N / 8 kDa subunit.  
Q#26085 - 	CGI_10000050	superfamily	221911	1	45	7.46E-12	58.3539	cl18625	Fer2_3 superfamily	N	 - 	2Fe-2S iron-sulfur cluster binding domain; The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.
Q#26086 - 	CGI_10000052	superfamily	241874	1	212	2.06E-46	161.848	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#26090 - 	CGI_10000055	superfamily	241592	1	136	1.63E-82	240.962	cl00074	H2A superfamily	 - 	 - 	"Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins."
Q#26091 - 	CGI_10000056	superfamily	243058	4	89	0.00922513	31.516	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#26092 - 	CGI_10000057	superfamily	222090	51	238	2.75E-17	77.313	cl18636	Methyltransf_22 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#26093 - 	CGI_10000058	superfamily	203444	19	59	2.46E-15	66.5527	cl05761	PRP1_N superfamily	C	 - 	"PRP1 splicing factor, N-terminal; This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1. It is involved in mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression."
Q#26097 - 	CGI_10000062	superfamily	243064	19	62	1.53E-05	38.1087	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#26098 - 	CGI_10000063	superfamily	241594	1	158	1.22E-69	216.277	cl00077	HECTc superfamily	N	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#26099 - 	CGI_10000064	superfamily	243141	1	35	4.35E-06	39.9922	cl02687	RWD superfamily	C	 - 	"RWD domain; This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices."
Q#26100 - 	CGI_10000067	superfamily	247044	1	94	9.34E-33	112.344	cl15697	ADF_gelsolin superfamily	 - 	 - 	Actin depolymerization factor/cofilin- and gelsolin-like domains; Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Q#26101 - 	CGI_10000069	superfamily	248289	39	96	0.00122727	34.3219	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#26102 - 	CGI_10000070	superfamily	248469	47	153	1.45E-13	63.9283	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#26104 - 	CGI_10000071	superfamily	245010	2	88	1.80E-15	66.6417	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#26106 - 	CGI_10000073	superfamily	245206	4	274	1.29E-103	303.775	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#26107 - 	CGI_10000074	superfamily	245013	13	63	0.00886898	31.8469	cl09115	Ribosomal_L32p superfamily	C	 - 	Ribosomal L32p protein family; Ribosomal L32p protein family.  
Q#26108 - 	CGI_10000075	superfamily	194545	1	89	2.08E-62	186.166	cl03131	Dynein_light superfamily	 - 	 - 	Dynein light chain type 1; Dynein light chain type 1.  
Q#26111 - 	CGI_10000078	superfamily	247741	1	131	1.02E-69	215.196	cl17187	Aldolase_Class_I superfamily	N	 - 	"Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin."
Q#26112 - 	CGI_10000080	superfamily	242849	3	76	4.29E-27	96.1188	cl02041	Cyt-b5 superfamily	 - 	 - 	Cytochrome b5-like Heme/Steroid binding domain; This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
Q#26115 - 	CGI_10000082	superfamily	198827	1	89	6.91E-56	169.532	cl03803	BAF superfamily	 - 	 - 	Barrier to autointegration factor; The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.
Q#26116 - 	CGI_10000077	superfamily	241788	16	106	1.67E-14	64.4342	cl00327	Ribosomal_L22 superfamily	C	 - 	"Ribosomal protein L22/L17e.  L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit.  It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA.  L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes.  L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome."
Q#26117 - 	CGI_10000083	superfamily	243146	68	115	1.52E-08	46.7827	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#26118 - 	CGI_10000084	superfamily	191369	1	109	5.72E-27	99.8741	cl05372	DUF837 superfamily	C	 - 	Protein of unknown function (DUF837); This family consists of several eukaryotic proteins of unknown function. One of the family members is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke).
Q#26119 - 	CGI_10000085	superfamily	202823	1	47	3.71E-15	65.2529	cl08408	Ribosomal_L2_C superfamily	N	 - 	"Ribosomal Proteins L2, C-terminal domain; Ribosomal Proteins L2, C-terminal domain.  "
Q#26120 - 	CGI_10000086	superfamily	247866	37	125	6.83E-09	50.5288	cl17312	PhyH superfamily	C	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#26122 - 	CGI_10000088	superfamily	241600	54	187	7.42E-55	175.507	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26125 - 	CGI_10000093	superfamily	241888	86	216	5.46E-40	139.053	cl00473	BI-1-like superfamily	C	 - 	"BAX inhibitor (BI)-1/YccA-like protein family; Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes."
Q#26129 - 	CGI_10000098	superfamily	247057	40	128	7.87E-44	140.951	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#26130 - 	CGI_10000100	superfamily	247755	1	53	1.51E-24	91.8883	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26135 - 	CGI_10000110	superfamily	245864	3	179	3.30E-10	56.903	cl12078	p450 superfamily	C	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#26137 - 	CGI_10000112	superfamily	243778	45	68	0.00010507	37.2035	cl04503	HA2 superfamily	C	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#26141 - 	CGI_10000113	superfamily	219316	1	154	3.80E-62	192.436	cl06268	B9-C2 superfamily	 - 	 - 	"Ciliary basal body-associated, B9 protein; The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains. There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease. All the three distinct types of B9-C2 proteins cooperatively localise to the basal body or centrosome of cilia."
Q#26142 - 	CGI_10000115	superfamily	241879	93	339	1.37E-24	99.9388	cl00462	TM_ABC_iron-siderophores_like superfamily	 - 	 - 	"Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The TMs are bundles of alpha helices that transverse the cytoplasmic membrane multiple times. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Each TM has a prominent cytoplasmic loop which contacts an ABC and represents a conserved motif. The two TMs form either a homodimer (e.g. in the case of the BtuC subunits of the Escherichia coli BtuCD vitamin B12 transporter), a heterodimer (e.g. the TroC and TroD subunits of the Treponema pallidum general transition metal transporter, TroBCD), or a pseudo-heterodimer (e.g. the FhuB protein of the E. coli ferrichrome transporter, FhuBC). FhuB contains two tandem TMs which associate to form the pseudo-heterodimer. Both FhuB TMs are found in this hierarchy."
Q#26148 - 	CGI_10000124	superfamily	243175	53	172	1.14E-59	183.989	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#26148 - 	CGI_10000124	superfamily	241832	2	45	1.43E-20	81.6636	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26150 - 	CGI_10000126	superfamily	241584	49	107	4.25E-08	46.3355	cl00065	FN3 superfamily	C	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#26152 - 	CGI_10000129	superfamily	247905	1	63	2.03E-17	72.6556	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#26153 - 	CGI_10000130	superfamily	238211	28	142	2.74E-42	141.645	cl18908	TS_Pyrimidine_HMase superfamily	C	 - 	"Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the biosynthesis of DNA precursors and are active as homodimers. However, they exhibit distinct pyrimidine base specificities and differ in the details of their catalyzed reactions. TS is biologically ubiquitous and catalyzes the conversion of dUMP and methylene-tetrahydrofolate (CH2THF) to dTMP and dihydrofolate (DHF). It also acts as a regulator of its own expression by binding and inactivating its own RNA. Due to its key role in the de novo pathway for thymidylate synthesis and, hence, DNA synthesis, it is one of the most conserved enzymes across species and phyla. TS is a well-recognized target for anticancer chemotherapy, as well as a valuable new target against infectious diseases. Interestingly, in several protozoa, a single polypeptide chain codes for both, dihydrofolate reductase (DHFR) and thymidylate synthase (TS), forming a bifunctional enzyme (DHFR-TS), possibly through gene fusion at a single evolutionary point. DHFR-TS is also active as a dimer. Virus encoded dCMP-HMase catalyzes the reversible conversion of dCMP and CH2THF to hydroxymethyl-dCMP and THF. This family also includes dUMP hydroxymethylase, which is encoded by several bacteriophages that infect Bacillus subtilis, for their own protection against the host restriction system,  and contain hydroxymethyl-dUMP instead of dTMP in their DNA."
Q#26154 - 	CGI_10000131	superfamily	242559	30	371	0	535.743	cl01529	GH99_GH71_like superfamily	 - 	 - 	"Glycoside hydrolase families 71, 99, and related domains; This superfamily of glycoside hydrolases contains families GH71 and GH99 (following the CAZY nomenclature), as well as other members with undefined function and specificity."
Q#26159 - 	CGI_10000135	superfamily	247692	17	100	1.76E-28	107.247	cl17068	AFD_class_I superfamily	NC	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#26161 - 	CGI_10000136	superfamily	198738	1	46	1.02E-20	77.6934	cl02599	Ets superfamily	N	 - 	Ets-domain; Ets-domain.  
Q#26162 - 	CGI_10000138	superfamily	247725	1	45	8.46E-14	64.6495	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#26162 - 	CGI_10000138	superfamily	247725	113	201	3.76E-12	59.7978	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#26163 - 	CGI_10000137	superfamily	241572	16	91	3.75E-17	71.886	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#26165 - 	CGI_10000141	superfamily	218556	1	330	2.20E-33	132.427	cl05076	RRN3 superfamily	N	 - 	RNA polymerase I specific transcription initiation factor RRN3; This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae.
Q#26166 - 	CGI_10000144	superfamily	221913	49	255	4.92E-67	210.089	cl18626	AAA_12 superfamily	 - 	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Q#26166 - 	CGI_10000144	superfamily	222258	2	38	9.08E-06	44.096	cl18656	AAA_30 superfamily	NC	 - 	AAA domain; This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Q#26167 - 	CGI_10000140	superfamily	241619	33	100	0.000914271	34.4801	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#26168 - 	CGI_10000145	superfamily	197504	1	48	6.21E-17	72.7073	cl18192	PBPe superfamily	N	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#26170 - 	CGI_10000147	superfamily	242205	1	160	2.58E-60	186.356	cl00937	Ribosomal_L21e superfamily	 - 	 - 	Ribosomal protein L21e; Ribosomal protein L21e.  
Q#26173 - 	CGI_10000096	superfamily	147609	12	176	1.24E-17	75.4707	cl05205	p25-alpha superfamily	 - 	 - 	"p25-alpha; This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila."
Q#26176 - 	CGI_10000158	superfamily	247755	2	239	9.92E-96	283.239	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26177 - 	CGI_10000159	superfamily	241914	1	181	2.47E-70	215.742	cl00510	Permease superfamily	 - 	 - 	Permease; This domain functions as a permease. In a hypothetical protein from Neisseria it is involved in L-glutamate import into the cell. In Arabidopsis ABC transporter I family member 14 it is involved in lipid transfer within the cell.
Q#26178 - 	CGI_10000156	superfamily	242730	162	203	0.00535667	36.4703	cl01825	Phage_Mu_Gam superfamily	C	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#26182 - 	CGI_10000162	superfamily	241879	81	326	1.09E-35	131.14	cl00462	TM_ABC_iron-siderophores_like superfamily	 - 	 - 	"Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The TMs are bundles of alpha helices that transverse the cytoplasmic membrane multiple times. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Each TM has a prominent cytoplasmic loop which contacts an ABC and represents a conserved motif. The two TMs form either a homodimer (e.g. in the case of the BtuC subunits of the Escherichia coli BtuCD vitamin B12 transporter), a heterodimer (e.g. the TroC and TroD subunits of the Treponema pallidum general transition metal transporter, TroBCD), or a pseudo-heterodimer (e.g. the FhuB protein of the E. coli ferrichrome transporter, FhuBC). FhuB contains two tandem TMs which associate to form the pseudo-heterodimer. Both FhuB TMs are found in this hierarchy."
Q#26183 - 	CGI_10000163	superfamily	239148	13	161	7.37E-73	218.648	cl02780	MIT_C superfamily	 - 	 - 	"MIT_C; domain found C-terminal to MIT (contained within Microtubule Interacting and Trafficking molecules) domains, as well as in some bacterial proteins. The function of this domain is unknown."
Q#26186 - 	CGI_10000164	superfamily	216363	2	57	1.02E-09	49.7762	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#26189 - 	CGI_10023130	superfamily	245862	258	318	1.47E-06	46.8045	cl12076	THUMP superfamily	N	 - 	"THUMP domain, predicted to bind RNA; The THUMP domain is named after THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases. It is predicted to be an RNA-binding domain and  probably functions by delivering a variety of RNA modification enzymes to their targets."
Q#26189 - 	CGI_10023130	superfamily	245862	18	105	3.38E-06	45.6489	cl12076	THUMP superfamily	C	 - 	"THUMP domain, predicted to bind RNA; The THUMP domain is named after THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases. It is predicted to be an RNA-binding domain and  probably functions by delivering a variety of RNA modification enzymes to their targets."
Q#26189 - 	CGI_10023130	superfamily	247727	323	497	4.13E-37	135.117	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#26191 - 	CGI_10023132	superfamily	247098	60	190	3.98E-74	222.401	cl15841	COG0229 superfamily	 - 	 - 	"Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]"
Q#26192 - 	CGI_10023133	superfamily	247775	1	63	2.46E-07	46.5651	cl17221	ArsB_NhaD_permease superfamily	N	 - 	"Anion permease ArsB/NhaD.  These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life.  A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump."
Q#26193 - 	CGI_10023134	superfamily	207690	127	151	3.57E-05	39.9937	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#26194 - 	CGI_10023135	superfamily	241624	22	182	8.40E-49	177.904	cl00120	PP2Cc superfamily	C	 - 	"Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity."
Q#26195 - 	CGI_10023136	superfamily	241574	413	623	1.16E-89	286.019	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#26195 - 	CGI_10023136	superfamily	241574	674	853	1.89E-17	82.2485	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#26196 - 	CGI_10023137	superfamily	241750	2	182	2.44E-33	120.371	cl00281	metallo-dependent_hydrolases superfamily	N	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#26198 - 	CGI_10023139	superfamily	245864	154	259	3.66E-27	108.135	cl12078	p450 superfamily	NC	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#26200 - 	CGI_10023141	superfamily	243263	38	427	1.55E-55	192.238	cl02990	ASC superfamily	 - 	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#26201 - 	CGI_10023142	superfamily	243045	227	326	6.80E-16	74.5919	cl02459	PAS superfamily	 - 	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#26201 - 	CGI_10023142	superfamily	243045	86	156	1.41E-10	59.1839	cl02459	PAS superfamily	C	 - 	"PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction."
Q#26201 - 	CGI_10023142	superfamily	241596	8	52	4.61E-07	47.9791	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#26202 - 	CGI_10023143	superfamily	243161	3	60	2.42E-05	40.0702	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#26203 - 	CGI_10023144	superfamily	248097	104	134	7.19E-06	41.0966	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26205 - 	CGI_10023146	superfamily	241596	67	124	2.26E-11	57.2239	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#26206 - 	CGI_10023147	superfamily	241758	52	237	3.79E-84	256.791	cl00292	AANH_like superfamily	 - 	 - 	"Adenine nucleotide alpha hydrolases superfamily  including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which  binds to Adenosine nucleotide."
Q#26206 - 	CGI_10023147	superfamily	129370	201	302	7.13E-16	72.921	cl11741	TIGR00269 superfamily	 - 	 - 	"TIGR00269 family protein; [Hypothetical proteins, Conserved]."
Q#26207 - 	CGI_10023148	superfamily	241900	93	345	2.24E-150	426.968	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#26208 - 	CGI_10023149	superfamily	243072	137	263	7.49E-25	97.8394	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26208 - 	CGI_10023149	superfamily	243072	54	194	2.33E-12	63.1714	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26208 - 	CGI_10023149	superfamily	243073	335	379	3.08E-06	43.9981	cl02533	SOCS superfamily	 - 	 - 	"SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions."
Q#26209 - 	CGI_10023150	superfamily	247097	106	142	0.000406166	35.1194	cl15839	ShK superfamily	 - 	 - 	ShK domain-like; This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone.
Q#26211 - 	CGI_10023152	superfamily	243066	327	355	2.14E-05	42.1549	cl02518	BTB superfamily	C	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#26214 - 	CGI_10023156	superfamily	243039	1	153	2.99E-98	284.148	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#26216 - 	CGI_10023158	superfamily	243039	319	492	2.74E-100	302.252	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#26218 - 	CGI_10023160	superfamily	241754	34	704	0	1253.26	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#26218 - 	CGI_10023160	superfamily	247683	1070	1121	9.81E-31	116.745	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#26218 - 	CGI_10023160	superfamily	218855	731	936	1.88E-62	211.777	cl10652	Myosin_TH1 superfamily	 - 	 - 	Myosin tail; Myosin tail.  
Q#26219 - 	CGI_10023161	superfamily	241820	11	89	3.20E-16	69.9511	cl00368	Ribosomal_S16 superfamily	 - 	 - 	Ribosomal protein S16; Ribosomal protein S16.  
Q#26220 - 	CGI_10023162	superfamily	245847	127	184	5.39E-12	59.2881	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#26224 - 	CGI_10023166	superfamily	241733	54	135	1.13E-39	130.038	cl00259	Sm_like superfamily	 - 	 - 	"Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes."
Q#26226 - 	CGI_10023168	superfamily	217617	23	69	0.00317808	33.5437	cl15988	Sulfotransfer_2 superfamily	N	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#26233 - 	CGI_10000174	superfamily	242161	1	41	2.71E-18	72.4319	cl00875	PTZ00255 superfamily	NC	 - 	60S ribosomal protein L37a; Provisional
Q#26236 - 	CGI_10000180	superfamily	241783	1	42	3.71E-07	47.1788	cl00322	Ribosomal_L1 superfamily	N	 - 	"Ribosomal protein L1.  The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA.  In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA.  Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity.  L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site."
Q#26237 - 	CGI_10000175	superfamily	245205	19	96	6.78E-17	70.7297	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26243 - 	CGI_10005236	superfamily	241594	68	141	0.000142987	38.8256	cl00077	HECTc superfamily	N	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#26245 - 	CGI_10005238	superfamily	218735	4	243	3.49E-16	75.3219	cl15681	IER superfamily	 - 	 - 	"Immediate early response protein (IER); This family consists of several eukaryotic immediate early response (IER) 2 and 5 proteins. The role of IER5 is unclear although it play an important role in mediating the cellular response to mitogenic signals. Again, little is known about the function of IER2 although it is thought to play a role in mediating the cellular responses to a variety of extracellular signals."
Q#26246 - 	CGI_10005239	superfamily	245814	377	455	7.21E-06	44.7368	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#26246 - 	CGI_10005239	superfamily	245814	287	361	0.0021379	37.0997	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#26248 - 	CGI_10000190	superfamily	241563	18	50	0.00365979	35.3907	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26248 - 	CGI_10000190	superfamily	128778	66	161	0.00853797	35.3183	cl17972	BBC superfamily	C	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#26249 - 	CGI_10000191	superfamily	247740	4	79	9.07E-34	119.521	cl17186	TIM_phosphate_binding superfamily	N	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#26252 - 	CGI_10000194	superfamily	241786	3	171	5.12E-60	193.515	cl00325	Ribosomal_L4 superfamily	N	 - 	Ribosomal protein L4/L1 family; This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA.
Q#26252 - 	CGI_10000194	superfamily	222716	181	260	1.11E-26	100.372	cl16836	Ribos_L4_asso_C superfamily	 - 	 - 	60S ribosomal protein L4 C-terminal domain; This family is found at the very C-terminal of 60 ribosomal L4 proteins.
Q#26255 - 	CGI_10000195	superfamily	246597	1	72	6.51E-24	91.5662	cl13995	MPP_superfamily superfamily	NC	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#26258 - 	CGI_10000199	superfamily	247792	184	236	3.12E-16	70.4427	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#26258 - 	CGI_10000199	superfamily	214806	73	159	1.98E-14	66.1649	cl15966	CRA superfamily	 - 	 - 	"CT11-RanBPM; protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)"
Q#26258 - 	CGI_10000199	superfamily	128914	14	66	1.68E-09	52.1882	cl15352	CTLH superfamily	 - 	 - 	C-terminal to LisH motif; Alpha-helical motif of unknown function.
Q#26263 - 	CGI_10000206	superfamily	243035	76	116	7.36E-08	46.459	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26263 - 	CGI_10000206	superfamily	243061	17	60	6.56E-06	40.9131	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#26265 - 	CGI_10000210	superfamily	242031	5	183	3.47E-57	180.081	cl00689	TYW3 superfamily	 - 	 - 	Methyltransferase TYW3; The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis. yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3' position adjacent the anticodon of phenylalanine tRNA. TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner.
Q#26267 - 	CGI_10000212	superfamily	241600	7	187	2.61E-89	263.332	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26268 - 	CGI_10000213	superfamily	243072	30	118	2.22E-09	52.0006	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26268 - 	CGI_10000213	superfamily	149414	169	198	7.97E-05	38.4066	cl07091	TRP_2 superfamily	N	 - 	Transient receptor ion channel II; This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023).
Q#26269 - 	CGI_10000214	superfamily	245847	25	167	1.34E-18	77.9821	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#26273 - 	CGI_10000215	superfamily	243092	42	284	1.46E-13	69.286	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#26277 - 	CGI_10020228	superfamily	241571	383	502	6.23E-12	62.4298	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#26277 - 	CGI_10020228	superfamily	245213	345	375	0.00067863	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26277 - 	CGI_10020228	superfamily	241583	149	333	1.28E-46	161.585	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#26278 - 	CGI_10020229	superfamily	201778	3	114	3.32E-18	78.4046	cl18219	GFO_IDH_MocA superfamily	 - 	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#26279 - 	CGI_10020230	superfamily	242406	704	854	5.09E-57	192.421	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#26279 - 	CGI_10020230	superfamily	247742	196	488	3.34E-36	141.851	cl17188	enolase_like superfamily	N	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#26281 - 	CGI_10020232	superfamily	241578	255	411	2.41E-26	105.837	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26281 - 	CGI_10020232	superfamily	241578	27	194	2.19E-41	147.818	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26281 - 	CGI_10020232	superfamily	241578	452	623	4.65E-11	61.25	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26282 - 	CGI_10020233	superfamily	241578	115	277	4.59E-40	144.742	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26282 - 	CGI_10020233	superfamily	241578	306	457	5.91E-24	99.2882	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26282 - 	CGI_10020233	superfamily	241578	505	653	2.14E-09	56.0823	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26285 - 	CGI_10020236	superfamily	243054	527	706	8.93E-33	126.791	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26285 - 	CGI_10020236	superfamily	243054	316	523	2.30E-27	110.998	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26285 - 	CGI_10020236	superfamily	241559	67	171	4.84E-26	103.93	cl00030	CH superfamily	 - 	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#26285 - 	CGI_10020236	superfamily	243054	207	417	3.49E-14	71.7079	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26285 - 	CGI_10020236	superfamily	241559	1	48	5.81E-06	45.3843	cl00030	CH superfamily	N	 - 	"Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav)."
Q#26287 - 	CGI_10020238	superfamily	247725	2952	3053	2.54E-40	147.741	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#26287 - 	CGI_10020238	superfamily	243054	2346	2556	1.30E-37	143.74	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	1924	2133	1.28E-36	141.044	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	544	753	1.54E-33	132.184	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	1817	2027	8.91E-33	129.873	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	754	962	1.51E-32	129.103	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	1607	1816	2.49E-31	125.636	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	2136	2343	1.64E-30	123.325	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	228	436	5.94E-30	121.399	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	1284	1495	5.96E-30	121.399	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	437	646	7.89E-30	121.013	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	122	330	1.23E-28	117.547	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	1501	1710	1.29E-27	114.85	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	860	1066	3.90E-27	113.309	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	2558	2747	1.20E-25	108.687	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	243054	1074	1281	2.11E-24	105.22	cl02488	SPEC superfamily	 - 	 - 	"Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here"
Q#26287 - 	CGI_10020238	superfamily	247683	2	30	1.53E-05	45.3838	cl17036	SH3 superfamily	N	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#26288 - 	CGI_10020239	superfamily	241694	3	99	6.47E-18	76.5587	cl00216	L-asparaginase_like superfamily	NC	 - 	"Bacterial L-asparaginases and related enzymes; Asparaginases (amidohydrolases, E.C. 3.5.1.1) are dimeric or tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localized to the periplasm (type II L-asparaginase), and a second (asparaginase- glutaminase) present in the cytosol (type I L-asparaginase) that hydrolyzes both asparagine and glutamine with similar specificities and has a lower affinity for its substrate. Bacterial L-asparaginases (type II) are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL). A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. This wider family also includes a subunit of an archaeal Glu-tRNA amidotransferase."
Q#26290 - 	CGI_10020241	superfamily	201616	33	61	3.88E-08	45.005	cl03112	ER superfamily	N	 - 	Enhancer of rudimentary; Enhancer of rudimentary is a protein of unknown function that is highly conserved in plants and animals. This protein is found to be an enhancer of the rudimentary gene.
Q#26293 - 	CGI_10020244	superfamily	216653	99	227	5.53E-30	112.305	cl08331	Na_Ca_ex superfamily	 - 	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#26294 - 	CGI_10020245	superfamily	216653	60	149	7.64E-16	71.0891	cl08331	Na_Ca_ex superfamily	C	 - 	"Sodium/calcium exchanger protein; This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3."
Q#26296 - 	CGI_10020247	superfamily	241874	90	453	4.90E-164	481.405	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#26296 - 	CGI_10020247	superfamily	241874	11	86	1.93E-31	126.637	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#26297 - 	CGI_10020248	superfamily	218118	147	180	0.00290619	34.5121	cl04552	CD225 superfamily	NC	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#26298 - 	CGI_10020249	superfamily	241874	11	110	8.95E-42	144.356	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#26303 - 	CGI_10000216	superfamily	221397	18	116	1.50E-05	45.3891	cl14983	DUF3535 superfamily	NC	 - 	"Domain of unknown function (DUF3535); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with pfam00271, pfam02985, pfam00176. This domain has two completely conserved residues (P and K) that may be functionally important."
Q#26303 - 	CGI_10000216	superfamily	110440	352	379	0.00882847	33.9205	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26306 - 	CGI_10000220	superfamily	247856	42	98	0.000139865	35.9865	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#26306 - 	CGI_10000220	superfamily	247856	5	65	0.000455243	34.8309	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#26307 - 	CGI_10000222	superfamily	248438	34	138	1.70E-05	44.5405	cl17884	COG1214 superfamily	C	 - 	"Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]"
Q#26308 - 	CGI_10000224	superfamily	245106	1	52	3.32E-22	83.0772	cl09615	UBA_e1_C superfamily	N	 - 	Ubiquitin-activating enzyme e1 C-terminal domain; This presumed domain found at the C-terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterized.
Q#26309 - 	CGI_10003877	superfamily	247797	9	130	9.22E-49	157.577	cl17243	PRK13975 superfamily	N	 - 	thymidylate kinase; Provisional
Q#26310 - 	CGI_10003878	superfamily	247797	4	111	4.95E-51	163.355	cl17243	PRK13975 superfamily	C	 - 	thymidylate kinase; Provisional
Q#26311 - 	CGI_10003879	superfamily	245201	80	350	8.30E-180	504.458	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26312 - 	CGI_10000226	superfamily	243064	23	114	1.03E-27	100.953	cl02512	NTR_like superfamily	C	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#26314 - 	CGI_10000229	superfamily	241563	51	87	7.98E-05	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26314 - 	CGI_10000229	superfamily	110440	477	503	0.000237115	38.9281	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26316 - 	CGI_10000235	superfamily	241659	58	129	1.38E-21	83.4667	cl00175	alpha-crystallin-Hsps_p23-like superfamily	C	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#26316 - 	CGI_10000235	superfamily	149931	1	61	0.000236439	35.8923	cl07592	Siah-Interact_N superfamily	 - 	 - 	"Siah interacting protein, N terminal; The N terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N terminal domain."
Q#26319 - 	CGI_10000241	superfamily	247724	32	123	0.00155986	35.51	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26320 - 	CGI_10000242	superfamily	247724	20	191	5.05E-46	153.963	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26323 - 	CGI_10006299	superfamily	248020	30	296	4.02E-35	133.744	cl17466	Sulfatase superfamily	C	 - 	Sulfatase; Sulfatase.  
Q#26324 - 	CGI_10006300	superfamily	242206	364	455	9.32E-50	170.881	cl00938	Rieske superfamily	 - 	 - 	"Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis."
Q#26324 - 	CGI_10006300	superfamily	215691	621	701	2.74E-11	61.0626	cl15766	Pyr_redox superfamily	 - 	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#26324 - 	CGI_10006300	superfamily	248054	567	649	9.04E-08	51.9195	cl17500	NAD_binding_8 superfamily	N	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#26325 - 	CGI_10006301	superfamily	247727	55	185	1.22E-08	51.2767	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#26325 - 	CGI_10006301	superfamily	221654	240	300	2.87E-21	85.8128	cl13964	WBS_methylT superfamily	N	 - 	"Methyltransferase involved in Williams-Beuren syndrome; This domain family is found in eukaryotes, and is typically between 72 and 83 amino acids in length. The family is found in association with pfam08241. This family is made up of S-adenosylmethionine-dependent methyltransferases. The proteins are deleted in Williams-Beuren syndrome (WBS), a complex developmental disorder with multisystemic manifestations including supravalvular aortic stenosis (SVAS) and a specific cognitive phenotype."
Q#26325 - 	CGI_10006301	superfamily	247727	19	89	0.000227619	40.7173	cl17173	AdoMet_MTases superfamily	C	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#26326 - 	CGI_10006302	superfamily	243077	39	91	3.74E-13	61.0221	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#26327 - 	CGI_10006303	superfamily	220904	2	122	6.21E-26	96.2121	cl12494	DUF2781 superfamily	N	 - 	Protein of unknown function (DUF2781); This is a eukaryotic family of uncharacterized proteins. Some of the proteins in this family are annotated as membrane proteins.
Q#26333 - 	CGI_10000246	superfamily	246748	70	126	2.57E-13	65.3065	cl14876	Zinc_peptidase_like superfamily	C	 - 	"Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This family corresponds to several clans in the MEROPS database, including the MH clan, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carbxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metalloaminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some of M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacylpeptidase activity (i.e. hydrolysis of acylated N-terminal residues)."
Q#26334 - 	CGI_10000248	superfamily	214507	348	399	6.29E-08	48.9656	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#26335 - 	CGI_10000256	superfamily	241884	1	128	7.10E-59	183.229	cl00467	Ntn_hydrolase superfamily	N	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#26336 - 	CGI_10000257	superfamily	241884	18	61	1.49E-08	47.6387	cl00467	Ntn_hydrolase superfamily	NC	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#26338 - 	CGI_10000249	superfamily	248264	2	87	2.17E-06	43.3798	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#26339 - 	CGI_10000258	superfamily	246918	115	161	2.28E-08	47.1963	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#26339 - 	CGI_10000258	superfamily	241610	1	25	1.53E-05	39.5893	cl00101	KU superfamily	N	 - 	BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
Q#26342 - 	CGI_10000265	superfamily	242173	15	155	8.33E-23	88.8482	cl00891	Cu-Zn_Superoxide_Dismutase superfamily	 - 	 - 	"Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730]."
Q#26343 - 	CGI_10000266	superfamily	148061	77	256	4.74E-77	234.642	cl18026	FRG1 superfamily	 - 	 - 	"FRG1-like family; The human FRG1 gene maps to human chromosome 4q35 and has been identified as a candidate for facioscapulohumeral muscular dystrophy. Currently, the function of FRG1 is unknown."
Q#26344 - 	CGI_10000267	superfamily	243519	1	121	2.07E-68	216.704	cl03757	phosphohexomutase superfamily	N	 - 	"The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model."
Q#26345 - 	CGI_10000268	superfamily	242885	10	68	8.49E-26	94.5866	cl02106	IF4E superfamily	C	 - 	Eukaryotic initiation factor 4E; Eukaryotic initiation factor 4E.  
Q#26347 - 	CGI_10000273	superfamily	243179	76	177	8.91E-23	88.7154	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#26349 - 	CGI_10000271	superfamily	206009	29	61	7.20E-16	66.8078	cl16430	Clathrin_H_link superfamily	N	 - 	"Clathrin-H-link; This short domain is found on clathrins, and often appears on proteins directly downstream from the Clathrin-link domain pfam09268."
Q#26351 - 	CGI_10000283	superfamily	241670	1	93	9.46E-11	55.0567	cl00188	BPI superfamily	N	 - 	"BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide."
Q#26355 - 	CGI_10000289	superfamily	241563	61	112	0.00136106	37.844	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26356 - 	CGI_10004197	superfamily	215839	575	642	1.38E-06	46.7762	cl15968	GHMP_kinases_N superfamily	 - 	 - 	"GHMP kinases N terminal domain; This family includes homoserine kinases, galactokinases and mevalonate kinases."
Q#26356 - 	CGI_10004197	superfamily	193687	107	163	0.00439801	36.4507	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#26357 - 	CGI_10004198	superfamily	217293	2	201	1.62E-42	150.861	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#26357 - 	CGI_10004198	superfamily	202474	219	329	1.59E-10	59.5897	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#26358 - 	CGI_10004199	superfamily	217293	34	240	8.43E-43	152.017	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#26358 - 	CGI_10004199	superfamily	202474	247	378	9.05E-09	54.5821	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#26359 - 	CGI_10004200	superfamily	152695	26	82	3.13E-05	39.3155	cl13667	PIP49_C superfamily	C	 - 	Pancreatitis induced protein 49 C terminal; This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 344 to 431 amino acids in length. This protein has a single completely conserved residue C that may be functionally important. PIP49 is a putative transmembrane protein which is induced to express during pancreatitis.
Q#26360 - 	CGI_10004201	superfamily	152695	126	318	2.01E-20	87.0803	cl13667	PIP49_C superfamily	 - 	 - 	Pancreatitis induced protein 49 C terminal; This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 344 to 431 amino acids in length. This protein has a single completely conserved residue C that may be functionally important. PIP49 is a putative transmembrane protein which is induced to express during pancreatitis.
Q#26361 - 	CGI_10004202	superfamily	219779	17	80	5.04E-08	46.4915	cl07044	DPM3 superfamily	 - 	 - 	"Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex."
Q#26362 - 	CGI_10004203	superfamily	222150	451	476	8.55E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26362 - 	CGI_10004203	superfamily	222150	541	566	0.00309464	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26362 - 	CGI_10004203	superfamily	246975	557	577	0.00390938	37.3265	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#26362 - 	CGI_10004203	superfamily	222150	569	594	0.0049237	36.9861	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26364 - 	CGI_10004205	superfamily	247739	6	76	1.89E-06	42.6433	cl17185	LPLAT superfamily	N	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#26365 - 	CGI_10000294	superfamily	247069	14	43	0.00155365	36.456	cl15787	SEC14 superfamily	NC	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#26367 - 	CGI_10000295	superfamily	248264	85	202	7.80E-08	50.3134	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#26369 - 	CGI_10000296	superfamily	243092	3	98	9.27E-07	45.0184	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#26371 - 	CGI_10000299	superfamily	241568	17	42	0.000395032	33.5904	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#26371 - 	CGI_10000299	superfamily	243035	53	73	0.000854508	33.8706	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26372 - 	CGI_10000300	superfamily	247805	233	327	9.83E-08	51.184	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26372 - 	CGI_10000300	superfamily	217017	492	578	0.00833588	38.1273	cl17780	Herpes_ori_bp superfamily	NC	 - 	"Origin of replication binding protein; This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication."
Q#26374 - 	CGI_10000301	superfamily	241563	62	102	0.000446566	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26375 - 	CGI_10000303	superfamily	241607	57	71	0.00263411	31.5363	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#26376 - 	CGI_10000304	superfamily	247805	47	82	3.68E-14	64.4281	cl17251	DEXDc superfamily	C	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26378 - 	CGI_10000307	superfamily	241786	2	191	9.27E-43	144.162	cl00325	Ribosomal_L4 superfamily	 - 	 - 	Ribosomal protein L4/L1 family; This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA.
Q#26381 - 	CGI_10018665	superfamily	245040	65	87	0.000116897	37.0684	cl09238	CY superfamily	NC	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#26382 - 	CGI_10018666	superfamily	245040	26	88	0.000143548	36.5107	cl09238	CY superfamily	C	 - 	"Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains."
Q#26384 - 	CGI_10018668	superfamily	220239	573	713	6.96E-28	110.021	cl09673	DUF2013 superfamily	 - 	 - 	Protein of unknown function (DUF2013); This region is found at the C terminal of a group of cytoskeletal proteins.
Q#26384 - 	CGI_10018668	superfamily	247683	1	54	1.99E-13	66.1846	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#26385 - 	CGI_10018669	superfamily	198738	51	134	1.16E-46	155.889	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#26386 - 	CGI_10018670	superfamily	241645	714	803	1.10E-20	88.7004	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#26386 - 	CGI_10018670	superfamily	241566	107	139	4.60E-06	45.1379	cl00040	C1 superfamily	C	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#26387 - 	CGI_10018671	superfamily	111929	157	244	1.18E-24	95.9306	cl03885	Str_synth superfamily	 - 	 - 	Strictosidine synthase; Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyzes the condensation of tryptamine with secologanin to form strictosidine.
Q#26388 - 	CGI_10018672	superfamily	222340	13	30	0.0024068	32.4429	cl18665	GNAT_acetyltr_2 superfamily	C	 - 	GNAT acetyltransferase 2; This domain has N-acetyltransferase activity. It has a GCN5-related N-acetyltransferase (GNAT) fold.
Q#26389 - 	CGI_10018673	superfamily	217293	4	163	8.30E-29	107.719	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#26390 - 	CGI_10018674	superfamily	217293	4	196	2.98E-37	135.068	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#26390 - 	CGI_10018674	superfamily	202474	204	291	1.46E-10	59.2045	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#26391 - 	CGI_10018675	superfamily	245213	1573	1610	1.83E-05	44.5498	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	1952	1985	0.000225252	41.4682	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	1357	1390	0.000303919	41.083	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	1658	1694	0.000337492	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	1824	1864	0.000448451	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	1530	1563	0.00287516	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	1487	1520	0.00322858	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	162	199	0.0033161	38.0014	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	245213	359	396	0.00450282	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26391 - 	CGI_10018675	superfamily	246918	1999	2050	4.85E-13	66.8415	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#26391 - 	CGI_10018675	superfamily	243065	812	976	9.75E-09	55.9109	cl02516	VWD superfamily	 - 	 - 	von Willebrand factor type D domain; Luciferin-2-monooxygenase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
Q#26391 - 	CGI_10018675	superfamily	243124	506	663	8.06E-07	50.1181	cl02648	NIDO superfamily	 - 	 - 	Nidogen-like; This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Q#26391 - 	CGI_10018675	superfamily	246918	206	257	1.68E-06	47.9667	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#26391 - 	CGI_10018675	superfamily	241578	1909	1949	4.68E-06	48.5352	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26391 - 	CGI_10018675	superfamily	241578	1860	1908	7.73E-06	48.15	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26391 - 	CGI_10018675	superfamily	221695	1638	1661	1.83E-05	44.3682	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#26391 - 	CGI_10018675	superfamily	241578	1390	1437	3.21E-05	46.224	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26391 - 	CGI_10018675	superfamily	221695	1294	1317	0.000239616	41.2866	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#26391 - 	CGI_10018675	superfamily	221695	1719	1740	0.000462472	40.5162	cl18612	cEGF superfamily	 - 	 - 	"Complement Clr-like EGF-like; cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue."
Q#26391 - 	CGI_10018675	superfamily	245213	1783	1822	0.000513518	40.41	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26395 - 	CGI_10018680	superfamily	241782	47	346	1.70E-17	81.358	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#26397 - 	CGI_10018683	superfamily	245201	523	775	7.76E-90	289.437	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26397 - 	CGI_10018683	superfamily	241613	252	286	1.02E-06	46.8162	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#26397 - 	CGI_10018683	superfamily	247764	842	976	2.80E-27	110.261	cl17210	AtpH superfamily	N	 - 	"F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]"
Q#26398 - 	CGI_10018684	superfamily	245814	734	798	0.000798041	39.7799	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#26398 - 	CGI_10018684	superfamily	243061	1506	1606	2.02E-39	144.407	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#26398 - 	CGI_10018684	superfamily	215647	1180	1396	8.80E-39	147.37	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#26398 - 	CGI_10018684	superfamily	243086	1109	1152	1.31E-13	68.1705	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#26398 - 	CGI_10018684	superfamily	243086	1796	1833	1.38E-09	56.6146	cl02559	GPS superfamily	 - 	 - 	"Latrophilin/CL-1-like GPS domain; Domain present in latrophilin/CL-1, sea urchin REJ and polycystin."
Q#26399 - 	CGI_10018685	superfamily	243092	47	201	2.96E-20	92.0128	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#26400 - 	CGI_10018686	superfamily	247805	102	242	1.06E-27	109.349	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26400 - 	CGI_10018686	superfamily	247905	267	425	8.73E-07	47.6177	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#26400 - 	CGI_10018686	superfamily	219532	569	670	1.41E-31	119.341	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#26400 - 	CGI_10018686	superfamily	243778	478	549	1.12E-16	76.4939	cl04503	HA2 superfamily	C	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#26401 - 	CGI_10018687	superfamily	241600	102	313	2.93E-98	291.452	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26404 - 	CGI_10000302	superfamily	243161	4	61	1.38E-05	40.4962	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#26409 - 	CGI_10000314	superfamily	243035	22	62	0.00872661	31.051	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26410 - 	CGI_10000317	superfamily	217473	72	295	1.66E-27	112.458	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#26413 - 	CGI_10000321	superfamily	215754	38	132	4.52E-24	92.3164	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26413 - 	CGI_10000321	superfamily	215754	155	196	6.49E-09	50.3296	cl02813	Mito_carr superfamily	NC	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26418 - 	CGI_10000324	superfamily	247038	58	94	0.00607227	32.389	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#26419 - 	CGI_10000325	superfamily	243094	49	102	9.45E-19	79.39	cl02569	RasGAP superfamily	N	 - 	"Ras GTPase Activating Domain; RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator."
Q#26420 - 	CGI_10000331	superfamily	247947	3	36	0.0039478	30.8157	cl17393	HTH_Hin_like superfamily	 - 	 - 	"Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a DNA-binding domain (HTH_Hin) and a catalytic domain."
Q#26423 - 	CGI_10000318	superfamily	216981	175	204	0.00183692	35.5862	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#26426 - 	CGI_10000339	superfamily	242730	9	87	0.00794311	35.3147	cl01825	Phage_Mu_Gam superfamily	C	 - 	Bacteriophage Mu Gam like protein; This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Q#26427 - 	CGI_10000338	superfamily	241564	32	99	6.61E-31	111.974	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#26427 - 	CGI_10000338	superfamily	247792	262	301	4.24E-05	40.1216	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#26428 - 	CGI_10000290	superfamily	247736	12	45	0.000131603	35.5883	cl17182	NAT_SF superfamily	N	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#26429 - 	CGI_10000291	superfamily	247736	36	119	2.60E-15	67.8077	cl17182	NAT_SF superfamily	C	 - 	"N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included."
Q#26434 - 	CGI_10000350	superfamily	110440	484	510	9.36E-05	40.0837	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26434 - 	CGI_10000350	superfamily	241563	59	95	0.000455243	38.2292	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26434 - 	CGI_10000350	superfamily	110440	525	552	0.00441933	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26437 - 	CGI_10000349	superfamily	247725	1	86	9.97E-38	125.097	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#26447 - 	CGI_10000374	superfamily	192604	229	282	4.62E-14	67.7094	cl11135	PACT_coil_coil superfamily	C	 - 	"Pericentrin-AKAP-450 domain of centrosomal targeting protein; This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly."
Q#26450 - 	CGI_10000375	superfamily	245847	6	126	5.52E-23	88.7677	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#26454 - 	CGI_10000381	superfamily	240425	6	148	8.85E-05	40.9555	cl18912	PTZ00464 superfamily	C	 - 	SNF-7-like protein; Provisional
Q#26455 - 	CGI_10000384	superfamily	241792	1	120	1.00E-77	228.978	cl00332	Ribosomal_S11 superfamily	 - 	 - 	Ribosomal protein S11; Ribosomal protein S11.  
Q#26457 - 	CGI_10000286	superfamily	245213	192	227	1.47E-05	40.6978	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26457 - 	CGI_10000286	superfamily	245213	1	37	2.06E-05	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26457 - 	CGI_10000286	superfamily	245213	78	113	4.26E-05	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26457 - 	CGI_10000286	superfamily	245213	153	189	9.67E-05	38.3866	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26457 - 	CGI_10000286	superfamily	245213	115	151	0.000192385	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26457 - 	CGI_10000286	superfamily	245213	39	75	0.000222918	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26464 - 	CGI_10000369	superfamily	218149	16	80	1.72E-21	83.0848	cl04588	tRNA_synt_1c_R1 superfamily	N	 - 	"Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1; This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function."
Q#26466 - 	CGI_10000401	superfamily	238191	1	332	1.09E-59	200.636	cl18907	Esterase_lipase superfamily	N	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#26468 - 	CGI_10000404	superfamily	242274	6	165	3.61E-05	41.629	cl01053	SGNH_hydrolase superfamily	 - 	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#26469 - 	CGI_10000405	superfamily	243069	44	171	3.61E-58	181.6	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#26470 - 	CGI_10000402	superfamily	241591	44	117	2.54E-28	102.699	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#26473 - 	CGI_10000416	superfamily	248009	4	118	4.07E-37	131.953	cl17455	UPF0027 superfamily	NC	 - 	Uncharacterized protein family UPF0027; Uncharacterized protein family UPF0027.  
Q#26476 - 	CGI_10000414	superfamily	242406	55	190	4.54E-24	94.1953	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#26480 - 	CGI_10000423	superfamily	245202	39	126	1.32E-32	113.799	cl09927	S1_like superfamily	 - 	 - 	"S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold."
Q#26486 - 	CGI_10000430	superfamily	219525	74	119	2.63E-06	42.021	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#26486 - 	CGI_10000430	superfamily	219525	126	175	0.000650476	35.4726	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#26488 - 	CGI_10000426	superfamily	241563	61	96	0.00500799	35.1476	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26493 - 	CGI_10000441	superfamily	222150	432	457	1.93E-05	41.9937	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26493 - 	CGI_10000441	superfamily	222150	402	420	0.00368209	35.4453	cl16282	zf-H2C2_2 superfamily	C	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26494 - 	CGI_10000437	superfamily	244574	11	37	0.000828521	35.058	cl06998	LEM_like superfamily	 - 	 - 	"LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and postmitotic reassembly. Some of the LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are nonmembrane nuclear polypeptides. All LAP2 isoforms contain an N-terminal lamina-associated polypeptide-Emerin-MAN1 (LEM)-domain that is connected to a highly divergent LEM-like domain by an unstructured linker. Both LEM and LEM-like domains share the same structural fold, mainly composed of two large parallel alpha helices. However, their biochemical nature of the solvent-accessible residues is completely different, which indicates the two domains may target different protein surfaces. The LEM domain is responsible for the interaction with the nonspecific DNA binding protein barrier-to-autointegration factor (BAF), and the LEM-like domain is involved in chromosome binding. The family also includes the yeast helix-extension-helix domain-containing proteins, Heh1p (formerly called Src1p) and Heh2p, and their uncharacterized homologs found mainly in fungi and several in bacteria. Heh1p and Heh2p are inner nuclear membrane proteins that might interact with nuclear pore complexes (NPCs). Heh1p is involved in mitosis. It functions at the interface between subtelomeric gene expression and transcription export (TREX)-dependent messenger RNA export through NPCs. The function of Heh2p remains ill-defined. Both Heh1p and Heh2p contain a LEM-like domain (also termed HeH domain), but lack a LEM domain."
Q#26499 - 	CGI_10000454	superfamily	216363	7	73	2.53E-13	60.5618	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#26502 - 	CGI_10000453	superfamily	247858	19	68	5.51E-09	49.3086	cl17304	2OG-FeII_Oxy_3 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#26503 - 	CGI_10000464	superfamily	241554	12	124	4.86E-22	85.3899	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#26506 - 	CGI_10000466	superfamily	245201	16	239	3.57E-83	252.457	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26507 - 	CGI_10000462	superfamily	247723	59	137	6.30E-47	150.848	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#26507 - 	CGI_10000462	superfamily	247723	166	198	5.73E-17	72.2668	cl17169	RRM_SF superfamily	C	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#26507 - 	CGI_10000462	superfamily	247723	3	34	1.53E-06	43.3315	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#26508 - 	CGI_10000469	superfamily	248420	101	302	1.04E-16	76.5889	cl17866	ABC2_membrane_2 superfamily	 - 	 - 	ABC-2 family transporter protein; This family is related to the ABC-2 membrane transporter family.
Q#26509 - 	CGI_10000470	superfamily	247755	313	520	2.80E-78	246.54	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26509 - 	CGI_10000470	superfamily	247755	2	198	6.88E-63	206.095	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26510 - 	CGI_10000471	superfamily	222128	205	317	6.30E-13	63.5511	cl18638	HlyD_3 superfamily	 - 	 - 	HlyD family secretion protein; This is a family of largely bacterial haemolysin translocator HlyD proteins.
Q#26510 - 	CGI_10000471	superfamily	205711	42	90	1.36E-08	50.5649	cl18273	Biotin_lipoyl_2 superfamily	 - 	 - 	Biotin-lipoyl like; Biotin-lipoyl like.  
Q#26511 - 	CGI_10000473	superfamily	243179	1	92	3.02E-07	44.2609	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#26512 - 	CGI_10000475	superfamily	246683	21	186	1.48E-77	237.404	cl14648	Aldose_epim superfamily	C	 - 	"aldose 1-epimerase superfamily; Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen."
Q#26516 - 	CGI_10000478	superfamily	217293	19	89	4.06E-10	57.2575	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#26516 - 	CGI_10000478	superfamily	202474	98	176	4.10E-07	48.8041	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#26518 - 	CGI_10000485	superfamily	218267	160	249	1.00E-25	104.054	cl04754	LMBR1 superfamily	N	 - 	"LMBR1-like membrane protein; Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought. Vertebrate members of this family may play a role in limb development. A member of this family has been shown to be a lipocalin membrane receptor"
Q#26519 - 	CGI_10000488	superfamily	245225	24	361	5.42E-55	189.444	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#26521 - 	CGI_10000434	superfamily	241600	2	133	1.82E-55	174.736	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26522 - 	CGI_10000491	superfamily	245596	32	55	6.25E-07	43.347	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#26523 - 	CGI_10000494	superfamily	245206	4	227	4.83E-94	277.668	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#26524 - 	CGI_10000492	superfamily	247856	106	154	8.14E-07	42.9201	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#26527 - 	CGI_10000497	superfamily	247856	47	100	3.83E-07	42.9201	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#26528 - 	CGI_10000501	superfamily	241600	1	73	8.95E-19	76.1251	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26529 - 	CGI_10000507	superfamily	218182	14	217	1.39E-66	207.302	cl18445	ERG2_Sigma1R superfamily	 - 	 - 	"ERG2 and Sigma1 receptor like protein; This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyzes a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum, which interacts with endogenous steroid hormones, such as progesterone and testosterone. It also binds the sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia."
Q#26531 - 	CGI_10000508	superfamily	245213	265	295	0.00475853	34.9198	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#26531 - 	CGI_10000508	superfamily	241583	1	94	1.74E-16	76.841	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#26531 - 	CGI_10000508	superfamily	241571	160	257	0.00833294	34.6955	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#26535 - 	CGI_10000510	superfamily	247805	52	94	2.20E-05	41.554	cl17251	DEXDc superfamily	N	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26539 - 	CGI_10000523	superfamily	241563	75	115	1.43E-06	45.9332	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26541 - 	CGI_10000526	superfamily	242274	72	166	1.03E-07	48.771	cl01053	SGNH_hydrolase superfamily	N	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#26543 - 	CGI_10000534	superfamily	243263	48	126	6.68E-13	63.581	cl02990	ASC superfamily	C	 - 	Amiloride-sensitive sodium channel; Amiloride-sensitive sodium channel.  
Q#26544 - 	CGI_10000535	superfamily	245814	237	310	1.65E-05	42.0911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#26544 - 	CGI_10000535	superfamily	245814	141	208	1.98E-05	41.7059	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#26549 - 	CGI_10000546	superfamily	241600	1	53	3.55E-21	82.6735	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26550 - 	CGI_10000543	superfamily	244819	9	63	0.000508951	36.2234	cl07874	zf-AD superfamily	C	 - 	"Zinc-finger associated domain (zf-AD); The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA."
Q#26552 - 	CGI_10000547	superfamily	199156	48	63	0.00251462	31.2596	cl15298	zf-CCHC superfamily	 - 	 - 	"Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger."
Q#26553 - 	CGI_10000545	superfamily	245612	1	116	6.57E-43	147.459	cl11426	Amidase superfamily	N	 - 	Amidase; Amidase.  
Q#26555 - 	CGI_10000552	superfamily	242889	59	103	5.16E-06	41.8198	cl02111	PCI superfamily	N	 - 	"PCI domain; This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)."
Q#26556 - 	CGI_10000555	superfamily	241754	29	118	1.15E-35	126.917	cl00286	Motor_domain superfamily	NC	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#26560 - 	CGI_10000560	superfamily	216363	297	392	3.17E-14	68.2658	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#26561 - 	CGI_10000573	superfamily	201369	1	37	6.78E-12	56.485	cl02914	EF1G superfamily	N	 - 	"Elongation factor 1 gamma, conserved domain; Elongation factor 1 gamma, conserved domain.  "
Q#26563 - 	CGI_10000577	superfamily	222150	327	352	0.000310078	38.5269	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26563 - 	CGI_10000577	superfamily	222150	467	490	0.0023613	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26563 - 	CGI_10000577	superfamily	222150	355	380	0.00794783	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26566 - 	CGI_10000579	superfamily	241691	202	328	1.56E-05	43.2696	cl00213	DNA_BRE_C superfamily	N	 - 	"DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region.  Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity."
Q#26569 - 	CGI_10000585	superfamily	197729	29	47	0.00102316	34.2049	cl11732	LRRcap superfamily	 - 	 - 	occurring C-terminal to leucine-rich repeats; A motif occurring C-terminal to leucine-rich repeats in "sds22-like" and "typical" LRR-containing proteins.
Q#26570 - 	CGI_10000591	superfamily	213393	191	231	1.12E-14	68.4336	cl17094	talin-RS superfamily	C	 - 	rod-segment of the talin C-terminal domain; The talin rod-segment characterize by this model interacts with its N-terminal FERM domain to mask its integrin-binding site and interferes with interactions between the FERM domain and the cellular membrane. Talin is a large and ubiquitous cytoskeletal protein concentrated at focal adhesion sites. It is involved in linking integrins to the actin cytoskeleton.
Q#26573 - 	CGI_10000590	superfamily	247724	43	323	3.49E-139	410.73	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26573 - 	CGI_10000590	superfamily	243185	338	420	2.91E-25	100.64	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#26573 - 	CGI_10000590	superfamily	243187	543	623	1.03E-07	50.4715	cl02789	EFG_like_IV superfamily	C	 - 	"Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm."
Q#26574 - 	CGI_10000596	superfamily	216152	110	376	9.62E-49	170.572	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#26575 - 	CGI_10000595	superfamily	195671	13	143	1.14E-44	145.672	cl08257	Ribosomal_L11 superfamily	 - 	 - 	"Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation."
Q#26578 - 	CGI_10000594	superfamily	241576	50	119	3.48E-45	145.288	cl00055	MH1 superfamily	C	 - 	"N-terminal Mad Homology 1 (MH1) domain; The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure.  It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. Receptor-regulated SMAD proteins (R-SMADs, including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by phosphorylation by transforming growth factor (TGF)-beta type I receptors. The active R-SMAD associates with a common mediator SMAD (Co-SMAD or SMAD4) and other cofactors, which together translocate to the nucleus to regulate gene expression. The inhibitory or antagonistic SMADs (I-SMADs, including SMAD6 and SMAD7) negatively regulate TGF-beta signaling by competing with R-SMADs for type I receptor or Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a nuclear localization signal as well as DNA-binding activity. The activated R-SMAD/SMAD4 complex then binds with very low affinity to a DNA sequence CAGAC called SMAD-binding element (SBE) via the MH1 domain."
Q#26584 - 	CGI_10000588	superfamily	218425	171	305	2.12E-39	144.763	cl04931	eIF-3_zeta superfamily	C	 - 	"Eukaryotic translation initiation factor 3 subunit 7 (eIF-3); This family is made up of eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is a multi-subunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. These functions and the complex nature of eIF3 suggest multiple interactions with many components of the translational machinery. The gene coding for the protein has been implicated in cancer in mammals."
Q#26585 - 	CGI_10010457	superfamily	247805	261	393	7.69E-16	73.9108	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26586 - 	CGI_10010458	superfamily	221155	146	259	9.30E-19	79.334	cl13152	RIG-I_C-RD superfamily	 - 	 - 	"C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity."
Q#26587 - 	CGI_10010459	superfamily	247805	235	385	9.18E-22	93.1708	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26587 - 	CGI_10010459	superfamily	247905	585	696	1.18E-18	83.8264	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#26587 - 	CGI_10010459	superfamily	221155	772	880	1.73E-13	68.5484	cl13152	RIG-I_C-RD superfamily	 - 	 - 	"C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity."
Q#26587 - 	CGI_10010459	superfamily	246680	2	75	0.00801799	35.7402	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#26590 - 	CGI_10010462	superfamily	193687	4	149	6.01E-62	190.614	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#26591 - 	CGI_10010463	superfamily	243555	21	207	4.26E-20	85.1354	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#26592 - 	CGI_10010464	superfamily	243134	348	459	2.08E-22	95.0235	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#26592 - 	CGI_10010464	superfamily	243134	641	748	9.67E-19	84.238	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#26592 - 	CGI_10010464	superfamily	243134	9	130	4.36E-13	67.6744	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#26592 - 	CGI_10010464	superfamily	243134	501	605	1.87E-11	62.6668	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#26592 - 	CGI_10010464	superfamily	243134	762	895	1.19E-09	57.274	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#26592 - 	CGI_10010464	superfamily	243134	929	1048	4.29E-09	55.7332	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#26592 - 	CGI_10010464	superfamily	243134	213	319	1.21E-08	54.1924	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#26598 - 	CGI_10010470	superfamily	220704	57	269	1.92E-122	353.507	cl11011	DUF2419 superfamily	C	 - 	"Protein of unknown function (DUF2419); This is a family of conserved proteins found from plants to humans. The function is not known. A few members are annotated as being cobyrinic acid a,c-diamide synthetase but this could not be confirmed."
Q#26599 - 	CGI_10000605	superfamily	118307	6	118	3.90E-44	142.223	cl10754	Keratin_assoc superfamily	 - 	 - 	"Keratinocyte-associated protein 2; Members of this family comprise various keratinocyte-associated proteins. Their exact function has not, as yet, been determined."
Q#26600 - 	CGI_10000607	superfamily	247856	44	93	2.34E-08	46.3869	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#26602 - 	CGI_10000611	superfamily	218216	8	150	9.20E-59	181.678	cl04685	P16-Arc superfamily	 - 	 - 	"ARP2/3 complex 16 kDa subunit (p16-Arc); The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices."
Q#26604 - 	CGI_10000614	superfamily	219316	1	55	4.36E-15	66.0907	cl06268	B9-C2 superfamily	N	 - 	"Ciliary basal body-associated, B9 protein; The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains. There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease. All the three distinct types of B9-C2 proteins cooperatively localise to the basal body or centrosome of cilia."
Q#26604 - 	CGI_10000614	superfamily	248445	33	79	0.00420777	32.9903	cl17891	ProX superfamily	C	 - 	"ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]"
Q#26605 - 	CGI_10000615	superfamily	242996	5	89	9.07E-22	82.6432	cl02346	Tmemb_14 superfamily	 - 	 - 	Transmembrane proteins 14C; This family of short membrane proteins are as yet uncharacterized.
Q#26607 - 	CGI_10000613	superfamily	110440	481	508	0.00129764	37.0021	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26607 - 	CGI_10000613	superfamily	110440	523	550	0.00933853	34.3057	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#26608 - 	CGI_10000624	superfamily	242046	59	221	1.44E-63	197.477	cl00718	TOPRIM superfamily	 - 	 - 	"Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function."
Q#26609 - 	CGI_10000619	superfamily	241563	148	190	5.29E-06	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26609 - 	CGI_10000619	superfamily	128778	204	306	0.00336968	35.7035	cl17972	BBC superfamily	 - 	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#26610 - 	CGI_10000627	superfamily	209366	21	45	5.62E-11	53.35	cl11604	zf-A20 superfamily	 - 	 - 	A20-like zinc finger; The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation.
Q#26612 - 	CGI_10000630	superfamily	245205	10	82	7.45E-16	71.0572	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26612 - 	CGI_10000630	superfamily	241739	97	315	6.29E-61	198.944	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#26614 - 	CGI_10000629	superfamily	248264	1	107	1.87E-11	58.0174	cl17710	DDE_4 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#26618 - 	CGI_10000631	superfamily	241629	38	112	9.39E-22	84.569	cl00133	SCP superfamily	C	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#26622 - 	CGI_10000661	superfamily	247724	41	201	0.000314242	38.9768	cl17170	Ras_like_GTPase superfamily	C	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26624 - 	CGI_10000639	superfamily	245836	101	258	6.50E-75	232.913	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#26624 - 	CGI_10000639	superfamily	151975	25	63	3.37E-08	49.401	cl13054	Snurportin1 superfamily	 - 	 - 	Snurportin1; Snurportin1 is a novel nuclear import receptor which contains an N-terminal importin beta binding domain which is essential for its function of a snRNP-specific nuclear import receptor. Snurportin1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells.
Q#26629 - 	CGI_10000668	superfamily	245225	4	120	2.66E-15	70.0328	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	NC	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#26631 - 	CGI_10000677	superfamily	245814	101	169	0.00046786	37.0012	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#26632 - 	CGI_10000688	superfamily	241563	38	77	5.78E-05	40.7336	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26632 - 	CGI_10000688	superfamily	197380	290	347	0.0078335	36.8309	cl16909	SdiA-regulated superfamily	C	 - 	"SdiA-regulated; This model represents a bacterial family of proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators. The C-terminal domain included in the alignment forms a five-bladed beta-propeller structure. The X-ray structure of Escherichia coli yjiK (C-terminal domain) exhibits binding of calcium ions (Ca++) in what appears to be an evolutionarily conserved site. Sequence analysis suggests a distant relationship to proteins that are characterized as containing NHL-repeats. The latter also form beta-propeller structures, with several examples known to form six-bladed beta-propellers. Several of the six-bladed beta-propellers containing NHL repeats have been characterized functionally, including members with enzymatic functions that are dependent on metal ions. No functional characterization is available for this family of five-bladed propellers, though."
Q#26633 - 	CGI_10000689	superfamily	243035	38	85	9.81E-06	39.1402	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26634 - 	CGI_10000690	superfamily	241817	21	186	1.42E-48	161.976	cl00365	F1-ATPase_gamma superfamily	C	 - 	"mitochondrial ATP synthase gamma subunit; The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain of F-ATPases is composed of alpha, beta, gamma, delta, and epsilon (not present in bacteria) subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain."
Q#26635 - 	CGI_10000692	superfamily	241563	8	52	0.00998834	34.3772	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26636 - 	CGI_10000695	superfamily	243072	251	362	1.53E-20	86.2834	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26636 - 	CGI_10000695	superfamily	115363	4	65	9.06E-05	40.0478	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#26637 - 	CGI_10000696	superfamily	218676	125	411	1.98E-16	79.2995	cl14911	Peptidase_M13_N superfamily	C	 - 	"Peptidase family M13; M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk."
Q#26638 - 	CGI_10000697	superfamily	244307	71	421	3.13E-112	340.191	cl06123	DHR2_DOCK superfamily	 - 	 - 	"Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins; DOCK proteins comprise a family of atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. They are also called the CZH (CED-5, Dock180, and MBC-zizimin homology) family, after the first family members identified. Dock180 was first isolated as a binding partner for the adaptor protein Crk. The Caenorhabditis elegans protein, Ced-5, is essential for cell migration and phagocytosis, while the Drosophila ortholog, Myoblast city (MBC), is necessary for myoblast fusion and dorsal closure. DOCKs are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1 (or Dock180), 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1, and DHR-2 (also called CZH2 or Docker). This alignment model represents the DHR-2 domain of DOCK proteins, which contains the catalytic GEF activity for Rac and/or Cdc42."
Q#26639 - 	CGI_10000698	superfamily	241547	84	186	3.97E-19	81.9455	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#26641 - 	CGI_10000704	superfamily	245248	1	116	1.26E-29	110.01	cl10080	RPE65 superfamily	N	 - 	"Retinal pigment epithelial membrane protein; This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria."
Q#26642 - 	CGI_10000705	superfamily	242274	61	174	7.73E-05	40.5725	cl01053	SGNH_hydrolase superfamily	N	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#26644 - 	CGI_10000699	superfamily	248264	312	438	3.24E-05	42.6094	cl17710	DDE_4 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#26646 - 	CGI_10000709	superfamily	247724	8	208	1.37E-83	255.153	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26649 - 	CGI_10000718	superfamily	241584	54	96	0.000232046	36.3203	cl00065	FN3 superfamily	N	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#26651 - 	CGI_10000720	superfamily	222428	104	416	1.71E-162	462.821	cl18675	AAA_34 superfamily	 - 	 - 	P-loop containing NTP hydrolase pore-1; P-loop containing NTP hydrolase pore-1.  
Q#26654 - 	CGI_10000736	superfamily	241600	2	128	3.96E-36	125.431	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#26656 - 	CGI_10000731	superfamily	244083	22	138	4.32E-33	115.04	cl05417	PLA2_like superfamily	 - 	 - 	"PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers."
Q#26658 - 	CGI_10000682	superfamily	183292	83	149	0.00313386	35.5676	cl18135	PRK11728 superfamily	NC	 - 	hydroxyglutarate oxidase; Provisional
Q#26660 - 	CGI_10000745	superfamily	183292	1	35	0.00153896	36.7232	cl18135	PRK11728 superfamily	C	 - 	hydroxyglutarate oxidase; Provisional
Q#26661 - 	CGI_10000749	superfamily	245596	86	147	2.89E-24	94.1857	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#26663 - 	CGI_10000757	superfamily	241578	1	124	6.54E-22	85.8062	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26664 - 	CGI_10000758	superfamily	248293	46	115	0.000447463	38.1038	cl17739	MADF_DNA_bdg superfamily	 - 	 - 	Alcohol dehydrogenase transcription factor Myb/SANT-like; The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains.
Q#26667 - 	CGI_10000766	superfamily	243635	139	192	3.11E-10	55.0333	cl04085	uDENN superfamily	N	 - 	uDENN domain; This region is always found associated with pfam02141. It is predicted to form an all beta domain.
Q#26667 - 	CGI_10000766	superfamily	245670	236	261	0.00238243	36.7898	cl11519	DENN superfamily	NC	 - 	DENN (AEX-3) domain; DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
Q#26669 - 	CGI_10000761	superfamily	220672	80	274	1.55E-37	133.526	cl10957	Frag1 superfamily	 - 	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#26669 - 	CGI_10000761	superfamily	220672	2	46	4.86E-05	42.2338	cl10957	Frag1 superfamily	N	 - 	"Frag1/DRAM/Sfk1 family; This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton."
Q#26670 - 	CGI_10000779	superfamily	245225	12	378	8.58E-96	291.868	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#26677 - 	CGI_10000795	superfamily	247684	4	149	8.07E-23	96.6476	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#26678 - 	CGI_10000794	superfamily	247941	115	255	0.000111174	40.3969	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#26679 - 	CGI_10000806	superfamily	241619	8	42	0.00332337	31.6378	cl00112	PAN_APPLE superfamily	NC	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#26687 - 	CGI_10000818	superfamily	241563	61	96	0.000156612	40.9256	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26689 - 	CGI_10000788	superfamily	207668	80	113	1.52E-13	60.283	cl02609	TFIIS_C superfamily	 - 	 - 	Transcription factor S-II (TFIIS); Transcription factor S-II (TFIIS).  
Q#26690 - 	CGI_10000823	superfamily	248097	72	185	2.02E-20	83.0834	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26691 - 	CGI_10000824	superfamily	248097	5	95	8.19E-17	70.3718	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26692 - 	CGI_10000755	superfamily	241563	89	124	0.00242239	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26693 - 	CGI_10000829	superfamily	245205	8	103	1.30E-33	115.402	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26694 - 	CGI_10000825	superfamily	245205	3	47	8.94E-06	39.9137	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26695 - 	CGI_10000821	superfamily	245201	92	241	9.63E-37	131.525	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26695 - 	CGI_10000821	superfamily	247824	8	117	5.10E-05	42.2115	cl17270	APH_ChoK_like superfamily	NC	 - 	"Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine."
Q#26696 - 	CGI_10000836	superfamily	242406	83	123	0.000414434	36.4153	cl01271	DUF1768 superfamily	C	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#26699 - 	CGI_10000840	superfamily	152473	1	47	1.69E-15	71.8264	cl12034	DUF3524 superfamily	N	 - 	Domain of unknown function (DUF3524); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is about 170 amino acids in length. This domain is found associated with pfam00534. This domain has two conserved sequence motifs: HENQ and FNS. This domain has a single completely conserved residue S that may be functionally important.
Q#26699 - 	CGI_10000840	superfamily	245227	179	273	1.09E-08	54.7002	cl10013	Glycosyltransferase_GTB_type superfamily	NC	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#26700 - 	CGI_10000841	superfamily	152473	12	123	1.07E-49	158.111	cl12034	DUF3524 superfamily	C	 - 	Domain of unknown function (DUF3524); This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is about 170 amino acids in length. This domain is found associated with pfam00534. This domain has two conserved sequence motifs: HENQ and FNS. This domain has a single completely conserved residue S that may be functionally important.
Q#26703 - 	CGI_10000811	superfamily	241832	60	172	7.18E-64	196.255	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26704 - 	CGI_10000812	superfamily	248020	1	263	1.05E-18	83.9499	cl17466	Sulfatase superfamily	N	 - 	Sulfatase; Sulfatase.  
Q#26705 - 	CGI_10000822	superfamily	245201	42	132	8.33E-09	54.5202	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26707 - 	CGI_10000851	superfamily	191331	148	334	3.75E-29	113.662	cl05293	RNA_pol_Rpc82 superfamily	 - 	 - 	"RNA polymerase III subunit RPC82; This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa."
Q#26707 - 	CGI_10000851	superfamily	191971	7	68	7.71E-11	57.9932	cl07012	HTH_9 superfamily	 - 	 - 	"RNA polymerase III subunit RPC82 helix-turn-helix domain; This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix."
Q#26708 - 	CGI_10000869	superfamily	245206	3	271	5.35E-139	396.817	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#26710 - 	CGI_10000871	superfamily	149426	8	157	1.18E-26	104.4	cl18038	SEFIR superfamily	 - 	 - 	"SEFIR domain; This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways."
Q#26712 - 	CGI_10000872	superfamily	245205	19	77	0.000284618	36.0617	cl09930	RPA_2b-aaRSs_OBF_like superfamily	C	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26715 - 	CGI_10000883	superfamily	241578	17	135	4.21E-09	51.6864	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26717 - 	CGI_10000887	superfamily	246680	84	151	0.00486941	33.0778	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#26723 - 	CGI_10000874	superfamily	245205	151	225	1.36E-06	46.0769	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26723 - 	CGI_10000874	superfamily	245531	404	480	0.000480543	38.499	cl11158	BEN superfamily	 - 	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#26725 - 	CGI_10000893	superfamily	241832	74	177	4.58E-41	141.686	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26725 - 	CGI_10000893	superfamily	241832	198	299	6.22E-37	130.516	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26725 - 	CGI_10000893	superfamily	241832	321	373	3.05E-24	95.4624	cl00388	Thioredoxin_like superfamily	C	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26725 - 	CGI_10000893	superfamily	241832	17	61	7.52E-08	49.7791	cl00388	Thioredoxin_like superfamily	N	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26727 - 	CGI_10000902	superfamily	217836	2	47	4.33E-11	55.3645	cl09556	Sas10_Utp3 superfamily	N	 - 	"Sas10/Utp3/C1D family; This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex. It also includes the human C1D protein and Saccharomyces cerevisiae YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs, and Sas10 which has been identified as a regulator of chromatin silencing. This family also includes the human protein Neuroguidin an initiation factor 4E (eIF4E) binding protein."
Q#26730 - 	CGI_10000897	superfamily	217648	328	646	1.44E-76	253.429	cl15557	Glyco_hydro_65m superfamily	 - 	 - 	"Glycosyl hydrolase family 65 central catalytic domain; This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu. The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom. The catalytic domain also forms the majority of the dimerisation interface."
Q#26732 - 	CGI_10000912	superfamily	217473	163	307	3.05E-26	108.992	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#26732 - 	CGI_10000912	superfamily	216981	641	670	0.00763493	35.5862	cl17087	OTU superfamily	C	 - 	"OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases."
Q#26733 - 	CGI_10000908	superfamily	242406	1	63	0.0029917	34.1041	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#26735 - 	CGI_10000913	superfamily	215647	969	1191	5.68E-10	59.9297	cl18338	7tm_2 superfamily	 - 	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#26736 - 	CGI_10000910	superfamily	248097	13	106	1.19E-19	81.9278	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26736 - 	CGI_10000910	superfamily	248097	129	173	8.96E-06	43.0226	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26737 - 	CGI_10000916	superfamily	216363	72	177	6.20E-25	94.0741	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#26739 - 	CGI_10000932	superfamily	218118	31	80	1.10E-08	47.6089	cl04552	CD225 superfamily	C	 - 	"Interferon-induced transmembrane protein; This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression."
Q#26740 - 	CGI_10000934	superfamily	247905	228	387	1.18E-23	95.3824	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#26740 - 	CGI_10000934	superfamily	247805	8	217	8.41E-56	185.766	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26741 - 	CGI_10000935	superfamily	247805	86	226	8.00E-29	112.431	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26741 - 	CGI_10000935	superfamily	243778	469	559	2.14E-39	139.667	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#26741 - 	CGI_10000935	superfamily	247905	313	372	2.45E-06	46.0509	cl17351	HELICc superfamily	C	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#26741 - 	CGI_10000935	superfamily	219532	593	633	7.35E-06	44.6126	cl06657	OB_NTP_bind superfamily	C	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#26745 - 	CGI_10007265	superfamily	241554	1346	1485	7.44E-38	141.244	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#26745 - 	CGI_10007265	superfamily	247723	386	454	8.72E-18	81.1596	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#26745 - 	CGI_10007265	superfamily	247723	294	365	2.26E-17	80.0388	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#26745 - 	CGI_10007265	superfamily	247723	473	541	0.00130316	39.2105	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#26745 - 	CGI_10007265	superfamily	241554	1153	1305	1.86E-45	164.366	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#26745 - 	CGI_10007265	superfamily	241554	1662	1773	1.75E-21	93.8643	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#26745 - 	CGI_10007265	superfamily	247723	548	616	6.08E-10	58.0476	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#26745 - 	CGI_10007265	superfamily	219837	109	176	0.000354025	41.5003	cl07160	Fork_head_N superfamily	C	 - 	"Forkhead N-terminal region; The region described in this family is found towards the N-terminus of various eukaryotic fork head/HNF-3-related transcription factors (which contain the pfam00250 domain). These proteins play key roles in embryogenesis, maintenance of differentiated cell states, and tumorigenesis."
Q#26747 - 	CGI_10007267	superfamily	192997	1042	1198	1.20E-34	133.091	cl18184	Sterol-sensing superfamily	 - 	 - 	"Sterol-sensing domain of SREBP cleavage-activation; Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus."
Q#26747 - 	CGI_10007267	superfamily	243092	2335	2483	7.28E-06	49.2556	cl02567	WD40 superfamily	N	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#26748 - 	CGI_10007268	superfamily	241862	268	430	6.54E-19	85.1004	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#26749 - 	CGI_10007269	superfamily	241596	12	55	7.71E-05	35.6527	cl00081	HLH superfamily	N	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#26750 - 	CGI_10007270	superfamily	220692	26	326	3.39E-15	74.5481	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#26753 - 	CGI_10000920	superfamily	215691	237	286	2.07E-06	44.499	cl15766	Pyr_redox superfamily	N	 - 	Pyridine nucleotide-disulphide oxidoreductase; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
Q#26753 - 	CGI_10000920	superfamily	248054	60	85	0.00613321	33.9848	cl17500	NAD_binding_8 superfamily	C	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#26754 - 	CGI_10000921	superfamily	243066	41	172	4.12E-08	48.7677	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#26755 - 	CGI_10000906	superfamily	218713	120	299	2.89E-74	228.766	cl05332	MRG superfamily	 - 	 - 	"MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif."
Q#26756 - 	CGI_10000947	superfamily	215754	231	322	9.87E-22	87.694	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26756 - 	CGI_10000947	superfamily	215754	134	225	8.40E-20	82.3012	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26756 - 	CGI_10000947	superfamily	215754	26	132	2.26E-13	64.582	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26758 - 	CGI_10000936	superfamily	245206	5	61	2.37E-08	47.8269	cl09931	NADB_Rossmann superfamily	NC	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#26760 - 	CGI_10000950	superfamily	248097	1	61	5.55E-09	47.645	cl17543	C1q superfamily	N	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26761 - 	CGI_10000958	superfamily	245201	173	216	2.02E-06	45.7914	cl09925	PKc_like superfamily	NC	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26762 - 	CGI_10000953	superfamily	245201	1	157	1.21E-104	306.649	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26763 - 	CGI_10000960	superfamily	243040	1	57	2.40E-30	107.497	cl02447	CRD_FZ superfamily	N	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#26765 - 	CGI_10000889	superfamily	245227	16	68	4.93E-35	122.704	cl10013	Glycosyltransferase_GTB_type superfamily	C	 - 	"Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility."
Q#26766 - 	CGI_10000975	superfamily	241748	1	191	1.79E-75	230.537	cl00279	APP_MetAP superfamily	N	 - 	"A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation."
Q#26770 - 	CGI_10000993	superfamily	248469	65	154	3.02E-16	73.9435	cl17915	HAD_like superfamily	C	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#26770 - 	CGI_10000993	superfamily	248469	259	311	1.46E-07	48.9055	cl17915	HAD_like superfamily	N	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#26772 - 	CGI_10000954	superfamily	245206	61	307	1.06E-117	343.03	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#26773 - 	CGI_10000955	superfamily	241831	62	124	8.46E-16	67.5814	cl00386	BolA superfamily	 - 	 - 	BolA-like protein; This family consist of the morphoprotein BolA from E. coli and its various homologues. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5.
Q#26775 - 	CGI_10000877	superfamily	238012	26	64	7.78E-05	40.4154	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#26775 - 	CGI_10000877	superfamily	238012	122	153	0.00627126	34.6374	cl11390	EGF_Lam superfamily	N	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#26776 - 	CGI_10001003	superfamily	243146	256	302	4.89E-09	51.8934	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#26776 - 	CGI_10001003	superfamily	243146	218	267	6.24E-07	46.0123	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#26777 - 	CGI_10001007	superfamily	241568	151	206	4.46E-05	40.1388	cl00043	CCP superfamily	 - 	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#26777 - 	CGI_10001007	superfamily	241619	45	116	0.00397976	34.4801	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#26782 - 	CGI_10001001	superfamily	247724	2	187	6.27E-75	226.005	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26783 - 	CGI_10001013	superfamily	202711	40	204	2.39E-56	179.856	cl04190	Mob1_phocein superfamily	 - 	 - 	"Mob1/phocein family; Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin."
Q#26787 - 	CGI_10000977	superfamily	241578	1	77	1.12E-11	56.531	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#26789 - 	CGI_10001031	superfamily	243175	91	206	1.99E-57	179.315	cl02776	GST_C_family superfamily	 - 	 - 	"C-terminal, alpha helical domain of the Glutathione S-transferase family; Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of  glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction  and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases."
Q#26789 - 	CGI_10001031	superfamily	241832	2	73	4.98E-36	123.064	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#26790 - 	CGI_10001033	superfamily	247794	2	334	8.29E-164	464.957	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#26791 - 	CGI_10001034	superfamily	241952	57	520	0	567.378	cl00566	PntB superfamily	 - 	 - 	NAD/NADP transhydrogenase beta subunit [Energy production and conversion]
Q#26791 - 	CGI_10001034	superfamily	204792	6	76	3.08E-06	45.7822	cl13395	DUF3464 superfamily	NC	 - 	Protein of unknown function (DUF3464); This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 137 to 196 amino acids in length.
Q#26794 - 	CGI_10001009	superfamily	245596	36	139	5.05E-45	148.114	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#26798 - 	CGI_10001014	superfamily	218802	117	146	0.00671562	35.415	cl05462	DUF862 superfamily	N	 - 	"PPPDE putative peptidase domain; The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)."
Q#26799 - 	CGI_10001039	superfamily	247755	1	112	7.40E-41	138.068	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26800 - 	CGI_10001017	superfamily	191582	22	99	0.00024704	36.4385	cl05954	DUF1180 superfamily	NC	 - 	Protein of unknown function (DUF1180); This family consists of several hypothetical mammalian proteins of around 190 residues in length. The function of this family is unknown.
Q#26802 - 	CGI_10001041	superfamily	241609	29	97	2.89E-24	88.9743	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#26803 - 	CGI_10001044	superfamily	245205	134	208	4.91E-07	46.0769	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26803 - 	CGI_10001044	superfamily	245205	19	98	0.000532639	37.2173	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26805 - 	CGI_10001025	superfamily	241868	5	85	1.17E-10	54.0702	cl00447	Nudix_Hydrolase superfamily	N	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#26806 - 	CGI_10000854	superfamily	128937	3	69	7.55E-15	65.3616	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#26806 - 	CGI_10000854	superfamily	128937	79	142	5.63E-10	51.8796	cl02743	DM9 superfamily	 - 	 - 	Repeats found in Drosophila proteins; Repeats found in Drosophila proteins.  
Q#26807 - 	CGI_10001070	superfamily	241583	125	285	8.69E-30	113.05	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#26807 - 	CGI_10001070	superfamily	241571	290	352	0.000751857	37.3919	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#26809 - 	CGI_10001112	superfamily	220662	81	141	0.00444554	34.7386	cl10947	DUF2217 superfamily	NC	 - 	Uncharacterized conserved protein (DUF2217); This is a family of conserved proteins of from 500 - 600 residues found from worms to humans. Its function is not known.
Q#26813 - 	CGI_10001111	superfamily	217925	206	286	1.18E-05	43.2637	cl04417	Ctr superfamily	N	 - 	"Ctr copper transporter family; The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport."
Q#26817 - 	CGI_10001094	superfamily	222150	59	84	0.00148518	33.1342	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#26820 - 	CGI_10001130	superfamily	247794	6	160	3.14E-23	92.5848	cl17240	FDH_GDH_like superfamily	C	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#26821 - 	CGI_10001131	superfamily	247794	11	82	4.01E-34	119.549	cl17240	FDH_GDH_like superfamily	N	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#26822 - 	CGI_10001132	superfamily	247792	20	70	5.61E-07	47.0552	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#26822 - 	CGI_10001132	superfamily	241563	157	199	0.0017981	36.6884	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26826 - 	CGI_10001193	superfamily	218200	1	107	4.80E-29	112.075	cl04660	Glyco_transf_54 superfamily	N	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#26827 - 	CGI_10001194	superfamily	218200	30	258	8.60E-81	253.058	cl04660	Glyco_transf_54 superfamily	 - 	 - 	"N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region; The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein."
Q#26827 - 	CGI_10001194	superfamily	242729	329	346	0.00881929	36.4795	cl01823	DUF2331 superfamily	N	 - 	Uncharacterized protein conserved in bacteria (DUF2331); Members of this family of hypothetical bacterial proteins have no known function.
Q#26831 - 	CGI_10001157	superfamily	220704	17	291	5.19E-142	404.353	cl11011	DUF2419 superfamily	 - 	 - 	"Protein of unknown function (DUF2419); This is a family of conserved proteins found from plants to humans. The function is not known. A few members are annotated as being cobyrinic acid a,c-diamide synthetase but this could not be confirmed."
Q#26832 - 	CGI_10001158	superfamily	243064	28	58	5.56E-06	39.7062	cl02512	NTR_like superfamily	NC	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#26834 - 	CGI_10001078	superfamily	217685	10	114	7.93E-20	83.1524	cl04225	Cu2_monoox_C superfamily	N	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#26835 - 	CGI_10001225	superfamily	245201	219	335	2.89E-17	78.0473	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26838 - 	CGI_10001221	superfamily	247861	104	214	1.61E-15	69.8479	cl17307	SpoU_methylase superfamily	C	 - 	SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
Q#26838 - 	CGI_10001221	superfamily	244541	10	81	1.23E-13	62.9388	cl06870	SpoU_sub_bind superfamily	 - 	 - 	RNA 2'-O ribose methyltransferase substrate binding; This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.
Q#26840 - 	CGI_10001223	superfamily	247792	189	230	3.93E-10	55.5296	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#26842 - 	CGI_10001235	superfamily	241563	61	97	0.000168337	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26843 - 	CGI_10001236	superfamily	192604	217	264	8.36E-11	56.5386	cl11135	PACT_coil_coil superfamily	C	 - 	"Pericentrin-AKAP-450 domain of centrosomal targeting protein; This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly."
Q#26846 - 	CGI_10001244	superfamily	247038	152	213	0.000306295	38.2046	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#26846 - 	CGI_10001244	superfamily	247038	32	92	0.000708734	37.0114	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#26847 - 	CGI_10001263	superfamily	219849	168	283	1.19E-38	140.397	cl09597	RIH_assoc superfamily	 - 	 - 	"RyR and IP3R Homology associated; This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815."
Q#26849 - 	CGI_10001262	superfamily	241565	467	518	2.49E-11	60.0278	cl00038	BRCT superfamily	C	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#26853 - 	CGI_10001270	superfamily	248458	59	387	1.32E-17	82.3617	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#26854 - 	CGI_10001281	superfamily	243250	190	609	9.16E-175	506.801	cl02959	Glyco_hydro_9 superfamily	 - 	 - 	Glycosyl hydrolase family 9; Glycosyl hydrolase family 9.  
Q#26854 - 	CGI_10001281	superfamily	248295	77	172	0.000687539	38.543	cl17741	CBM_2 superfamily	 - 	 - 	Cellulose binding domain; Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria.
Q#26857 - 	CGI_10001297	superfamily	245819	299	476	4.47E-65	216.291	cl11967	Nucleotidyl_cyc_III superfamily	 - 	 - 	"Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's).  The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways."
Q#26857 - 	CGI_10001297	superfamily	245201	3	228	3.64E-30	120.719	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26857 - 	CGI_10001297	superfamily	219526	245	286	4.68E-06	47.2287	cl06648	HNOBA superfamily	N	 - 	"Heme NO binding associated; The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals."
Q#26858 - 	CGI_10001287	superfamily	245823	1	441	1.07E-154	454.047	cl11976	SNF superfamily	 - 	 - 	Sodium:neurotransmitter symporter family; Sodium:neurotransmitter symporter family.  
Q#26859 - 	CGI_10001190	superfamily	238191	25	499	1.45E-121	368.968	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#26860 - 	CGI_10001191	superfamily	220695	102	239	9.89E-09	54.5071	cl18571	7TM_GPCR_Srx superfamily	NC	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#26861 - 	CGI_10001300	superfamily	192604	72	99	0.00139536	33.0414	cl11135	PACT_coil_coil superfamily	C	 - 	"Pericentrin-AKAP-450 domain of centrosomal targeting protein; This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly."
Q#26865 - 	CGI_10001310	superfamily	245206	133	371	1.63E-113	334.957	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#26865 - 	CGI_10001310	superfamily	243072	1	119	1.71E-25	99.7654	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26866 - 	CGI_10001311	superfamily	243072	305	431	1.75E-26	105.543	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26866 - 	CGI_10001311	superfamily	243072	502	600	1.58E-17	79.735	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26866 - 	CGI_10001311	superfamily	243072	180	330	1.32E-15	74.3422	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#26874 - 	CGI_10001329	superfamily	241563	72	108	5.08E-05	41.1188	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26875 - 	CGI_10001305	superfamily	243035	8	45	4.31E-05	36.809	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26878 - 	CGI_10001346	superfamily	248012	2	125	6.24E-11	55.3573	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#26879 - 	CGI_10001347	superfamily	245201	11	110	0.00146832	40.5432	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26880 - 	CGI_10001348	superfamily	216599	11	325	3.89E-157	450.574	cl18372	B56 superfamily	 - 	 - 	"Protein phosphatase 2A regulatory B subunit (B56 family); Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also pfam01240), this family is called the B56 family."
Q#26884 - 	CGI_10001375	superfamily	183292	1	32	0.00633887	36.338	cl18135	PRK11728 superfamily	C	 - 	hydroxyglutarate oxidase; Provisional
Q#26886 - 	CGI_10001397	superfamily	245814	17	74	3.17E-05	42.0911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#26888 - 	CGI_10001428	superfamily	248097	179	305	3.44E-23	92.3282	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26890 - 	CGI_10001293	superfamily	217380	131	408	4.60E-103	313.492	cl18406	TTL superfamily	 - 	 - 	"Tubulin-tyrosine ligase family; Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain."
Q#26891 - 	CGI_10001331	superfamily	245622	176	338	6.35E-30	112.703	cl11446	Rhomboid superfamily	 - 	 - 	"Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite."
Q#26891 - 	CGI_10001331	superfamily	247856	63	90	0.000666924	37.5273	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#26893 - 	CGI_10001431	superfamily	247057	102	138	5.17E-07	47.0888	cl15755	SAM_superfamily superfamily	N	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#26894 - 	CGI_10001432	superfamily	243146	291	336	3.16E-06	44.5746	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#26894 - 	CGI_10001432	superfamily	243146	340	385	0.000145861	39.739	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#26894 - 	CGI_10001432	superfamily	243146	259	302	0.000335913	38.6935	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#26900 - 	CGI_10001456	superfamily	245603	307	374	0.00107496	37.5716	cl11403	pepsin_retropepsin_like superfamily	C	 - 	"Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family)."
Q#26901 - 	CGI_10001457	superfamily	243179	90	147	1.37E-13	63.1542	cl02781	tetraspanin_LEL superfamily	N	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#26903 - 	CGI_10001459	superfamily	220695	31	147	0.00211045	37.9435	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#26904 - 	CGI_10001382	superfamily	247755	839	1060	1.45E-104	330.236	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26904 - 	CGI_10001382	superfamily	247755	2	209	1.59E-102	324.843	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26908 - 	CGI_10001505	superfamily	218284	110	171	3.53E-07	46.4787	cl04786	SOUL superfamily	NC	 - 	SOUL heme-binding protein; This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Q#26909 - 	CGI_10001506	superfamily	246679	42	169	2.35E-57	178.1	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#26914 - 	CGI_10001325	superfamily	193257	61	283	6.81E-65	219.857	cl15086	AAA_9 superfamily	 - 	 - 	"ATP-binding dynein motor region D5; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop."
Q#26914 - 	CGI_10001325	superfamily	193253	4	35	0.00669367	38.4793	cl15084	MT superfamily	N	 - 	"Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component."
Q#26915 - 	CGI_10001550	superfamily	243037	282	335	1.27E-20	86.6203	cl02440	DAGK_acc superfamily	C	 - 	Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
Q#26915 - 	CGI_10001550	superfamily	248019	1	18	0.00177641	36.4933	cl17465	DAGK_cat superfamily	NC	 - 	"Diacylglycerol kinase catalytic domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family."
Q#26916 - 	CGI_10001551	superfamily	243037	1	74	2.07E-27	104.339	cl02440	DAGK_acc superfamily	N	 - 	Diacylglycerol kinase accessory domain; Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
Q#26917 - 	CGI_10001552	superfamily	247057	17	81	4.14E-32	109.039	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#26918 - 	CGI_10001553	superfamily	247805	82	279	8.30E-88	268.969	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26918 - 	CGI_10001553	superfamily	247905	290	415	7.03E-32	118.109	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#26919 - 	CGI_10001554	superfamily	247805	1	168	3.94E-82	250.48	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#26919 - 	CGI_10001554	superfamily	247905	179	308	1.31E-32	118.88	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#26920 - 	CGI_10001578	superfamily	241580	2	71	6.60E-10	54.6267	cl00061	FH superfamily	 - 	 - 	"Forkhead (FH), also known as a "winged helix".  FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix."
Q#26923 - 	CGI_10001581	superfamily	241563	35	77	3.69E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26924 - 	CGI_10001562	superfamily	241574	292	346	1.54E-17	81.0929	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#26924 - 	CGI_10001562	superfamily	241574	416	500	9.01E-10	57.5957	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#26925 - 	CGI_10001630	superfamily	245840	35	139	0.00262846	35.7904	cl12022	Ribosomal_L18e superfamily	C	 - 	Ribosomal protein L18e/L15; This family includes eukaryotic L18 as well as prokaryotic L15.
Q#26926 - 	CGI_10001722	superfamily	245211	301	886	0	621.485	cl09939	RNR_PFL superfamily	 - 	 - 	"Ribonucleotide reductase and Pyruvate formate lyase; Ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL) are believed to have diverged from a common ancestor. They have a structurally similar ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs use a diiron-tyrosyl radical while Class II RNRs use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. PFL, an essential enzyme in anaerobic bacteria, catalyzes the conversion of pyruvate and CoA to acteylCoA and formate in a mechanism that uses a glycyl radical."
Q#26926 - 	CGI_10001722	superfamily	217585	23	114	8.06E-22	91.9244	cl12279	ATP-cone superfamily	 - 	 - 	ATP cone domain; ATP cone domain.  
Q#26928 - 	CGI_10001726	superfamily	218479	149	284	5.04E-46	153.424	cl04965	DapB_C superfamily	 - 	 - 	"Dihydrodipicolinate reductase, C-terminus; Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain."
Q#26928 - 	CGI_10001726	superfamily	216304	4	145	2.08E-12	61.8772	cl18363	DapB_N superfamily	 - 	 - 	"Dihydrodipicolinate reductase, N-terminus; Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH."
Q#26929 - 	CGI_10001729	superfamily	247861	40	183	5.76E-38	129.554	cl17307	SpoU_methylase superfamily	 - 	 - 	SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
Q#26930 - 	CGI_10001730	superfamily	241550	211	312	1.07E-55	186.631	cl00015	nt_trans superfamily	N	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#26930 - 	CGI_10001730	superfamily	241550	5	116	2.40E-45	158.896	cl00015	nt_trans superfamily	C	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#26930 - 	CGI_10001730	superfamily	245839	371	482	9.75E-15	71.439	cl12020	Anticodon_Ia_like superfamily	N	 - 	"Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway."
Q#26931 - 	CGI_10001731	superfamily	247740	75	291	1.69E-57	185.415	cl17186	TIM_phosphate_binding superfamily	 - 	 - 	"TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN."
Q#26932 - 	CGI_10001732	superfamily	244842	149	572	0	813.611	cl08031	ThiC superfamily	 - 	 - 	"ThiC family; ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis. The precise catalytic function of ThiC is still not known. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis."
Q#26932 - 	CGI_10001732	superfamily	222303	18	108	2.43E-20	86.3897	cl16343	ThiC-associated superfamily	 - 	 - 	"ThiC-associated domain; This domain is most frequently found at the N-terminus of the ThiC family of proteins, pfam01964. The function is not known."
Q#26934 - 	CGI_10001549	superfamily	218280	33	63	1.66E-06	42.2065	cl04781	Rad21_Rec8_N superfamily	NC	 - 	"N terminus of Rad21 / Rec8 like protein; This family represents a conserved N-terminal region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Members of this family mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation."
Q#26935 - 	CGI_10001743	superfamily	243035	31	145	9.44E-14	66.4893	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26935 - 	CGI_10001743	superfamily	243035	169	279	4.74E-07	47.2294	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26936 - 	CGI_10001744	superfamily	242274	421	534	1.11E-06	47.7922	cl01053	SGNH_hydrolase superfamily	N	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#26937 - 	CGI_10001603	superfamily	248469	13	123	4.40E-09	52.7575	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#26937 - 	CGI_10001603	superfamily	248469	166	231	7.24E-08	49.2907	cl17915	HAD_like superfamily	N	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#26938 - 	CGI_10001604	superfamily	245201	147	430	0	526.318	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#26938 - 	CGI_10001604	superfamily	243090	14	145	4.14E-38	136.561	cl02565	RGS superfamily	 - 	 - 	"Regulator of G protein signaling (RGS) domain superfamily; The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision."
Q#26939 - 	CGI_10001989	superfamily	215763	207	244	2.92E-07	45.6739	cl02815	HTH_AraC superfamily	 - 	 - 	"Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerisation domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilised when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added."
Q#26940 - 	CGI_10001990	superfamily	182155	1	296	1.66E-144	411.511	cl08072	PRK09936 superfamily	 - 	 - 	hypothetical protein; Provisional
Q#26941 - 	CGI_10001991	superfamily	241593	126	228	4.47E-28	103.495	cl00075	HATPase_c superfamily	 - 	 - 	"Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins"
Q#26941 - 	CGI_10001991	superfamily	241595	11	73	5.16E-12	58.378	cl00080	HisKA superfamily	 - 	 - 	"Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes."
Q#26942 - 	CGI_10001993	superfamily	248290	4	116	3.10E-35	122.684	cl17736	REC superfamily	 - 	 - 	"Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers"
Q#26942 - 	CGI_10001993	superfamily	247909	128	221	3.43E-33	116.78	cl17355	trans_reg_C superfamily	 - 	 - 	"Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase."
Q#26943 - 	CGI_10001995	superfamily	243005	1	102	4.29E-55	169.277	cl02363	CusF_Ec superfamily	 - 	 - 	"Copper binding periplasmic protein CusF; CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein."
Q#26944 - 	CGI_10001996	superfamily	222128	199	300	6.97E-12	61.2399	cl18638	HlyD_3 superfamily	 - 	 - 	HlyD family secretion protein; This is a family of largely bacterial haemolysin translocator HlyD proteins.
Q#26947 - 	CGI_10002000	superfamily	241917	2	211	8.39E-59	184.708	cl00514	Nitro_FMN_reductase superfamily	 - 	 - 	"Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer,  utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase."
Q#26948 - 	CGI_10002001	superfamily	242218	1	372	0	709.385	cl00954	GCS2 superfamily	 - 	 - 	"Glutamate-cysteine ligase family 2(GCS2); Also known as gamma-glutamylcysteine synthetase and gamma-ECS (EC:6.3.2.2). This enzyme catalyzes the first and rate limiting step in de novo glutathione biosynthesis. Members of this family are found in archaea, bacteria and plants. May and Leaver discuss the possible evolutionary origins of glutamate-cysteine ligase enzymes in different organisms and suggest that it evolved independently in different eukaryotes, from an ancestral bacterial enzyme. They also state that Arabidopsis thaliana gamma-glutamylcysteine synthetase is structurally unrelated to mammalian, yeast and Escherichia coli homologues. In plants, there are separate cytosolic and chloroplast forms of the enzyme."
Q#26949 - 	CGI_10002002	superfamily	247798	67	764	7.69E-117	369.088	cl17244	OM_channels superfamily	 - 	 - 	"Porin superfamily.  These outer membrane channels share a beta-barrel structure that differ in strand and shear number.  Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20), which associate as trimers. Maltoporin-like channels have specificities for various sugars and form 18 beta-stranded barrels (18,22), which associate as trimers. Ligand-gated protein channels cooperate with a TonB associated inner membrane complex to actively transport ligands via the proton motive force and they form monomeric, (22,24) barrels. The 150-200 N-terminal residues form a plug that blocks the channel from the periplasmic end."
Q#26950 - 	CGI_10002003	superfamily	221235	3	130	2.91E-39	137.12	cl13275	DUF3327 superfamily	 - 	 - 	Domain of unknown function (DUF3327); Domain of unknown function (DUF3327).  
Q#26950 - 	CGI_10002003	superfamily	225375	133	284	2.77E-10	58.9569	cl18715	COG2819 superfamily	C	 - 	Predicted hydrolase of the alpha/beta superfamily [General function prediction only]
Q#26951 - 	CGI_10002004	superfamily	247692	511	1000	0	567.843	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#26951 - 	CGI_10002004	superfamily	245209	1022	1084	1.05E-08	53.7126	cl09936	PP-binding superfamily	 - 	 - 	Phosphopantetheine attachment site; A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Vibrio anguillarum angR has the attachment serine replaced by an alanine.
Q#26952 - 	CGI_10002006	superfamily	247755	1	170	8.30E-56	177.628	cl17201	ABC_ATPase superfamily	N	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26954 - 	CGI_10001608	superfamily	241862	200	349	1.13E-21	91.6488	cl00437	COG0428 superfamily	N	 - 	Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]
Q#26955 - 	CGI_10001609	superfamily	247725	2	17	0.000819563	33.8994	cl17171	PH-like superfamily	N	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#26956 - 	CGI_10001115	superfamily	245205	139	217	8.29E-10	54.1661	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26956 - 	CGI_10001115	superfamily	245205	19	98	0.000822439	36.8321	cl09930	RPA_2b-aaRSs_OBF_like superfamily	 - 	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26958 - 	CGI_10001443	superfamily	247684	51	470	4.60E-87	279.933	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#26959 - 	CGI_10001444	superfamily	243035	1	64	0.00759993	31.051	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#26960 - 	CGI_10002078	superfamily	244888	1	274	1.20E-78	242.963	cl08282	Acyl_transf_1 superfamily	 - 	 - 	Acyl transferase domain; Acyl transferase domain.  
Q#26961 - 	CGI_10002080	superfamily	247755	206	435	1.53E-111	331.068	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26961 - 	CGI_10002080	superfamily	241857	64	192	3.62E-16	76.1632	cl00427	TM_PBP2 superfamily	C	 - 	"Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. For these transporters the ABCs and TMs are on independent polypeptide chains. These systems transport a diverse range of substrates. Most are specific for a single substrate or a group of related substrates; however some transporters are more promiscuous, transporting structurally diverse substrates such as the histidine/lysine and arginine transporter in Enterobacteriaceae. In the latter case, this is achieved through binding different PBPs with different specificities to the TMs. For other promiscuous transporters such as the multiple-sugar transporter Msm of Streptococcus mutans, the PBP has a wide substrate specificity. These transporters include the maltose-maltodextrin, phosphate and sulfate transporters, among others."
Q#26962 - 	CGI_10002081	superfamily	241857	406	613	2.55E-21	92.3416	cl00427	TM_PBP2 superfamily	 - 	 - 	"Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. For these transporters the ABCs and TMs are on independent polypeptide chains. These systems transport a diverse range of substrates. Most are specific for a single substrate or a group of related substrates; however some transporters are more promiscuous, transporting structurally diverse substrates such as the histidine/lysine and arginine transporter in Enterobacteriaceae. In the latter case, this is achieved through binding different PBPs with different specificities to the TMs. For other promiscuous transporters such as the multiple-sugar transporter Msm of Streptococcus mutans, the PBP has a wide substrate specificity. These transporters include the maltose-maltodextrin, phosphate and sulfate transporters, among others."
Q#26962 - 	CGI_10002081	superfamily	247850	35	347	6.99E-100	309.758	cl17296	PBP_like_2 superfamily	 - 	 - 	PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
Q#26963 - 	CGI_10002082	superfamily	247724	201	378	4.10E-65	208.852	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#26963 - 	CGI_10002082	superfamily	205348	33	125	0.00234039	35.9229	cl16145	GTP-bdg_N superfamily	 - 	 - 	"GTP-binding GTPase N-terminal; This is the N-terminal region of GTP-binding HflX-like proteins. The full-length members bind and interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP. This N-terminal region is necessary for stability of the whole protein."
Q#26964 - 	CGI_10002089	superfamily	247780	209	435	3.54E-102	306.385	cl17226	NAD_bind_amino_acid_DH superfamily	 - 	 - 	"NAD(P) binding domain of amino acid dehydrogenase-like proteins; Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel  domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts."
Q#26964 - 	CGI_10002089	superfamily	202408	63	190	1.77E-60	195.412	cl08368	ELFV_dehydrog_N superfamily	 - 	 - 	"Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Glu/Leu/Phe/Val dehydrogenase, dimerisation domain.  "
Q#26965 - 	CGI_10002090	superfamily	246713	3	120	1.63E-30	108.868	cl14786	ENDO3c superfamily	N	 - 	"endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases"
Q#26966 - 	CGI_10002091	superfamily	241739	104	249	8.59E-81	258.659	cl00268	class_II_aaRS-like_core superfamily	C	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#26966 - 	CGI_10002091	superfamily	241739	391	525	8.52E-56	191.635	cl00268	class_II_aaRS-like_core superfamily	N	 - 	"Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA.   PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial  ATP  phosphoribosyltransferase regulatory subunit HisZ."
Q#26966 - 	CGI_10002091	superfamily	245205	2	100	2.50E-31	118.778	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#26966 - 	CGI_10002091	superfamily	218125	525	614	2.41E-24	98.2955	cl18443	Bactofilin superfamily	 - 	 - 	"Polymer-forming cytoskeletal; This is a family of bactofilins, a functionally diverse class of cytoskeletal, polymer-forming, proteins that is widely conserved among bacteria. In the example species C. crescentus, two bactofilins assemble into a membrane-associated laminar structure that shows cell-cycle-dependent polar localisation and acts as a platform for the recruitment of a cell wall biosynthetic enzyme involved in polar morphogenesis. Bactofilins display distinct subcellular distributions and dynamics in different bacterial species, suggesting that they are versatile structural elements that have adopted a range of different cellular functions."
Q#26966 - 	CGI_10002091	superfamily	145868	282	371	3.56E-05	42.2402	cl08382	GAD superfamily	 - 	 - 	GAD domain; This domain is found in some members of the GatB and aspartyl tRNA synthetases.
Q#26967 - 	CGI_10002094	superfamily	247755	359	586	4.55E-95	293.363	cl17201	ABC_ATPase superfamily	 - 	 - 	"ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins."
Q#26967 - 	CGI_10002094	superfamily	216049	37	307	1.45E-33	128.943	cl18356	ABC_membrane superfamily	 - 	 - 	ABC transporter transmembrane region; This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions.
Q#26968 - 	CGI_10001813	superfamily	243034	276	372	2.02E-05	43.1376	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#26968 - 	CGI_10001813	superfamily	243034	161	270	0.000150165	40.4412	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#26968 - 	CGI_10001813	superfamily	248374	410	565	1.02E-61	202.999	cl17820	Asp_Arg_Hydrox superfamily	 - 	 - 	"Aspartyl/Asparaginyl beta-hydroxylase; Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyze oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalyzing oxidation of a free alpha-amino acid. The structure of proline 3-hydroxylase contains the conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. This family represent the arginine, asparagine and proline hydroxylases. The aspartyl/asparaginyl beta-hydroxylase (EC:1.14.11.16) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins."
Q#26970 - 	CGI_10001815	superfamily	248097	153	256	3.67E-09	52.6526	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#26970 - 	CGI_10001815	superfamily	221533	46	84	0.00354595	34.5948	cl13726	TMF_DNA_bd superfamily	N	 - 	"TATA element modulatory factor 1 DNA binding; This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells."
Q#26971 - 	CGI_10002228	superfamily	245818	57	212	4.33E-26	104.176	cl11966	Rel-Spo_like superfamily	 - 	 - 	"RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; The Rel-Spo superfamily includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain."
Q#26971 - 	CGI_10002228	superfamily	218331	367	505	5.71E-42	149.727	cl08427	PAP_RNA-bind superfamily	 - 	 - 	Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.
Q#26973 - 	CGI_10002230	superfamily	191179	3	437	0	538.418	cl04912	Menin superfamily	C	 - 	"Menin; MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23."
Q#26973 - 	CGI_10002230	superfamily	191179	614	712	5.79E-16	80.4153	cl04912	Menin superfamily	N	 - 	"Menin; MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23."
Q#26974 - 	CGI_10002231	superfamily	218652	39	86	0.000717403	36.5026	cl12311	CLPTM1 superfamily	C	 - 	"Cleft lip and palate transmembrane protein 1 (CLPTM1); This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family. This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis."
Q#26976 - 	CGI_10002026	superfamily	246612	44	281	2.93E-37	135.976	cl14057	BPL_LplA_LipB superfamily	 - 	 - 	"Biotin/lipoate A/B protein ligase family; This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Lipoate-protein ligase A (LPLA) catalyzes the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor."
Q#26978 - 	CGI_10002028	superfamily	241688	84	376	4.96E-89	271.732	cl00210	Isoprenoid_Biosyn_C1 superfamily	 - 	 - 	"Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD."
Q#26979 - 	CGI_10002029	superfamily	248388	3	167	2.50E-09	52.3309	cl17834	Ser_hydrolase superfamily	 - 	 - 	"Serine hydrolase; Members of this family have serine hydrolase activity. They contain a conserved serine hydrolase motif, GXSXG/A, where the serine is a putative nucleophile. This family has an alpha-beta hydrolase fold. Eukaryotic members of this family have a conserved LXCXE motif, which binds to retinoblastomas. This motif is absent from prokaryotic members of this family."
Q#26980 - 	CGI_10002030	superfamily	220792	6	104	1.22E-20	81.2983	cl11150	EPL1 superfamily	C	 - 	Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.
Q#26981 - 	CGI_10001734	superfamily	245862	54	266	5.10E-39	138.485	cl12076	THUMP superfamily	 - 	 - 	"THUMP domain, predicted to bind RNA; The THUMP domain is named after THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases. It is predicted to be an RNA-binding domain and  probably functions by delivering a variety of RNA modification enzymes to their targets."
Q#26982 - 	CGI_10001735	superfamily	192535	58	292	6.79E-06	46.0498	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#26984 - 	CGI_10001737	superfamily	215754	113	214	4.19E-17	74.5972	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26984 - 	CGI_10001737	superfamily	215754	21	112	6.54E-15	68.434	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26984 - 	CGI_10001737	superfamily	215754	216	303	2.09E-14	67.2784	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#26986 - 	CGI_10001749	superfamily	241563	68	109	2.84E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#26987 - 	CGI_10001716	superfamily	243092	37	318	4.28E-26	105.495	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#26989 - 	CGI_10001718	superfamily	207794	15	288	8.51E-123	363.841	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#26989 - 	CGI_10001718	superfamily	207794	291	422	2.06E-54	186.264	cl02948	GH20_hexosaminidase superfamily	N	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#26996 - 	CGI_10001856	superfamily	248458	124	220	1.37E-07	50.0049	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#26997 - 	CGI_10001857	superfamily	248458	34	99	2.55E-06	45.3825	cl17904	MFS superfamily	NC	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27002 - 	CGI_10002072	superfamily	243310	60	161	1.42E-27	104.628	cl03120	ELO superfamily	C	 - 	"GNS1/SUR4 family; Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1."
Q#27004 - 	CGI_10001058	superfamily	245226	16	115	1.03E-12	61.9329	cl10012	DnaQ_like_exo superfamily	N	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#27006 - 	CGI_10009783	superfamily	245847	2	92	3.94E-09	49.4774	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#27007 - 	CGI_10009784	superfamily	247742	2	97	1.40E-08	51.3289	cl17188	enolase_like superfamily	N	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#27008 - 	CGI_10009785	superfamily	247742	19	50	5.03E-09	51.3289	cl17188	enolase_like superfamily	N	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#27009 - 	CGI_10009786	superfamily	245201	32	311	1.74E-162	489.254	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27009 - 	CGI_10009786	superfamily	149105	1000	1103	0.00129413	41.2665	cl12353	TMPIT superfamily	C	 - 	"TMPIT-like protein; A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this."
Q#27010 - 	CGI_10009787	superfamily	245879	96	170	0.000104555	40.4194	cl12116	DUSP superfamily	 - 	 - 	DUSP domain; The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Q#27011 - 	CGI_10009788	superfamily	243066	12	104	2.05E-21	82.9861	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27012 - 	CGI_10009789	superfamily	248097	30	152	8.21E-18	74.9942	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#27013 - 	CGI_10009790	superfamily	246918	80	124	9.22E-08	44.8851	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27024 - 	CGI_10013283	superfamily	247941	6	146	1.54E-08	50.0269	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#27025 - 	CGI_10013284	superfamily	247941	52	192	1.37E-05	42.3229	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#27026 - 	CGI_10013285	superfamily	247856	50	104	7.52E-07	46.3869	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27026 - 	CGI_10013285	superfamily	247856	177	231	0.00180305	36.3717	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27027 - 	CGI_10013286	superfamily	247856	403	457	7.18E-07	46.7721	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27027 - 	CGI_10013286	superfamily	243056	121	298	8.95E-38	138.208	cl02495	RabGAP-TBC superfamily	N	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#27029 - 	CGI_10013288	superfamily	217293	16	224	1.11E-58	194.774	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#27029 - 	CGI_10013288	superfamily	202474	231	340	2.50E-17	80.3905	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#27032 - 	CGI_10000915	superfamily	241563	65	103	4.78E-07	46.8967	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27032 - 	CGI_10000915	superfamily	128778	121	200	0.00414063	36.0887	cl17972	BBC superfamily	C	 - 	B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
Q#27036 - 	CGI_10007289	superfamily	247684	65	230	9.95E-39	139.72	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	C	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#27037 - 	CGI_10007290	superfamily	247684	43	306	4.37E-40	145.883	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#27039 - 	CGI_10007292	superfamily	221825	168	294	5.89E-07	50.7022	cl15135	DUF3827 superfamily	NC	 - 	"Domain of unknown function (DUF3827); This family contains the human KIAA1549 protein which has been found to be fused fused to BRAF gene in many cases of pilocytic astrocytomas. The fusion is due mainly to a tandem duplication of 2 Mb at 7q34. Although nothing is known about the function of KIAA1549 protein, the BRAF protein is a well characterized oncoprotein. It is a serine/threonine protein kinase which is implicated in MAP/ERK signalling, a critical pathway for the regulation of cell division, differentiation and secretion."
Q#27041 - 	CGI_10007294	superfamily	243072	222	330	1.88E-30	115.559	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27041 - 	CGI_10007294	superfamily	241565	354	427	5.75E-07	47.3163	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#27041 - 	CGI_10007294	superfamily	241565	463	558	0.000350899	38.8958	cl00038	BRCT superfamily	 - 	 - 	"Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks."
Q#27042 - 	CGI_10007295	superfamily	241594	1344	1700	4.35E-142	444.7	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#27042 - 	CGI_10007295	superfamily	241647	947	972	1.11E-06	47.5226	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#27042 - 	CGI_10007295	superfamily	241647	1127	1157	0.000617718	39.4334	cl00157	WW superfamily	 - 	 - 	Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Q#27042 - 	CGI_10007295	superfamily	246669	191	317	4.25E-44	158.721	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27043 - 	CGI_10007296	superfamily	247684	5	118	9.67E-18	78.3995	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#27044 - 	CGI_10025282	superfamily	219502	312	556	2.02E-68	221.549	cl06625	Nucleos_tra2_C superfamily	 - 	 - 	Na+ dependent nucleoside transporter C-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Q#27044 - 	CGI_10025282	superfamily	201962	130	200	7.20E-18	78.5716	cl03347	Nucleos_tra2_N superfamily	 - 	 - 	Na+ dependent nucleoside transporter N-terminus; This family consists of nucleoside transport proteins. Rat CNT 2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. Rat CNT 1 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Q#27044 - 	CGI_10025282	superfamily	219507	209	309	1.50E-08	52.6267	cl18514	Gate superfamily	 - 	 - 	"Nucleoside recognition; This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'."
Q#27045 - 	CGI_10025283	superfamily	245596	748	934	1.30E-70	236.821	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#27045 - 	CGI_10025283	superfamily	245596	569	626	6.83E-08	53.4656	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#27045 - 	CGI_10025283	superfamily	245596	664	719	1.16E-06	49.9988	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#27049 - 	CGI_10025287	superfamily	216363	58	166	4.37E-12	58.6358	cl08312	UPF0029 superfamily	 - 	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#27050 - 	CGI_10025288	superfamily	243152	132	221	1.70E-11	58.4542	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#27050 - 	CGI_10025288	superfamily	248086	29	85	3.86E-07	45.2394	cl17532	SH3_3 superfamily	 - 	 - 	Bacterial SH3 domain; Bacterial SH3 domain.  
Q#27051 - 	CGI_10025289	superfamily	222150	512	538	0.000415004	39.2973	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27051 - 	CGI_10025289	superfamily	219837	321	430	0.000549895	39.9595	cl07160	Fork_head_N superfamily	 - 	 - 	"Forkhead N-terminal region; The region described in this family is found towards the N-terminus of various eukaryotic fork head/HNF-3-related transcription factors (which contain the pfam00250 domain). These proteins play key roles in embryogenesis, maintenance of differentiated cell states, and tumorigenesis."
Q#27051 - 	CGI_10025289	superfamily	222150	625	647	0.000644599	38.9121	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27051 - 	CGI_10025289	superfamily	222150	541	564	0.00216807	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27051 - 	CGI_10025289	superfamily	222150	652	677	0.002423	37.3713	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27051 - 	CGI_10025289	superfamily	222150	596	620	0.00486098	36.2157	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27052 - 	CGI_10025290	superfamily	245814	433	497	4.74E-10	56.7287	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27052 - 	CGI_10025290	superfamily	245814	250	320	5.22E-09	53.6471	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27052 - 	CGI_10025290	superfamily	245814	332	408	1.11E-11	61.3672	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27052 - 	CGI_10025290	superfamily	245814	195	229	0.00152348	37.0997	cl11960	Ig superfamily	N	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27053 - 	CGI_10025291	superfamily	222150	131	156	5.84E-05	40.8381	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27053 - 	CGI_10025291	superfamily	222150	160	184	0.000149526	39.6825	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27053 - 	CGI_10025291	superfamily	222150	43	65	0.00064615	38.1417	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27056 - 	CGI_10025294	superfamily	243066	13	117	7.09E-24	96.5325	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27056 - 	CGI_10025294	superfamily	198867	125	223	1.79E-16	75.6579	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#27056 - 	CGI_10025294	superfamily	243146	357	405	8.40E-06	43.419	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27056 - 	CGI_10025294	superfamily	243146	325	368	6.91E-05	41.0047	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27056 - 	CGI_10025294	superfamily	243146	505	554	0.00200877	36.6574	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27062 - 	CGI_10025300	superfamily	241754	209	482	1.01E-88	278.3	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#27062 - 	CGI_10025300	superfamily	243859	30	94	2.32E-11	60.8066	cl04722	PLAC8 superfamily	C	 - 	PLAC8 family; This family includes the Placenta-specific gene 8 protein.
Q#27063 - 	CGI_10025301	superfamily	242406	24	104	0.00284028	33.7189	cl01271	DUF1768 superfamily	C	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#27064 - 	CGI_10025302	superfamily	214507	24	77	1.50E-05	37.7948	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#27065 - 	CGI_10025303	superfamily	217617	580	755	3.05E-21	93.6348	cl15988	Sulfotransfer_2 superfamily	N	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#27066 - 	CGI_10025304	superfamily	248458	1	126	2.84E-11	63.8721	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27068 - 	CGI_10025306	superfamily	241584	141	243	3.60E-09	54.0395	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#27068 - 	CGI_10025306	superfamily	245201	347	509	8.52E-36	134.201	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27070 - 	CGI_10025308	superfamily	220695	30	200	0.000531205	39.4843	cl18571	7TM_GPCR_Srx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#27071 - 	CGI_10025309	superfamily	177822	2	290	1.01E-20	89.2089	cl18088	PLN02164 superfamily	 - 	 - 	sulfotransferase
Q#27072 - 	CGI_10025310	superfamily	241566	271	321	3.79E-07	47.4868	cl00040	C1 superfamily	 - 	 - 	"Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis)."
Q#27077 - 	CGI_10025315	superfamily	241763	128	347	2.52E-95	284.902	cl00298	Peptidase_C1 superfamily	 - 	 - 	"C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues."
Q#27077 - 	CGI_10025315	superfamily	244586	43	98	2.04E-12	61.4906	cl07031	Inhibitor_I29 superfamily	 - 	 - 	Cathepsin propeptide inhibitor domain (I29); This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
Q#27078 - 	CGI_10025316	superfamily	247769	221	403	3.16E-09	55.0381	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#27083 - 	CGI_10025321	superfamily	219080	15	105	1.05E-07	45.7946	cl05851	DUF1115 superfamily	 - 	 - 	Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function.
Q#27084 - 	CGI_10025322	superfamily	217473	187	373	1.30E-25	107.066	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#27085 - 	CGI_10025323	superfamily	246680	1714	1783	1.28E-11	63.76	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#27086 - 	CGI_10025324	superfamily	247059	42	212	4.77E-101	293.194	cl15763	Clp_protease_like superfamily	 - 	 - 	"Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Another family included in this class of enzymes is the signal peptide peptidase A (SppA; S49) which is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Mutagenesis studies suggest that the catalytic center of SppA comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain. Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain. The third family included in this hierarchy is nodulation formation efficiency D (NfeD) which is a membrane-bound Clp-class protease and only found in bacteria and archaea. Majority of the NfeD genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named stomatin operon partner protein (STOPP). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 from Pyrococcus horikoshii has been shown to possess serine protease activity having a Ser-Lys catalytic dyad."
Q#27087 - 	CGI_10025325	superfamily	247724	57	208	2.53E-93	274.397	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27089 - 	CGI_10025327	superfamily	245201	26	280	1.43E-52	172.806	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27090 - 	CGI_10025328	superfamily	241622	335	425	7.42E-15	71.829	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#27090 - 	CGI_10025328	superfamily	246669	490	611	7.83E-22	93.0811	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27090 - 	CGI_10025328	superfamily	246669	842	984	2.14E-20	89.3693	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27092 - 	CGI_10025330	superfamily	241642	172	226	5.59E-13	62.513	cl00152	t_SNARE superfamily	 - 	 - 	"Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent"
Q#27092 - 	CGI_10025330	superfamily	241634	32	119	5.29E-09	52.3481	cl00143	SynN superfamily	 - 	 - 	"Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain"
Q#27094 - 	CGI_10025332	superfamily	247769	515	688	2.25E-08	53.4973	cl17215	HDc superfamily	 - 	 - 	Metal dependent phosphohydrolases with conserved 'HD' motif
Q#27094 - 	CGI_10025332	superfamily	248010	277	421	5.46E-26	105.541	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#27094 - 	CGI_10025332	superfamily	248010	121	229	6.10E-09	55.08	cl17456	GAF superfamily	 - 	 - 	"GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54."
Q#27097 - 	CGI_10025335	superfamily	243061	8	107	1.38E-41	135.162	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27099 - 	CGI_10025337	superfamily	243061	1	59	6.88E-22	88.553	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27100 - 	CGI_10025338	superfamily	222263	62	112	0.00887463	33.0601	cl16321	DDE_4_2 superfamily	C	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#27101 - 	CGI_10025339	superfamily	243061	373	473	3.52E-43	149.029	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27101 - 	CGI_10025339	superfamily	243061	36	136	1.64E-40	141.711	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27101 - 	CGI_10025339	superfamily	243061	139	235	1.21E-36	130.925	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27105 - 	CGI_10021709	superfamily	216363	7	73	6.34E-09	48.2354	cl08312	UPF0029 superfamily	N	 - 	Uncharacterized protein family UPF0029; Uncharacterized protein family UPF0029.  
Q#27107 - 	CGI_10021711	superfamily	245864	97	456	2.96E-81	261.059	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#27108 - 	CGI_10021712	superfamily	247799	397	459	1.76E-15	72.5927	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27108 - 	CGI_10021712	superfamily	247799	194	257	2.37E-14	69.1259	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27108 - 	CGI_10021712	superfamily	247799	301	366	1.54E-12	64.1183	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27108 - 	CGI_10021712	superfamily	247799	512	575	1.66E-12	63.7331	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27108 - 	CGI_10021712	superfamily	149918	725	753	3.55E-09	53.6633	cl07567	DUF1897 superfamily	C	 - 	"Domain of unknown function (DUF1897); This domain is found in Psi proteins produced by Drosophila, and in various eukaryotic hypothetical proteins. It has no known function."
Q#27109 - 	CGI_10021713	superfamily	217617	91	346	1.08E-28	111.739	cl15988	Sulfotransfer_2 superfamily	 - 	 - 	"Sulfotransferase family; This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate."
Q#27110 - 	CGI_10021714	superfamily	248097	88	181	1.02E-12	66.1346	cl17543	C1q superfamily	C	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#27110 - 	CGI_10021714	superfamily	245213	321	361	0.00252437	36.9432	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27110 - 	CGI_10021714	superfamily	238012	469	531	0.00771948	35.4078	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#27114 - 	CGI_10021718	superfamily	241794	218	339	8.29E-37	129.847	cl00334	Ribosomal_S9 superfamily	 - 	 - 	Ribosomal protein S9/S16; This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes.
Q#27116 - 	CGI_10021720	superfamily	241607	910	945	1.66E-06	46.4942	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#27116 - 	CGI_10021720	superfamily	241607	1048	1068	7.02E-06	44.5682	cl00097	KAZAL_FS superfamily	C	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#27116 - 	CGI_10021720	superfamily	241607	979	1014	5.43E-05	42.3219	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#27118 - 	CGI_10021722	superfamily	243072	47	116	0.00267844	35.4371	cl02529	ANK superfamily	N	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27120 - 	CGI_10021724	superfamily	248458	311	491	1.67E-15	76.5837	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27121 - 	CGI_10021725	superfamily	241768	146	322	2.01E-44	151.493	cl00305	Sua5_yciO_yrdC superfamily	 - 	 - 	Telomere recombination; This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast.
Q#27121 - 	CGI_10021725	superfamily	243161	4	69	4.86E-07	46.6186	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#27122 - 	CGI_10021726	superfamily	246940	256	476	1.15E-05	45.4022	cl15377	Radical_SAM superfamily	 - 	 - 	"Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and  MoaA, an enzyme of the biosynthesis of molybdopterin."
Q#27122 - 	CGI_10021726	superfamily	216191	105	207	8.74E-30	113.364	cl03017	UPF0004 superfamily	 - 	 - 	Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.
Q#27122 - 	CGI_10021726	superfamily	242412	518	592	6.39E-06	44.1437	cl01282	TRAM superfamily	 - 	 - 	TRAM domain; This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).
Q#27125 - 	CGI_10021729	superfamily	201778	17	129	9.65E-24	93.8126	cl18219	GFO_IDH_MocA superfamily	 - 	 - 	"Oxidoreductase family, NAD-binding Rossmann fold; This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot."
Q#27126 - 	CGI_10021730	superfamily	247792	478	522	0.00546242	35.114	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27126 - 	CGI_10021730	superfamily	154937	93	168	9.45E-07	46.8275	cl02489	SWIB superfamily	 - 	 - 	SWIB/MDM2 domain; This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2.
Q#27129 - 	CGI_10021733	superfamily	246664	356	739	2.90E-173	508.653	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#27129 - 	CGI_10021733	superfamily	246664	206	302	2.10E-05	46.5088	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#27129 - 	CGI_10021733	superfamily	218628	699	836	0.00123979	41.0237	cl05221	Spheroidin superfamily	N	 - 	"Entomopoxvirus spheroidin protein; Entomopoxviruses (EPVs) are large (300-400 nm) oval-shaped viruses replicating in the cytoplasm of their insect host cells. At the end of their replicative cycle EPVs virions are occluded in a highly expressed protein called spheroidin. This protein forms large (5-20 mm long) oval-shaped occlusion bodies (OBs) called spherules. The infectious cycle of EPVs begins with the ingestion by the insect host of the spherules, their dissolution by the alkaline reducing conditions of the midgut fluid and the release of virions in the midgut lumen. The infective particles first replicate in midgut epithelial cells, then pass the gut barrier to colonise the internal tissues, mainly the fat body cells. Whilst spheroidin has been demonstrated to be non-essential for viral replication, it plays an essential role in the natural biological cycle of the virus in protecting virions from adverse environmental conditions (e.g. UV degradation) and thus improving transmission efficacy. In this respect, spheroidins are functionally similar to polyhedrins of baculoviruses or cypoviruses."
Q#27130 - 	CGI_10021734	superfamily	246664	127	478	3.35E-159	463.585	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#27130 - 	CGI_10021734	superfamily	245814	27	125	0.0043132	36.135	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27130 - 	CGI_10021734	superfamily	246918	521	564	0.00765362	34.8699	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27131 - 	CGI_10021735	superfamily	241900	1671	1920	5.26E-43	162.472	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#27132 - 	CGI_10021736	superfamily	248012	173	240	1.39E-05	42.6457	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27133 - 	CGI_10021737	superfamily	248012	3	99	1.11E-07	45.7273	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27135 - 	CGI_10021739	superfamily	248012	890	1011	1.58E-11	63.0613	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27135 - 	CGI_10021739	superfamily	246925	521	765	0.000333676	42.7278	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27137 - 	CGI_10021741	superfamily	248012	473	565	1.21E-09	56.5129	cl17458	TIR_2 superfamily	C	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27140 - 	CGI_10025139	superfamily	238191	23	524	3.34E-156	460.646	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#27142 - 	CGI_10025141	superfamily	248097	93	220	8.57E-16	70.3718	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#27144 - 	CGI_10025143	superfamily	242443	1	126	2.15E-42	146.333	cl01342	Peptidase_A22B superfamily	N	 - 	"Signal peptide peptidase; The members of this family are membrane proteins. In some proteins this region is found associated with pfam02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with pfam01080."
Q#27149 - 	CGI_10025148	superfamily	247724	2	70	5.73E-16	70.6419	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27151 - 	CGI_10025150	superfamily	242902	42	104	4.07E-12	59.9531	cl02144	TLD superfamily	C	 - 	TLD; This domain is predicted to be an enzyme and is often found associated with pfam01476.
Q#27152 - 	CGI_10025151	superfamily	222150	408	433	9.60E-06	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27153 - 	CGI_10025152	superfamily	222150	77	102	0.00142044	32.749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27154 - 	CGI_10025153	superfamily	246597	28	303	1.77E-130	385.743	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#27154 - 	CGI_10025153	superfamily	217260	339	499	1.02E-38	138.926	cl03752	5_nucleotid_C superfamily	 - 	 - 	"5'-nucleotidase, C-terminal domain; 5'-nucleotidase, C-terminal domain.  "
Q#27156 - 	CGI_10025155	superfamily	243035	64	187	1.00E-21	86.1345	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27157 - 	CGI_10025156	superfamily	247683	327	381	1.32E-26	103.158	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#27157 - 	CGI_10025156	superfamily	247725	398	503	9.17E-42	148.178	cl17171	PH-like superfamily	C	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#27157 - 	CGI_10025156	superfamily	147559	549	642	1.02E-12	66.0674	cl05152	Tmemb_9 superfamily	 - 	 - 	"TMEM9; This family contains several eukaryotic transmembrane proteins which are homologous to human transmembrane protein 9. The TMEM9 gene encodes a 183 amino-acid protein that contains an N-terminal signal peptide, a single transmembrane region, three potential N-glycosylation sites and three conserved cys-rich domains in the N-terminus, but no known functional domains. The protein is highly conserved between species from Caenorhabditis elegans to man and belongs to a novel family of transmembrane proteins. The exact function of TMEM9 is unknown although it has been found to be widely expressed and localised to the late endosomes and lysosomes. Members of this family contain pfam03128 repeats in their N-terminal region."
Q#27158 - 	CGI_10025157	superfamily	191268	204	332	7.35E-05	41.1031	cl15960	Mt_ATP-synt_B superfamily	C	 - 	"Mitochondrial ATP synthase B chain precursor (ATP-synt_B); The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport. It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L)."
Q#27160 - 	CGI_10025159	superfamily	241619	31	93	6.12E-06	40.2581	cl00112	PAN_APPLE superfamily	 - 	 - 	"PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins,  plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions."
Q#27161 - 	CGI_10025160	superfamily	245213	60	90	2.33E-05	39.5422	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27162 - 	CGI_10025161	superfamily	243123	46	78	0.000415462	35.997	cl02638	Hairy_orange superfamily	 - 	 - 	"Hairy Orange; The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute."
Q#27164 - 	CGI_10025163	superfamily	247856	705	763	7.69E-08	50.6241	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27164 - 	CGI_10025163	superfamily	247856	292	347	0.000307237	39.8385	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27164 - 	CGI_10025163	superfamily	247856	796	853	0.000781083	38.6829	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27166 - 	CGI_10025165	superfamily	247723	65	146	4.49E-54	180.375	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27166 - 	CGI_10025165	superfamily	247723	153	233	9.07E-51	171.149	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27166 - 	CGI_10025165	superfamily	247723	555	646	2.79E-51	172.94	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27168 - 	CGI_10025169	superfamily	247905	777	900	3.87E-24	100.005	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#27168 - 	CGI_10025169	superfamily	247805	434	577	1.60E-23	98.5635	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#27168 - 	CGI_10025169	superfamily	243130	175	210	0.00032755	39.7559	cl02655	CUE superfamily	 - 	 - 	"CUE domain; CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2."
Q#27169 - 	CGI_10025170	superfamily	247637	8	348	0	512.039	cl16912	MDR superfamily	 - 	 - 	"Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH.  MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino acids of the MDR).  The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES.  The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc."
Q#27173 - 	CGI_10025174	superfamily	245235	1	220	2.37E-136	395.43	cl10023	POLBc superfamily	N	 - 	"DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y).  Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis."
Q#27173 - 	CGI_10025174	superfamily	222632	222	248	0.000931897	36.2293	cl16754	zf-C4pol superfamily	N	 - 	"C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1."
Q#27175 - 	CGI_10025176	superfamily	247804	96	140	2.44E-14	68.371	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#27175 - 	CGI_10025176	superfamily	247804	148	188	3.09E-11	59.5114	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#27175 - 	CGI_10025176	superfamily	247804	44	88	7.23E-11	58.3558	cl17250	SANT superfamily	 - 	 - 	"'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA."
Q#27175 - 	CGI_10025176	superfamily	220175	432	561	1.54E-11	62.9235	cl07814	Cmyb_C superfamily	 - 	 - 	"C-myb, C-terminal; Members of this family are predominantly found in the proto-oncogene c-myb and the viral transforming protein myb. Truncation of the domain results in 'activation' of c-myb and subsequent tumourigenesis."
Q#27178 - 	CGI_10025179	superfamily	247723	13	88	5.36E-50	159.703	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27179 - 	CGI_10025180	superfamily	241677	4	162	3.90E-114	323.44	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#27183 - 	CGI_10010961	superfamily	247038	554	595	3.24E-10	57.3255	cl15674	IPT superfamily	C	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#27183 - 	CGI_10010961	superfamily	247042	235	320	0.00100029	40.6853	cl15693	Sema superfamily	N	 - 	"The Sema domain, a protein interacting module, of semaphorins and plexins; Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors."
Q#27184 - 	CGI_10010963	superfamily	243060	163	251	5.46E-05	41.9808	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#27185 - 	CGI_10010964	superfamily	247984	21	203	7.38E-65	205.537	cl17430	FtsJ superfamily	 - 	 - 	"FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping."
Q#27186 - 	CGI_10010965	superfamily	247724	255	527	2.52E-152	453.487	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27186 - 	CGI_10010965	superfamily	243185	561	641	3.41E-46	160.909	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#27186 - 	CGI_10010965	superfamily	243187	733	841	3.45E-44	156.443	cl02789	EFG_like_IV superfamily	 - 	 - 	"Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2  promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm."
Q#27186 - 	CGI_10010965	superfamily	243183	854	931	5.80E-36	132.059	cl02785	Elongation_Factor_C superfamily	 - 	 - 	"Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p.  This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain.  EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner.  BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown."
Q#27187 - 	CGI_10010966	superfamily	243072	15	140	1.36E-31	115.173	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27189 - 	CGI_10005933	superfamily	111397	6	61	0.00196511	35.0095	cl03620	HYR superfamily	N	 - 	"HYR domain; This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion."
Q#27190 - 	CGI_10011897	superfamily	246669	366	485	2.95E-51	175.836	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27190 - 	CGI_10011897	superfamily	246669	500	613	7.87E-38	138.082	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27190 - 	CGI_10011897	superfamily	241578	635	861	1.28E-83	270.782	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27191 - 	CGI_10011898	superfamily	243066	18	121	2.95E-26	102.696	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27191 - 	CGI_10011898	superfamily	198867	130	230	8.38E-23	93.1748	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#27191 - 	CGI_10011898	superfamily	243146	369	415	1.91E-07	48.3235	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27191 - 	CGI_10011898	superfamily	243146	304	355	1.31E-06	45.7302	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27191 - 	CGI_10011898	superfamily	243146	406	448	1.87E-05	42.2634	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27192 - 	CGI_10011899	superfamily	246669	17	136	4.10E-40	141.938	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27192 - 	CGI_10011899	superfamily	246669	151	230	1.05E-26	104.57	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27192 - 	CGI_10011899	superfamily	241578	315	534	2.77E-81	256.915	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27193 - 	CGI_10011900	superfamily	246597	1	227	2.74E-69	214.452	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#27194 - 	CGI_10011901	superfamily	222269	174	331	0.00818049	36.1474	cl18657	Cupin_8 superfamily	C	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#27195 - 	CGI_10011902	superfamily	222269	49	249	3.29E-08	51.5554	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#27197 - 	CGI_10011904	superfamily	241570	581	697	3.44E-24	100.093	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#27199 - 	CGI_10011906	superfamily	241899	146	336	2.04E-32	121.496	cl00489	60KD_IMP superfamily	 - 	 - 	60Kd inner membrane protein; 60Kd inner membrane protein.  
Q#27200 - 	CGI_10011907	superfamily	150812	1	60	1.11E-16	68.1838	cl10884	Tmemb_170 superfamily	N	 - 	Putative transmembrane protein 170; Tmem170 is a family of putative transmembrane proteins conserved from nematodes to humans. The protein is only of approximately 130 amino acids in length. The function is unknown.
Q#27202 - 	CGI_10011909	superfamily	248097	117	242	1.83E-16	72.683	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#27203 - 	CGI_10011910	superfamily	243507	46	227	3.34E-28	108.597	cl03728	Alpha_kinase superfamily	 - 	 - 	"Alpha-kinase family; This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains."
Q#27204 - 	CGI_10011911	superfamily	215827	161	327	9.70E-23	96.3835	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#27205 - 	CGI_10011912	superfamily	215827	146	324	7.29E-37	136.829	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#27206 - 	CGI_10011913	superfamily	215827	148	325	2.35E-34	130.281	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#27209 - 	CGI_10011916	superfamily	215827	38	215	6.09E-38	139.141	cl02830	Tyrosinase superfamily	 - 	 - 	Common central domain of tyrosinase; This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372.
Q#27210 - 	CGI_10004096	superfamily	246723	149	693	0	603.141	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27212 - 	CGI_10004098	superfamily	243091	231	275	3.86E-09	53.65	cl02566	SET superfamily	N	 - 	"SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."
Q#27213 - 	CGI_10004099	superfamily	243092	37	334	7.46E-23	95.4796	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#27214 - 	CGI_10005452	superfamily	247743	2709	2854	1.89E-06	50.2223	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#27217 - 	CGI_10022109	superfamily	241574	11	55	0.0002775	34.2567	cl00053	PTPc superfamily	N	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27218 - 	CGI_10022110	superfamily	241584	109	221	2.31E-08	51.3431	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#27218 - 	CGI_10022110	superfamily	241574	348	451	4.76E-18	82.2485	cl00053	PTPc superfamily	C	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27219 - 	CGI_10022111	superfamily	245201	82	392	0	643.003	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27220 - 	CGI_10022112	superfamily	243058	879	982	0.00223277	38.8348	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#27220 - 	CGI_10022112	superfamily	243267	1	86	2.03E-14	75.728	cl03000	Innexin superfamily	N	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#27221 - 	CGI_10022113	superfamily	243267	582	670	0.00816303	37.5932	cl03000	Innexin superfamily	N	 - 	"Innexin; This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins."
Q#27223 - 	CGI_10022115	superfamily	241563	68	109	9.87E-06	44.0072	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27223 - 	CGI_10022115	superfamily	241563	24	59	0.00127207	37.844	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27223 - 	CGI_10022115	superfamily	241672	347	420	0.00297131	39.2596	cl00192	ribokinase_pfkB_like superfamily	C	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#27226 - 	CGI_10022118	superfamily	241874	9	548	0	714.066	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#27227 - 	CGI_10022119	superfamily	241874	9	528	0	692.11	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#27230 - 	CGI_10022122	superfamily	245206	269	497	1.85E-79	249.905	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#27231 - 	CGI_10022123	superfamily	241599	1209	1264	5.62E-13	66.498	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#27231 - 	CGI_10022123	superfamily	202226	1102	1180	5.37E-29	113.542	cl08348	CUT superfamily	 - 	 - 	"CUT domain; The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein ."
Q#27231 - 	CGI_10022123	superfamily	202226	926	1002	7.68E-29	112.772	cl08348	CUT superfamily	 - 	 - 	"CUT domain; The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein ."
Q#27231 - 	CGI_10022123	superfamily	202226	538	622	7.65E-26	104.297	cl08348	CUT superfamily	 - 	 - 	"CUT domain; The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein ."
Q#27232 - 	CGI_10022124	superfamily	222430	565	653	0.000940792	38.7664	cl16445	Nup54 superfamily	N	 - 	"Nucleoporin complex subunit 54; This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them."
Q#27233 - 	CGI_10022125	superfamily	241868	60	148	1.23E-11	58.6599	cl00447	Nudix_Hydrolase superfamily	C	 - 	"Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase."
Q#27234 - 	CGI_10022126	superfamily	244824	8	378	4.55E-124	371.896	cl07893	AmyAc_family superfamily	 - 	 - 	"Alpha amylase catalytic domain family; The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase."
Q#27234 - 	CGI_10022126	superfamily	241832	407	577	5.28E-46	159.988	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#27235 - 	CGI_10022127	superfamily	241832	32	202	1.72E-47	155.366	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#27236 - 	CGI_10022128	superfamily	245864	27	481	2.96E-136	403.968	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#27237 - 	CGI_10022129	superfamily	215859	175	308	3.46E-07	49.5223	cl18347	Peptidase_S9 superfamily	C	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#27238 - 	CGI_10022130	superfamily	247941	259	406	1.51E-17	78.9168	cl17387	Methyltransf_21 superfamily	 - 	 - 	"Methyltransferase FkbM domain; This family has members from bacteria to human, and appears to be a methyltransferase."
Q#27241 - 	CGI_10022133	superfamily	219125	441	632	1.29E-85	268.427	cl05941	C5-epim_C superfamily	 - 	 - 	D-glucuronyl C5-epimerase C-terminus; This family represents the C-terminus of D-glucuronyl C5-epimerase (EC:5.1.3.-). Glucuronyl C5-epimerases catalyze the conversion of D-glucuronic acid (GlcUA) to L-iduronic acid (IdceA) units during the biosynthesis of glycosaminoglycans.
Q#27242 - 	CGI_10011551	superfamily	241546	12	124	8.96E-26	100.106	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#27242 - 	CGI_10011551	superfamily	215847	224	362	3.80E-27	112.155	cl09510	Lipoxygenase superfamily	NC	 - 	Lipoxygenase; Lipoxygenase.  
Q#27243 - 	CGI_10011552	superfamily	241546	3	108	6.52E-22	85.8536	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#27244 - 	CGI_10011553	superfamily	241546	6	110	1.04E-28	104.174	cl00011	PLAT superfamily	 - 	 - 	"PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2)  domain.  It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates."
Q#27245 - 	CGI_10011554	superfamily	241659	70	163	1.45E-27	101.956	cl00175	alpha-crystallin-Hsps_p23-like superfamily	 - 	 - 	"alpha-crystallin domain (ACD) found in alpha-crystallin-type small heat shock proteins, and a similar domain found in p23 (a cochaperone for Hsp90) and in other p23-like proteins.; The alpha-crystallin-Hsps_p23-like superfamily includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12-43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this superfamily is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR)."
Q#27245 - 	CGI_10011554	superfamily	218373	190	217	2.26E-07	46.2445	cl04882	SGS superfamily	NC	 - 	"SGS domain; This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins."
Q#27245 - 	CGI_10011554	superfamily	149931	3	73	3.13E-07	45.9075	cl07592	Siah-Interact_N superfamily	 - 	 - 	"Siah interacting protein, N terminal; The N terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N terminal domain."
Q#27246 - 	CGI_10011555	superfamily	215859	294	342	0.00794524	36.4255	cl18347	Peptidase_S9 superfamily	NC	 - 	Prolyl oligopeptidase family; Prolyl oligopeptidase family.  
Q#27249 - 	CGI_10011558	superfamily	241884	40	228	1.75E-144	406.198	cl00467	Ntn_hydrolase superfamily	 - 	 - 	"The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid.  N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences."
Q#27249 - 	CGI_10011558	superfamily	204931	231	269	4.96E-10	53.6172	cl13849	Pr_beta_C superfamily	 - 	 - 	"Proteasome beta subunits C terminal; This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00227. There is a conserved GTT sequence motif. There is a single completely conserved residue Y that may be functionally important. This family includes the C terminal of the beta-type subunits of the proteasome, a multimeric complex that degrades proteins into peptides as part of the MHC class I-mediated Ag-presenting pathway."
Q#27251 - 	CGI_10011560	superfamily	241889	21	178	9.22E-36	124.738	cl00474	PAP2_like superfamily	 - 	 - 	"PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins."
Q#27252 - 	CGI_10011561	superfamily	245201	29	257	8.06E-161	451.504	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27254 - 	CGI_10011563	superfamily	241572	117	202	5.68E-14	66.108	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#27254 - 	CGI_10011563	superfamily	241572	216	296	2.41E-05	41.4553	cl00050	CYCLIN superfamily	 - 	 - 	"Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain."
Q#27254 - 	CGI_10011563	superfamily	203895	16	53	0.000924894	36.4926	cl07036	TF_Zn_Ribbon superfamily	 - 	 - 	TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Q#27255 - 	CGI_10011564	superfamily	241603	93	325	1.45E-74	231.875	cl00089	NUC superfamily	 - 	 - 	DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.  They exists as monomers and homodimers.
Q#27256 - 	CGI_10011565	superfamily	247948	406	457	2.56E-12	62.4086	cl17394	RINGv superfamily	 - 	 - 	RING-variant domain; RING-variant domain.  
Q#27257 - 	CGI_10011566	superfamily	241570	515	632	2.07E-21	90.8481	cl00047	CAP_ED superfamily	 - 	 - 	"effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels.  Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels"
Q#27258 - 	CGI_10011567	superfamily	247069	81	210	2.24E-22	93.2186	cl15787	SEC14 superfamily	 - 	 - 	"Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits."
Q#27258 - 	CGI_10011567	superfamily	201362	265	368	1.42E-15	72.7831	cl08277	Motile_Sperm superfamily	 - 	 - 	MSP (Major sperm protein) domain; Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
Q#27259 - 	CGI_10011568	superfamily	152683	246	327	2.12E-13	67.3129	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#27263 - 	CGI_10011572	superfamily	247805	563	695	3.87E-29	113.972	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#27264 - 	CGI_10011573	superfamily	247905	10	122	6.76E-08	49.5437	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#27264 - 	CGI_10011573	superfamily	243778	176	266	3.94E-39	134.274	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#27266 - 	CGI_10011575	superfamily	248458	16	408	2.46E-11	63.4869	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27267 - 	CGI_10011576	superfamily	221187	1	123	2.13E-40	137.038	cl13212	Malectin superfamily	N	 - 	"Di-glucose binding within endoplasmic reticulum; Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. It carries a signal peptide from residues 1-26, a C-terminal transmembrane helix from residues 255-274, and a highly conserved central part of approximately 190 residues followed by an acidic, glutamate-rich region. Carbohydrate-binding is mediated by the four aromatic residues, Y67, Y89, Y116, and F117 and the aspartate at D186. NMR-based ligand-screening studies has shown binding of the protein to maltose and related oligosaccharides, on the basis of which the protein has been designated "malectin", and its endogenous ligand is found to be Glc2-high-mannose N-glycan."
Q#27268 - 	CGI_10011577	superfamily	248472	1	112	8.08E-29	101.956	cl17918	Ribosomal_P1_P2_L12p superfamily	 - 	 - 	"Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have two copies each of P1 and P2 (two heterodimers). Bacteria may have four or six copies (two or three homodimers), depending on the species. As in bacteria, the stalk is crucial for binding of initiation, elongation, and release factors in eukaryotes and archaea."
Q#27269 - 	CGI_10011578	superfamily	241578	69	241	1.70E-43	150.616	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27270 - 	CGI_10010574	superfamily	247724	91	285	1.50E-76	240.13	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27270 - 	CGI_10010574	superfamily	207690	17	43	0.00193577	36.1737	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#27271 - 	CGI_10023791	superfamily	203134	388	451	0.00917297	34.9649	cl04866	CHORD superfamily	 - 	 - 	"CHORD; CHORD represents a Zn binding domain. Silencing of the C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development."
Q#27273 - 	CGI_10023793	superfamily	217865	2047	2410	0	578.041	cl12285	Not1 superfamily	 - 	 - 	"CCR4-Not complex component, Not1; The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID."
Q#27273 - 	CGI_10023793	superfamily	221802	1414	1567	2.05E-56	195.103	cl15117	DUF3819 superfamily	 - 	 - 	Domain of unknown function (DUF3819); This is an uncharacterized domain that is found on the CCR4-Not complex component Not1. Not1 is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID.
Q#27274 - 	CGI_10023794	superfamily	241666	3	158	4.53E-16	71.594	cl00184	CAS_like superfamily	N	 - 	"Clavaminic acid synthetase (CAS) -like;  CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to succinate and CO2"
Q#27275 - 	CGI_10023795	superfamily	248360	13	205	1.88E-57	183.631	cl17806	DER1 superfamily	 - 	 - 	"Der1-like family; The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localised to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.)."
Q#27276 - 	CGI_10023796	superfamily	243092	41	336	4.13E-34	134	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#27276 - 	CGI_10023796	superfamily	243056	420	601	9.28E-12	65.0729	cl02495	RabGAP-TBC superfamily	 - 	 - 	"Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases."
Q#27277 - 	CGI_10023797	superfamily	241770	210	272	4.44E-11	58.9464	cl00309	PRTases_typeI superfamily	N	 - 	"Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP).  PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22."
Q#27277 - 	CGI_10023797	superfamily	222383	37	121	1.17E-06	45.8654	cl16402	Pribosyltran_N superfamily	N	 - 	"N-terminal domain of ribose phosphate pyrophosphokinase; This family is frequently found N-terminal to the Pribosyltran, pfam00156."
Q#27278 - 	CGI_10023798	superfamily	245835	209	421	5.00E-69	223.731	cl12013	BAR superfamily	 - 	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#27282 - 	CGI_10023802	superfamily	243035	566	683	1.73E-33	125.04	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27283 - 	CGI_10023803	superfamily	243555	23	212	3.19E-11	58.5566	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#27284 - 	CGI_10023804	superfamily	243555	23	212	1.94E-14	67.8014	cl03871	Chitin_bind_3 superfamily	 - 	 - 	"Chitin binding domain; This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function."
Q#27285 - 	CGI_10023805	superfamily	243033	79	198	1.24E-08	50.7797	cl02428	Ependymin superfamily	 - 	 - 	Ependymin; Ependymin.  
Q#27287 - 	CGI_10023807	superfamily	247639	1	100	8.38E-24	92.5243	cl16914	O-FucT_like superfamily	N	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#27288 - 	CGI_10023808	superfamily	243039	1645	1783	8.12E-88	284.439	cl02446	MATH superfamily	 - 	 - 	"MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains."
Q#27288 - 	CGI_10023808	superfamily	243035	344	472	4.82E-09	56.4741	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27288 - 	CGI_10023808	superfamily	241584	1121	1215	8.96E-07	49.0319	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#27288 - 	CGI_10023808	superfamily	241584	1335	1431	4.36E-06	47.1059	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#27288 - 	CGI_10023808	superfamily	241584	1440	1531	8.35E-06	46.3355	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#27288 - 	CGI_10023808	superfamily	222608	4	124	2.42E-25	104.259	cl18680	DIOX_N superfamily	 - 	 - 	non-haem dioxygenase in morphine synthesis N-terminal; This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.
Q#27288 - 	CGI_10023808	superfamily	217403	175	278	4.31E-22	94.4117	cl18408	2OG-FeII_Oxy superfamily	 - 	 - 	"2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalyzing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB."
Q#27288 - 	CGI_10023808	superfamily	243066	1807	1911	1.35E-21	93.0657	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27288 - 	CGI_10023808	superfamily	245814	933	1006	6.71E-17	78.6402	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27288 - 	CGI_10023808	superfamily	245814	830	911	1.31E-15	74.944	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27288 - 	CGI_10023808	superfamily	245814	1029	1101	2.73E-13	68.2896	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27288 - 	CGI_10023808	superfamily	245814	502	598	3.29E-13	68.241	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27288 - 	CGI_10023808	superfamily	245814	733	802	4.54E-08	52.8646	cl11960	Ig superfamily	C	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27288 - 	CGI_10023808	superfamily	245814	607	695	6.67E-08	52.5576	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27289 - 	CGI_10023809	superfamily	222438	220	283	1.28E-11	60.189	cl16459	zf-C3Hc3H superfamily	 - 	 - 	Potential DNA-binding domain; This domain is likely to be the DNA-binding domain of chromatin re-modelling proteins and helicases.
Q#27291 - 	CGI_10023811	superfamily	245225	39	493	0	613.096	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	 - 	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#27291 - 	CGI_10023811	superfamily	215648	588	800	5.91E-71	234.412	cl02802	7tm_3 superfamily	 - 	 - 	"7 transmembrane sweet-taste receptor of 3 GCPR; This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness."
Q#27291 - 	CGI_10023811	superfamily	219467	506	557	1.19E-12	64.2767	cl08456	NCD3G superfamily	 - 	 - 	"Nine Cysteines Domain of family 3 GPCR; This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins."
Q#27293 - 	CGI_10023813	superfamily	248009	32	472	1.09E-172	505.211	cl17455	UPF0027 superfamily	 - 	 - 	Uncharacterized protein family UPF0027; Uncharacterized protein family UPF0027.  
Q#27293 - 	CGI_10023813	superfamily	248009	468	740	3.44E-107	335.724	cl17455	UPF0027 superfamily	N	 - 	Uncharacterized protein family UPF0027; Uncharacterized protein family UPF0027.  
Q#27294 - 	CGI_10023814	superfamily	248009	392	639	3.97E-77	254.061	cl17455	UPF0027 superfamily	N	 - 	Uncharacterized protein family UPF0027; Uncharacterized protein family UPF0027.  
Q#27294 - 	CGI_10023814	superfamily	220964	125	211	0.000580219	39.1213	cl12630	DUF2869 superfamily	C	 - 	Protein of unknown function (DUF2869); This bacterial family of proteins has no known function.
Q#27296 - 	CGI_10023816	superfamily	207794	321	769	0	654.361	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#27296 - 	CGI_10023816	superfamily	243574	11	160	1.12E-32	124.75	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#27297 - 	CGI_10023817	superfamily	247639	23	267	1.63E-37	134.896	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#27298 - 	CGI_10023818	superfamily	247639	77	327	5.36E-36	132.585	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#27299 - 	CGI_10023819	superfamily	247639	83	347	3.43E-28	110.629	cl16914	O-FucT_like superfamily	 - 	 - 	"GDP-fucose protein O-fucosyltransferase and related proteins; O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes."
Q#27302 - 	CGI_10023822	superfamily	247683	324	375	4.07E-20	82.6926	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#27302 - 	CGI_10023822	superfamily	245835	2	111	5.83E-44	154.333	cl12013	BAR superfamily	N	 - 	"The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively."
Q#27302 - 	CGI_10023822	superfamily	241602	191	230	3.46E-08	50.3033	cl00087	HR1 superfamily	N	 - 	"Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases; The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and Rho-associated kinase (ROCK). Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 domains may occur in repeat arrangements (PKN contains three HR1 domains), separated by a short linker region."
Q#27303 - 	CGI_10023823	superfamily	241571	12	105	1.46E-15	70.519	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#27304 - 	CGI_10023824	superfamily	241571	42	137	4.94E-08	51.2591	cl00049	CUB superfamily	N	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#27304 - 	CGI_10023824	superfamily	242323	385	491	8.37E-19	82.5563	cl01132	FA_hydroxylase superfamily	 - 	 - 	"Fatty acid hydroxylase superfamily; This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins."
Q#27306 - 	CGI_10023826	superfamily	247856	489	549	3.55E-11	59.4837	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27306 - 	CGI_10023826	superfamily	246925	189	344	3.53E-17	81.2477	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27310 - 	CGI_10023830	superfamily	243179	133	241	1.01E-18	79.8843	cl02781	tetraspanin_LEL superfamily	 - 	 - 	"Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web", which may also include integrins."
Q#27311 - 	CGI_10023831	superfamily	246679	27	170	3.69E-67	203.143	cl14632	Glo_EDI_BRP_like superfamily	 - 	 - 	"This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases."
Q#27312 - 	CGI_10023832	superfamily	247724	25	164	3.04E-60	189.204	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27313 - 	CGI_10023833	superfamily	215754	272	368	5.97E-10	56.1076	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27314 - 	CGI_10023834	superfamily	199528	4	115	0.000146301	40.8496	cl15392	PRK10429 superfamily	C	 - 	melibiose:sodium symporter; Provisional
Q#27318 - 	CGI_10024101	superfamily	241645	237	302	0.00179972	35.579	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#27319 - 	CGI_10024102	superfamily	247986	216	296	0.00189382	37.7378	cl17432	PBPb superfamily	N	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#27321 - 	CGI_10024104	superfamily	247792	28	73	4.30E-13	66.3152	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27322 - 	CGI_10024105	superfamily	243072	473	589	9.13E-33	124.803	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27322 - 	CGI_10024105	superfamily	243072	602	717	1.85E-25	104.003	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27322 - 	CGI_10024105	superfamily	243072	669	773	2.50E-12	65.4826	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27322 - 	CGI_10024105	superfamily	247792	802	844	0.00086172	38.5808	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27322 - 	CGI_10024105	superfamily	115363	15	83	2.86E-29	112.85	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#27322 - 	CGI_10024105	superfamily	115363	166	233	1.41E-21	90.8941	cl05972	MIB_HERC2 superfamily	 - 	 - 	Mib_herc2; Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Q#27322 - 	CGI_10024105	superfamily	241760	92	136	4.13E-19	83.2767	cl00295	ZZ superfamily	 - 	 - 	"Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins."
Q#27322 - 	CGI_10024105	superfamily	247792	866	895	0.000139667	41.2113	cl17238	RING superfamily	C	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27323 - 	CGI_10024106	superfamily	243038	421	504	2.94E-52	177.15	cl02442	DEP superfamily	 - 	 - 	"DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction."
Q#27323 - 	CGI_10024106	superfamily	241622	252	339	1.30E-21	90.7038	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#27323 - 	CGI_10024106	superfamily	198670	1	82	7.36E-41	145.632	cl02426	DIX superfamily	 - 	 - 	DIX domain; The DIX domain is present in Dishevelled and axin. This domain is involved in homo- and hetero-oligomerisation. It is involved in the homo- oligomerisation of mouse axin. The axin DIX domain also interacts with the dishevelled DIX domain. The DIX domain has also been called the DAX domain.
Q#27323 - 	CGI_10024106	superfamily	221526	508	572	0.000259091	41.8735	cl13715	Dsh_C superfamily	C	 - 	"Segment polarity protein dishevelled (Dsh) C terminal; This domain family is found in eukaryotes, and is typically between 177 and 207 amino acids in length. The family is found in association with pfam00778, pfam02377, pfam00610, pfam00595. The segment polarity gene dishevelled (dsh) is required for pattern formation of the embryonic segments. It is involved in the determination of body organisation through the Wingless pathway (analogous to the Wnt-1 pathway)."
Q#27323 - 	CGI_10024106	superfamily	221526	833	857	0.00864878	37.2511	cl13715	Dsh_C superfamily	N	 - 	"Segment polarity protein dishevelled (Dsh) C terminal; This domain family is found in eukaryotes, and is typically between 177 and 207 amino acids in length. The family is found in association with pfam00778, pfam02377, pfam00610, pfam00595. The segment polarity gene dishevelled (dsh) is required for pattern formation of the embryonic segments. It is involved in the determination of body organisation through the Wingless pathway (analogous to the Wnt-1 pathway)."
Q#27324 - 	CGI_10024107	superfamily	247792	352	390	0.00897187	33.9584	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27324 - 	CGI_10024107	superfamily	248318	42	88	0.00214041	35.8338	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#27325 - 	CGI_10024108	superfamily	241548	51	443	0	609.547	cl00013	Lyase_I_like superfamily	 - 	 - 	"Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Lyase class I_like superfamily of enzymes that catalyze beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. This superfamily contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase. The lyase class I family comprises proteins similar to class II fumarase, aspartase, adenylosuccinate lyase, argininosuccinate lyase, and 3-carboxy-cis, cis-muconate lactonizing enzyme which, for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. Histidine or phenylalanine ammonia-lyase catalyze a beta-elimination of ammonia from histidine and phenylalanine, respectively."
Q#27328 - 	CGI_10024111	superfamily	241548	17	452	0	839.283	cl00013	Lyase_I_like superfamily	 - 	 - 	"Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Lyase class I_like superfamily of enzymes that catalyze beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. This superfamily contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase. The lyase class I family comprises proteins similar to class II fumarase, aspartase, adenylosuccinate lyase, argininosuccinate lyase, and 3-carboxy-cis, cis-muconate lactonizing enzyme which, for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. Histidine or phenylalanine ammonia-lyase catalyze a beta-elimination of ammonia from histidine and phenylalanine, respectively."
Q#27328 - 	CGI_10024111	superfamily	241983	497	754	1.27E-38	145.193	cl00614	ADP_ribosyl_GH superfamily	 - 	 - 	"ADP-ribosylglycohydrolase; This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues."
Q#27329 - 	CGI_10024112	superfamily	245230	3	455	0	868.497	cl10017	Tubulin_FtsZ superfamily	 - 	 - 	"Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis.  FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts."
Q#27330 - 	CGI_10024113	superfamily	245201	48	299	1.71E-67	217.773	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27331 - 	CGI_10024114	superfamily	247744	338	517	6.06E-54	181.949	cl17190	NK superfamily	 - 	 - 	"Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate."
Q#27331 - 	CGI_10024114	superfamily	241550	171	317	1.41E-49	168.998	cl00015	nt_trans superfamily	 - 	 - 	"nucleotidyl transferase superfamily; nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain."
Q#27333 - 	CGI_10024116	superfamily	203212	351	494	2.59E-32	125.204	cl04998	NDT80_PhoG superfamily	 - 	 - 	"NDT80 / PhoG like DNA-binding family; This family includes the DNA-binding region of NDT80 as well as PhoG and its homologues. The family contains VIB-1. VIB-1 is thought to be a regulator of conidiation in Neurospora crassa and shares a region of similarity to PHOG, a possible phosphate nonrepressible acid phosphatase in Aspergillus nidulans. It has been found that vib-1 is not the structural gene for nonrepressible acid phosphatase, but rather may regulate nonrepressible acid phosphatase activity."
Q#27333 - 	CGI_10024116	superfamily	206058	663	698	7.69E-15	70.9042	cl16455	MRF_C1 superfamily	 - 	 - 	"Myelin gene regulatory factor -C-terminal domain 1; This domain is found just downstream of Peptidase_S74, pfam13884. The function is not known."
Q#27333 - 	CGI_10024116	superfamily	222434	599	643	1.27E-05	44.1062	cl16452	Peptidase_S74 superfamily	N	 - 	"Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, pfam12219. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and presumably bind to DNA."
Q#27335 - 	CGI_10024118	superfamily	245206	4	102	2.92E-13	70.188	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#27335 - 	CGI_10024118	superfamily	248053	257	336	0.000127232	41.8837	cl17499	Peptidase_M14NE-CP-C_like superfamily	 - 	 - 	"Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity,  or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families."
Q#27336 - 	CGI_10024119	superfamily	245206	29	118	3.05E-23	92.6726	cl09931	NADB_Rossmann superfamily	C	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#27337 - 	CGI_10024120	superfamily	246925	136	410	6.36E-10	60.8322	cl15309	LRR_RI superfamily	 - 	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27337 - 	CGI_10024120	superfamily	220695	662	857	0.000181181	43.3363	cl18571	7TM_GPCR_Srx superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#27337 - 	CGI_10024120	superfamily	243030	25	49	0.00110261	38.4527	cl02423	LRRNT superfamily	C	 - 	Leucine rich repeat N-terminal domain; Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Q#27338 - 	CGI_10024121	superfamily	243084	746	853	3.52E-37	136.267	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#27338 - 	CGI_10024121	superfamily	247999	675	719	9.03E-12	61.7376	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#27338 - 	CGI_10024121	superfamily	241563	120	154	0.00200419	37.3167	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27339 - 	CGI_10024122	superfamily	243035	231	336	5.34E-19	81.5121	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27339 - 	CGI_10024122	superfamily	152683	128	198	4.73E-09	53.0605	cl13656	Methyltransf_FA superfamily	C	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#27339 - 	CGI_10024122	superfamily	243035	30	89	3.71E-07	47.5946	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27340 - 	CGI_10024123	superfamily	243035	252	326	6.98E-17	74.9637	cl02432	CLECT superfamily	N	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27340 - 	CGI_10024123	superfamily	152683	144	247	1.39E-14	68.4685	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#27340 - 	CGI_10024123	superfamily	243035	47	107	1.84E-10	57.2246	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27342 - 	CGI_10024125	superfamily	243072	819	924	5.48E-29	114.403	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27343 - 	CGI_10024126	superfamily	241613	499	533	3.98E-06	44.505	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#27343 - 	CGI_10024126	superfamily	246918	435	488	6.50E-15	69.9231	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27343 - 	CGI_10024126	superfamily	246918	369	423	8.28E-11	58.3671	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27344 - 	CGI_10024127	superfamily	241613	692	726	7.33E-05	41.0382	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#27344 - 	CGI_10024127	superfamily	246918	629	681	1.03E-11	61.4487	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27344 - 	CGI_10024127	superfamily	246918	203	247	7.91E-06	44.1147	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27344 - 	CGI_10024127	superfamily	246918	573	623	0.00148212	37.5663	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27345 - 	CGI_10024128	superfamily	221752	37	64	1.04E-08	47.7189	cl15069	SUZ superfamily	N	 - 	SUZ domain; The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterized in the C.elegans protein Szy-20 where it has been shown to bind RNA and allow their localization to the centrosome. Warning- the domain has a compositionally biased character.
Q#27348 - 	CGI_10024131	superfamily	188340	4	294	1.21E-48	175.459	cl18158	selen_PSTK_euk superfamily	 - 	 - 	"L-seryl-tRNA(Sec) kinase, eukaryotic; Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity."
Q#27348 - 	CGI_10024131	superfamily	245201	283	335	0.000487292	41.368	cl09925	PKc_like superfamily	N	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27349 - 	CGI_10024132	superfamily	217575	149	281	2.91E-46	157.821	cl04090	eRF1_2 superfamily	 - 	 - 	"eRF1 domain 2; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#27349 - 	CGI_10024132	superfamily	217574	13	145	6.17E-43	148.91	cl04089	eRF1_1 superfamily	 - 	 - 	"eRF1 domain 1; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#27349 - 	CGI_10024132	superfamily	146221	284	421	1.06E-34	124.972	cl04091	eRF1_3 superfamily	 - 	 - 	"eRF1 domain 3; The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification."
Q#27350 - 	CGI_10027125	superfamily	242571	1	310	5.97E-77	250.906	cl01544	Bestrophin superfamily	 - 	 - 	"Bestrophin, RFP-TM, chloride channel; Bestrophin is a 68-kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterized by a depressed light peak in the electrooculogram. VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif. Bestrophin is a plasma membrane protein, localised to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of chloride channels, indicating a direct role for bestrophin in generating the light peak. The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal RFP-TM domain implying important functional properties. The bestrophins are four-pass transmembrane chloride-channel proteins, and the RFP-TM or bestrophin domain extends from the N-terminus through approximately 350 amino acids and contains all of the TM domains as well as nearly all reported disease causing mutations. Interestingly, the RFP motif is not conserved evolutionarily back beyond Metazoa, neither is it in plant members."
Q#27351 - 	CGI_10027126	superfamily	247757	8	85	6.61E-23	87.9843	cl17203	Fer4_NifH superfamily	N	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#27352 - 	CGI_10027127	superfamily	217884	26	258	8.39E-55	187.652	cl04392	SRP-alpha_N superfamily	 - 	 - 	"Signal recognition particle, alpha subunit, N-terminal; SRP is a complex of six distinct polypeptides and a 7S RNA that is essential for transferring nascent polypeptide chains that are destined for export from the cell to the translocation apparatus of the endoplasmic reticulum (ER) membrane. SRP binds hydrophobic signal sequences as they emerge from the ribosome, and arrests translation."
Q#27352 - 	CGI_10027127	superfamily	247757	425	543	2.12E-43	153.083	cl17203	Fer4_NifH superfamily	C	 - 	"The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion."
Q#27352 - 	CGI_10027127	superfamily	243520	330	403	1.08E-07	49.472	cl03758	SRP54_N superfamily	 - 	 - 	"SRP54-type protein, helical bundle domain; SRP54-type protein, helical bundle domain.  "
Q#27353 - 	CGI_10027128	superfamily	241596	195	256	7.77E-14	64.9279	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#27354 - 	CGI_10027129	superfamily	247684	40	429	0	546.393	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#27356 - 	CGI_10027131	superfamily	243040	32	146	2.87E-75	236.924	cl02447	CRD_FZ superfamily	 - 	 - 	"CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain; CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines."
Q#27357 - 	CGI_10027132	superfamily	247724	585	790	2.97E-89	280.977	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27357 - 	CGI_10027132	superfamily	245820	1	148	5.40E-37	143.556	cl11970	PriL superfamily	N	 - 	"Archaeal/eukaryotic core primase: Large subunit, PriL; Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. The DNA replication machinery of archaeal organisms contains only the core primase, a simpler arrangement compared to eukaryotes. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL, such as the stabilization of PriS, involvement in the initiation of synthesis, the improvement of primase processivity, and the determination of product size."
Q#27357 - 	CGI_10027132	superfamily	191640	347	432	9.06E-28	108.512	cl06121	DUF1279 superfamily	 - 	 - 	Protein of unknown function (DUF1279); This family represents the C-terminus (approx. 120 residues) of a number of eukaryotic proteins of unknown function.
Q#27358 - 	CGI_10027133	superfamily	241583	249	362	3.07E-23	96.1535	cl00064	ZnMc superfamily	N	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#27359 - 	CGI_10027134	superfamily	248054	54	272	2.66E-14	70.7943	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#27360 - 	CGI_10027135	superfamily	248458	219	603	3.44E-22	97.3844	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27361 - 	CGI_10027136	superfamily	247723	333	403	6.90E-46	154.303	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27363 - 	CGI_10027138	superfamily	247723	17	30	0.000293904	33.7353	cl17169	RRM_SF superfamily	N	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27365 - 	CGI_10027140	superfamily	247684	4	383	8.84E-80	257.591	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#27366 - 	CGI_10027141	superfamily	214781	109	145	2.70E-12	63.9004	cl02747	NRF superfamily	C	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#27367 - 	CGI_10027142	superfamily	214781	110	146	9.03E-13	65.4412	cl02747	NRF superfamily	C	 - 	N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4); Also present in several other worm and fly proteins.
Q#27367 - 	CGI_10027142	superfamily	225813	416	582	0.00209966	39.2813	cl18725	COG3274 superfamily	N	 - 	Predicted O-acyltransferase [General function prediction only]
Q#27369 - 	CGI_10027144	superfamily	241584	209	292	5.00E-07	48.2615	cl00065	FN3 superfamily	 - 	 - 	"Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases."
Q#27369 - 	CGI_10027144	superfamily	245814	102	210	8.86E-14	68.4181	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27369 - 	CGI_10027144	superfamily	245814	17	102	3.71E-07	48.6557	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27370 - 	CGI_10027145	superfamily	245814	1	68	8.80E-09	50.7951	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27370 - 	CGI_10027145	superfamily	245814	175	249	2.35E-06	44.0333	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27370 - 	CGI_10027145	superfamily	245814	94	161	3.71E-06	43.5687	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27372 - 	CGI_10027147	superfamily	192535	140	165	0.00452151	35.6494	cl18179	7TM_GPCR_Srsx superfamily	C	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#27373 - 	CGI_10027148	superfamily	192535	141	219	0.00324442	36.4198	cl18179	7TM_GPCR_Srsx superfamily	N	 - 	Serpentine type 7TM GPCR chemoreceptor Srsx; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Q#27376 - 	CGI_10027151	superfamily	245814	197	278	6.10E-07	48.0987	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27376 - 	CGI_10027151	superfamily	245814	584	669	1.09E-06	47.3283	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27376 - 	CGI_10027151	superfamily	245814	698	765	3.17E-05	42.7792	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27376 - 	CGI_10027151	superfamily	245814	313	380	0.00038079	39.3124	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27377 - 	CGI_10027152	superfamily	245814	447	510	1.14E-05	45.1727	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27377 - 	CGI_10027152	superfamily	242406	1234	1371	8.55E-22	94.1953	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#27377 - 	CGI_10027152	superfamily	245814	782	869	3.55E-07	49.6395	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27377 - 	CGI_10027152	superfamily	245814	331	409	2.84E-06	46.9431	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27377 - 	CGI_10027152	superfamily	245814	897	963	0.000275331	40.972	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27378 - 	CGI_10027153	superfamily	242406	3	122	6.00E-18	76.4761	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#27380 - 	CGI_10027155	superfamily	222450	75	98	0.00762069	32.2167	cl16469	zf-H2C2_5 superfamily	 - 	 - 	C2H2-type zinc-finger domain; C2H2-type zinc-finger domain.  
Q#27382 - 	CGI_10027157	superfamily	247799	569	628	9.61E-20	85.6412	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	639	701	1.14E-17	79.478	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	713	775	7.08E-16	74.4705	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	1030	1092	8.30E-16	74.0853	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	423	482	1.19E-15	73.7001	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	493	555	2.18E-15	72.9297	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	1103	1165	2.51E-13	67.1517	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	950	1007	7.27E-13	65.6109	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	786	848	3.81E-12	63.6849	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	352	409	5.30E-12	63.2997	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	210	270	1.42E-09	55.9809	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	282	341	1.50E-09	55.9809	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	859	944	4.29E-09	54.8253	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27382 - 	CGI_10027157	superfamily	247799	137	198	8.95E-08	50.9733	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#27384 - 	CGI_10027159	superfamily	248458	131	311	3.37E-09	56.1681	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27385 - 	CGI_10027160	superfamily	248458	14	166	3.23E-08	51.5457	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27386 - 	CGI_10027161	superfamily	216897	30	108	3.66E-27	100.063	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#27386 - 	CGI_10027161	superfamily	216897	128	206	1.50E-25	95.826	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#27387 - 	CGI_10027162	superfamily	245531	94	175	7.47E-05	38.9115	cl11158	BEN superfamily	 - 	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#27388 - 	CGI_10027163	superfamily	241616	27	68	0.000119531	37.7516	cl00109	MADS superfamily	 - 	 - 	"MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers.  Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals.  Also found in fungi."
Q#27388 - 	CGI_10027163	superfamily	247999	131	182	0.000912949	35.2654	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#27389 - 	CGI_10027165	superfamily	243064	530	643	1.67E-41	146.237	cl02512	NTR_like superfamily	 - 	 - 	"NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex."
Q#27389 - 	CGI_10027165	superfamily	238012	436	484	4.02E-09	53.5122	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#27389 - 	CGI_10027165	superfamily	238012	254	299	8.35E-08	49.6602	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#27389 - 	CGI_10027165	superfamily	238012	373	426	0.000145069	40.0302	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#27389 - 	CGI_10027165	superfamily	243198	17	253	2.33E-101	311.602	cl02806	Laminin_N superfamily	 - 	 - 	Laminin N-terminal (Domain VI); Laminin N-terminal (Domain VI).  
Q#27392 - 	CGI_10027168	superfamily	152088	122	201	5.81E-11	55.6719	cl13155	DUF3259 superfamily	 - 	 - 	Protein of unknown function (DUF3259); This eukaryotic family of proteins has no known function.
Q#27393 - 	CGI_10027169	superfamily	243072	157	274	3.44E-23	96.6838	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27393 - 	CGI_10027169	superfamily	243072	332	453	4.22E-19	85.1278	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27393 - 	CGI_10027169	superfamily	243072	58	209	2.31E-11	62.401	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27393 - 	CGI_10027169	superfamily	217473	572	891	1.06E-12	68.1605	cl03978	Mab-21 superfamily	 - 	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#27394 - 	CGI_10027170	superfamily	245201	414	708	4.27E-177	512.345	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27394 - 	CGI_10027170	superfamily	245814	217	302	1.11E-28	110.793	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27394 - 	CGI_10027170	superfamily	245814	114	194	1.05E-17	79.3508	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27394 - 	CGI_10027170	superfamily	245814	3	83	1.36E-14	70.612	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27395 - 	CGI_10027171	superfamily	248241	32	482	0	526.055	cl17687	5_nucleotid superfamily	 - 	 - 	"5' nucleotidase family; This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5."
Q#27396 - 	CGI_10027172	superfamily	243092	84	373	3.92E-90	284.227	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#27400 - 	CGI_10027176	superfamily	246680	42	115	4.96E-06	44.8852	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#27400 - 	CGI_10027176	superfamily	246680	389	448	9.47E-06	44.1148	cl14633	DD_superfamily superfamily	C	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#27401 - 	CGI_10027177	superfamily	220374	40	140	1.14E-40	143.349	cl16011	MCM_bind superfamily	 - 	 - 	"Mini-chromosome maintenance replisome factor; This entry is of proteins of approximately 600 residues in length containing alternating regions of conservation and low complexity. The Arabidopsis protein is a replisome factor found to bind with the mini-chromosome maintenance, MCM-binding, complex and is crucial for efficient DNA replication."
Q#27401 - 	CGI_10027177	superfamily	222265	276	375	2.73E-37	133.115	cl16322	Racemase_4 superfamily	 - 	 - 	Putative alanine racemase; This is a family of eukaryotic proteins which are putatively alanine racemase.
Q#27402 - 	CGI_10027178	superfamily	241643	299	334	6.49E-10	54.0023	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#27403 - 	CGI_10027179	superfamily	216167	80	243	1.40E-37	135.792	cl02999	DNA_photolyase superfamily	 - 	 - 	DNA photolyase; This domain binds a light harvesting cofactor.
Q#27404 - 	CGI_10027180	superfamily	205718	214	242	1.07E-05	42.4774	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#27404 - 	CGI_10027180	superfamily	205718	320	348	0.000118369	39.3958	cl16296	RCC1_2 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#27404 - 	CGI_10027180	superfamily	201217	177	226	0.000414799	37.8904	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#27406 - 	CGI_10027182	superfamily	191444	81	161	2.10E-10	53.4821	cl05558	IL17 superfamily	 - 	 - 	Interleukin-17; IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution.
Q#27407 - 	CGI_10027183	superfamily	243060	143	235	4.56E-10	60.0852	cl02507	SEA superfamily	 - 	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#27408 - 	CGI_10027184	superfamily	241599	158	206	1.69E-18	77.6688	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#27409 - 	CGI_10027185	superfamily	242181	4	316	4.13E-78	254.864	cl00900	Ldh_2 superfamily	 - 	 - 	"Malate/L-lactate dehydrogenase; This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyzes the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyzes the reactions: (S)-malate + NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively."
Q#27409 - 	CGI_10027185	superfamily	242181	338	659	2.42E-68	228.671	cl00900	Ldh_2 superfamily	 - 	 - 	"Malate/L-lactate dehydrogenase; This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyzes the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyzes the reactions: (S)-malate + NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively."
Q#27410 - 	CGI_10027186	superfamily	243152	91	219	1.49E-37	129.331	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#27411 - 	CGI_10027187	superfamily	243152	91	218	9.15E-41	137.805	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#27412 - 	CGI_10027188	superfamily	243152	679	807	1.31E-39	143.198	cl02712	PGRP superfamily	 - 	 - 	"Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity."
Q#27412 - 	CGI_10027188	superfamily	246680	66	138	1.22E-06	47.1964	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#27414 - 	CGI_10011269	superfamily	245213	347	383	2.65E-06	45.3202	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27414 - 	CGI_10011269	superfamily	245213	310	345	7.54E-06	44.1646	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27414 - 	CGI_10011269	superfamily	246918	391	443	1.08E-15	73.0047	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27414 - 	CGI_10011269	superfamily	219525	685	722	5.06E-06	44.7174	cl06646	GCC2_GCC3 superfamily	N	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#27414 - 	CGI_10011269	superfamily	219525	210	252	1.16E-05	43.947	cl06646	GCC2_GCC3 superfamily	 - 	 - 	GCC2 and GCC3; GCC2 and GCC3.  
Q#27415 - 	CGI_10011270	superfamily	247866	48	249	7.31E-24	96.7528	cl17312	PhyH superfamily	 - 	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#27416 - 	CGI_10011271	superfamily	247866	3	142	2.55E-21	87.508	cl17312	PhyH superfamily	N	 - 	"Phytanoyl-CoA dioxygenase (PhyH); This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues."
Q#27417 - 	CGI_10011272	superfamily	247684	1	263	1.96E-130	384.354	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	N	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#27418 - 	CGI_10011273	superfamily	220692	29	332	9.68E-27	107.675	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#27419 - 	CGI_10011274	superfamily	220692	29	330	5.33E-15	73.7777	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#27420 - 	CGI_10011275	superfamily	220692	39	337	1.02E-20	90.3413	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#27421 - 	CGI_10011276	superfamily	220692	23	329	8.98E-22	93.0377	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#27422 - 	CGI_10011277	superfamily	241563	68	109	1.56E-06	46.3184	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27422 - 	CGI_10011277	superfamily	241563	28	59	0.000874048	38.2292	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27424 - 	CGI_10011279	superfamily	245596	35	209	7.15E-94	276	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#27428 - 	CGI_10027965	superfamily	241574	87	306	1.65E-60	205.127	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27428 - 	CGI_10027965	superfamily	241574	367	605	3.58E-42	154.281	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27429 - 	CGI_10027966	superfamily	241597	410	451	3.43E-06	45.3024	cl00082	HMG-box superfamily	C	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#27430 - 	CGI_10027967	superfamily	243092	6	294	4.27E-67	225.292	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#27430 - 	CGI_10027967	superfamily	219795	530	777	1.68E-49	174.871	cl08476	PUL superfamily	 - 	 - 	"PUL domain; The PUL (PLAP, Ufd3p and Lub1p) domain is a novel alpha-helical Ub-associated domain. It directly binds to Cdc48, a chaperone-like AAA ATPase that collects ubiquitylated substrates."
Q#27430 - 	CGI_10027967	superfamily	204121	339	455	1.37E-48	167.403	cl08519	PFU superfamily	 - 	 - 	PFU (PLAA family ubiquitin binding); This domain is found N terminal to pfam08324 and binds to ubiquitin.
Q#27432 - 	CGI_10027969	superfamily	218123	575	767	2.56E-74	245.301	cl04559	CP2 superfamily	 - 	 - 	CP2 transcription factor; This family represents a conserved region in the CP2 transcription factor family.
Q#27433 - 	CGI_10027970	superfamily	243092	545	859	1.44E-38	147.096	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#27433 - 	CGI_10027970	superfamily	247683	1065	1115	1.40E-24	99.1223	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#27435 - 	CGI_10027972	superfamily	242203	122	290	5.31E-51	169.067	cl00935	Brix superfamily	 - 	 - 	Brix domain; Brix domain.  
Q#27436 - 	CGI_10027973	superfamily	248145	12	231	2.98E-37	134.299	cl17591	CAF1 superfamily	C	 - 	CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Q#27438 - 	CGI_10027975	superfamily	241645	13	84	4.48E-16	72.1293	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#27439 - 	CGI_10027976	superfamily	241782	2	283	9.03E-54	180.23	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27440 - 	CGI_10027977	superfamily	243095	785	980	3.70E-81	263.558	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#27440 - 	CGI_10027977	superfamily	241622	82	165	1.27E-19	85.311	cl00117	PDZ superfamily	 - 	 - 	"PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1, a mammalian tight junction protein."
Q#27440 - 	CGI_10027977	superfamily	246669	658	730	7.17E-08	51.6839	cl14603	C2 superfamily	C	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27441 - 	CGI_10027978	superfamily	248458	96	404	7.88E-11	61.9461	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27442 - 	CGI_10027979	superfamily	248012	11	118	2.51E-07	48.7281	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27442 - 	CGI_10027979	superfamily	190233	262	320	5.16E-05	41.2858	cl08341	zf-TRAF superfamily	 - 	 - 	TRAF-type zinc finger; TRAF-type zinc finger.  
Q#27443 - 	CGI_10027981	superfamily	243035	24	135	2.19E-05	39.5254	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27444 - 	CGI_10027982	superfamily	247792	16	62	0.00126749	36.6548	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27445 - 	CGI_10027983	superfamily	214545	457	596	8.66E-59	196.772	cl10551	CULLIN superfamily	 - 	 - 	Cullin; Cullin.  
Q#27445 - 	CGI_10027983	superfamily	245539	704	771	1.01E-30	116.114	cl11186	Cullin_Nedd8 superfamily	 - 	 - 	"Cullin protein neddylation domain; This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue."
Q#27446 - 	CGI_10027984	superfamily	248097	295	417	3.98E-25	98.8766	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#27446 - 	CGI_10027984	superfamily	225368	68	166	0.00214554	36.2402	cl01058	NtpF superfamily	 - 	 - 	Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]
Q#27447 - 	CGI_10027985	superfamily	248097	63	172	3.14E-19	79.2314	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#27449 - 	CGI_10027987	superfamily	145577	58	83	4.25E-05	36.8786	cl03632	Spin-Ssty superfamily	N	 - 	Spin/Ssty Family; Spindlin (Spin) is a novel maternal transcript present in the unfertilised egg and early embryo. The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis and forms part of this Pfam family. Members of this family contain three copies of this 50 residue repeat. The repeat is predicted to contain four beta strands.
Q#27450 - 	CGI_10027988	superfamily	243166	18	155	8.34E-11	58.0738	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#27452 - 	CGI_10027990	superfamily	245226	197	365	2.02E-29	112.394	cl10012	DnaQ_like_exo superfamily	 - 	 - 	"DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer."
Q#27453 - 	CGI_10027991	superfamily	241818	107	150	0.000871686	36.4333	cl00366	PMSR superfamily	NC	 - 	Peptide methionine sulfoxide reductase; This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine.
Q#27455 - 	CGI_10027993	superfamily	241626	163	283	4.30E-59	188.197	cl00125	RHOD superfamily	 - 	 - 	"Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins."
Q#27457 - 	CGI_10027995	superfamily	212564	11	32	0.000185028	38.2143	cl17035	lambda-1 superfamily	C	 - 	"inner capsid protein lambda-1 or VP3; The reovirus inner capsid protein lambda-1 displays nucleoside triphosphate phosphohydrolase (NTPase), RNA-5'-triphosphatase (RTPase), and RNA helicase activity and may play a role in the transcription of the virus genome, the unwinding or reannealing of double-stranded RNA during RNA synthesis. The RTPase activity constitutes the first step in the capping of RNA, resulting in a 5'-diphosphorylated RNA plus-strand. lambda1 is an Orthoreovirus core protein, VP3 is the homologous core protein in Aquareoviruses."
Q#27459 - 	CGI_10027997	superfamily	243066	22	121	6.23E-09	54.1605	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27459 - 	CGI_10027997	superfamily	222150	752	777	2.22E-05	42.7641	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27459 - 	CGI_10027997	superfamily	246975	739	760	0.00464601	35.7857	cl15478	zf-C2H2 superfamily	 - 	 - 	"Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter."
Q#27460 - 	CGI_10027998	superfamily	243066	38	137	2.37E-10	58.3977	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27460 - 	CGI_10027998	superfamily	245531	697	771	5.01E-05	42.3783	cl11158	BEN superfamily	 - 	 - 	"BEN domain; The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription."
Q#27465 - 	CGI_10028003	superfamily	217293	38	103	7.69E-07	46.4719	cl03788	Neur_chan_LBD superfamily	C	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#27466 - 	CGI_10028004	superfamily	217293	33	238	2.76E-45	157.409	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#27466 - 	CGI_10028004	superfamily	202474	262	329	5.29E-08	51.8857	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#27467 - 	CGI_10028005	superfamily	245864	1	213	9.21E-71	225.235	cl12078	p450 superfamily	N	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#27468 - 	CGI_10028006	superfamily	216686	1	124	6.33E-26	98.9345	cl18377	Galactosyl_T superfamily	N	 - 	"Galactosyltransferase; This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2."
Q#27469 - 	CGI_10028007	superfamily	241629	76	212	6.11E-43	147.275	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#27469 - 	CGI_10028007	superfamily	241609	286	358	2.09E-14	67.8006	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#27470 - 	CGI_10028008	superfamily	247068	774	871	2.52E-12	65.0273	cl15786	CA_like superfamily	 - 	 - 	"Cadherin repeat-like domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan."
Q#27470 - 	CGI_10028008	superfamily	241629	74	212	2.81E-41	149.799	cl00133	SCP superfamily	 - 	 - 	"SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal SCP domains."
Q#27470 - 	CGI_10028008	superfamily	241609	264	334	2.39E-15	73.1934	cl00100	KR superfamily	 - 	 - 	"Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides."
Q#27471 - 	CGI_10028009	superfamily	247724	81	260	7.16E-98	286.835	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27474 - 	CGI_10028012	superfamily	247856	147	193	1.41E-08	50.6241	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27474 - 	CGI_10028012	superfamily	247856	60	112	5.22E-08	49.0833	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27474 - 	CGI_10028012	superfamily	247856	190	233	0.000213913	38.6829	cl17302	EFh superfamily	C	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27476 - 	CGI_10028014	superfamily	241578	648	703	1.85E-07	51.1382	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27476 - 	CGI_10028014	superfamily	243119	781	825	1.43E-05	43.9717	cl02629	CBM_14 superfamily	 - 	 - 	Chitin binding Peritrophin-A domain; This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Q#27479 - 	CGI_10028017	superfamily	241900	179	223	0.00320375	37.6565	cl00490	EEP superfamily	N	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#27480 - 	CGI_10028018	superfamily	243112	49	179	6.00E-52	167.428	cl02620	YDG_SRA superfamily	 - 	 - 	"YDG/SRA domain; The function of this domain is unknown, it contains a conserved motif YDG after which it has been named."
Q#27481 - 	CGI_10028019	superfamily	243032	668	989	5.24E-172	508.285	cl02427	Pumilio superfamily	 - 	 - 	"Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats."
Q#27481 - 	CGI_10028019	superfamily	247856	24	85	1.17E-14	70.6545	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27481 - 	CGI_10028019	superfamily	247856	99	149	7.50E-10	56.7873	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27485 - 	CGI_10028023	superfamily	218688	14	47	0.00139123	33.22	cl05315	ATP-synt_E superfamily	C	 - 	ATP synthase E chain; This family consists of several ATP synthase E chain sequences which are components of the CF(0) subunit.
Q#27486 - 	CGI_10028024	superfamily	247739	156	258	1.45E-35	128.108	cl17185	LPLAT superfamily	C	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#27487 - 	CGI_10028025	superfamily	247739	1	95	7.10E-37	138.893	cl17185	LPLAT superfamily	N	 - 	"Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene)."
Q#27488 - 	CGI_10028026	superfamily	193607	265	395	9.36E-76	233.618	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#27488 - 	CGI_10028026	superfamily	241554	72	197	1.13E-07	50.0367	cl00019	Macro superfamily	C	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#27489 - 	CGI_10028027	superfamily	248020	28	359	4.86E-50	176.501	cl17466	Sulfatase superfamily	 - 	 - 	Sulfatase; Sulfatase.  
Q#27490 - 	CGI_10028028	superfamily	241578	54	223	2.99E-13	68.7466	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27490 - 	CGI_10028028	superfamily	241578	447	510	1.43E-05	44.8642	cl00057	vWFA superfamily	C	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27490 - 	CGI_10028028	superfamily	241578	509	556	0.000413262	40.7938	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27491 - 	CGI_10028029	superfamily	241578	16	185	3.95E-13	66.8206	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27492 - 	CGI_10028030	superfamily	243095	1319	1502	4.98E-53	186.122	cl02570	RhoGAP superfamily	 - 	 - 	"RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins."
Q#27492 - 	CGI_10028030	superfamily	247724	153	245	5.14E-06	46.7315	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27493 - 	CGI_10028031	superfamily	245205	66	129	1.22E-05	40.6841	cl09930	RPA_2b-aaRSs_OBF_like superfamily	N	 - 	"Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism.  This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B,  of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases."
Q#27494 - 	CGI_10028032	superfamily	201810	84	161	7.94E-46	146.563	cl03226	Skp1 superfamily	 - 	 - 	"Skp1 family, dimerisation domain; Skp1 family, dimerisation domain.  "
Q#27494 - 	CGI_10028032	superfamily	248291	1	111	2.34E-27	99.6752	cl17737	Skp1_POZ superfamily	 - 	 - 	"Skp1 family, tetramerisation domain; Skp1 family, tetramerisation domain.  "
Q#27495 - 	CGI_10028033	superfamily	247724	225	442	5.42E-50	169.527	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27495 - 	CGI_10028033	superfamily	110047	141	223	1.72E-13	67.734	cl03072	GTP1_OBG superfamily	N	 - 	"GTP1/OBG; The N-terminal domain of B. subtilis GTPase obgE has the OBG fold, which is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich these regions form six left-handed collagen-like helices packed and H-bonded together."
Q#27496 - 	CGI_10028034	superfamily	242611	370	552	1.44E-70	232.038	cl01629	TPP_enzymes superfamily	 - 	 - 	"Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes."
Q#27496 - 	CGI_10028034	superfamily	245606	10	161	5.00E-57	193.517	cl11410	TPP_enzyme_PYR superfamily	 - 	 - 	"Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit."
Q#27496 - 	CGI_10028034	superfamily	247727	759	866	4.23E-11	61.2918	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#27496 - 	CGI_10028034	superfamily	215786	194	323	5.11E-41	148.083	cl18345	TPP_enzyme_M superfamily	 - 	 - 	"Thiamine pyrophosphate enzyme, central domain; The central domain of TPP enzymes contains a 2-fold Rossman fold."
Q#27496 - 	CGI_10028034	superfamily	216379	814	920	0.00251146	39.3011	cl18366	NNMT_PNMT_TEMT superfamily	N	 - 	NNMT/PNMT/TEMT family; NNMT/PNMT/TEMT family.  
Q#27497 - 	CGI_10028035	superfamily	219242	48	462	8.90E-74	245.678	cl06147	FPN1 superfamily	 - 	 - 	"Ferroportin1 (FPN1); This family represents a conserved region approximately 100 residues long within eukaryotic Ferroportin1 (FPN1), a protein that may play a role in iron export from the cell. This family may represent a number of transmembrane regions in Ferroportin1."
Q#27497 - 	CGI_10028035	superfamily	219242	529	609	3.22E-24	104.695	cl06147	FPN1 superfamily	N	 - 	"Ferroportin1 (FPN1); This family represents a conserved region approximately 100 residues long within eukaryotic Ferroportin1 (FPN1), a protein that may play a role in iron export from the cell. This family may represent a number of transmembrane regions in Ferroportin1."
Q#27500 - 	CGI_10028038	superfamily	241567	1	205	7.17E-23	92.6635	cl00042	CASc superfamily	 - 	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#27501 - 	CGI_10028039	superfamily	248012	13	94	4.45E-15	68.7585	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27503 - 	CGI_10028041	superfamily	247792	16	65	3.24E-06	43.9736	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27506 - 	CGI_10028044	superfamily	243034	498	597	8.16E-23	94.3691	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#27506 - 	CGI_10028044	superfamily	243034	566	665	5.02E-14	68.9459	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#27506 - 	CGI_10028044	superfamily	243034	449	529	4.72E-13	66.2496	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#27506 - 	CGI_10028044	superfamily	243034	636	709	5.17E-09	54.3084	cl02429	TPR superfamily	C	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#27506 - 	CGI_10028044	superfamily	149463	284	360	6.85E-20	85.3441	cl07144	DUF1736 superfamily	 - 	 - 	Domain of unknown function (DUF1736); This domain of unknown function is found in various hypothetical metazoan proteins.
Q#27508 - 	CGI_10028046	superfamily	247986	373	477	2.55E-09	56.9978	cl17432	PBPb superfamily	C	 - 	"Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD."
Q#27508 - 	CGI_10028046	superfamily	197504	599	758	4.27E-24	99.6712	cl18192	PBPe superfamily	 - 	 - 	Eukaryotic homologues of bacterial periplasmic substrate binding proteins; Prokaryotic homologues are represented by a separate alignment: PBPb
Q#27508 - 	CGI_10028046	superfamily	245225	31	205	8.79E-16	78.6924	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#27509 - 	CGI_10028047	superfamily	241984	74	358	2.34E-135	390.852	cl00615	Membrane-FADS-like superfamily	 - 	 - 	"The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase."
Q#27510 - 	CGI_10028048	superfamily	247803	323	513	1.43E-45	162.049	cl17249	YlqF_related_GTPase superfamily	 - 	 - 	"Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea.  They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases."
Q#27510 - 	CGI_10028048	superfamily	242415	4	172	1.26E-41	152.383	cl01287	AE_Prim_S_like superfamily	N	 - 	"AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro."
Q#27511 - 	CGI_10007854	superfamily	247999	192	243	1.15E-09	54.804	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#27512 - 	CGI_10007855	superfamily	241675	103	333	1.39E-115	350.778	cl00195	SIR2 superfamily	 - 	 - 	"SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines."
Q#27512 - 	CGI_10007855	superfamily	241672	493	630	0.000647248	41.5696	cl00192	ribokinase_pfkB_like superfamily	C	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#27513 - 	CGI_10007856	superfamily	207794	228	683	6.15E-132	402.826	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#27513 - 	CGI_10007856	superfamily	243574	2	91	0.000777845	39.6204	cl03918	CHB_HEX superfamily	N	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#27513 - 	CGI_10007856	superfamily	111707	166	230	0.00223049	37.7796	cl03741	Glyco_hydro_20b superfamily	N	 - 	"Glycosyl hydrolase family 20, domain 2; This domain has a zincin-like fold."
Q#27514 - 	CGI_10007857	superfamily	207794	323	774	2.90E-60	212.922	cl02948	GH20_hexosaminidase superfamily	 - 	 - 	"Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides.  These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase.  The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself."
Q#27514 - 	CGI_10007857	superfamily	243574	16	172	2.20E-07	50.406	cl03918	CHB_HEX superfamily	 - 	 - 	Putative carbohydrate binding domain; This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain.
Q#27517 - 	CGI_10007860	superfamily	198675	1109	1308	2.02E-46	167.437	cl02436	COLFI superfamily	 - 	 - 	"Fibrillar collagen C-terminal domain; Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc."
Q#27517 - 	CGI_10007860	superfamily	248289	35	102	5.36E-07	48.5743	cl17735	VWC superfamily	 - 	 - 	von Willebrand factor type C domain; The high cutoff was used to prevent overlap with pfam00094.
Q#27518 - 	CGI_10007861	superfamily	241782	62	290	6.78E-52	178.344	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27519 - 	CGI_10007862	superfamily	198675	1107	1312	4.77E-78	257.189	cl02436	COLFI superfamily	 - 	 - 	"Fibrillar collagen C-terminal domain; Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc."
Q#27520 - 	CGI_10007863	superfamily	241641	82	144	2.13E-13	65.1777	cl00150	TY superfamily	 - 	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#27521 - 	CGI_10028317	superfamily	241600	12	223	6.45E-98	286.829	cl00085	FReD superfamily	 - 	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#27522 - 	CGI_10028318	superfamily	247065	49	141	8.28E-18	75.459	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#27524 - 	CGI_10028320	superfamily	207627	1095	1183	4.08E-10	59.5707	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#27524 - 	CGI_10028320	superfamily	207627	1335	1427	4.20E-10	59.5707	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#27524 - 	CGI_10028320	superfamily	207627	1576	1668	1.23E-09	58.0347	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#27524 - 	CGI_10028320	superfamily	207627	1217	1308	2.20E-09	57.2595	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#27524 - 	CGI_10028320	superfamily	207627	1452	1546	8.06E-09	55.7187	cl02522	Calx-beta superfamily	 - 	 - 	Calx-beta domain; Calx-beta domain.  
Q#27526 - 	CGI_10028323	superfamily	245213	42	68	0.00196048	33.7642	cl09941	EGF_CA superfamily	N	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27529 - 	CGI_10028326	superfamily	241574	23	160	1.26E-53	168.941	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27530 - 	CGI_10028327	superfamily	241574	3	140	3.98E-47	151.607	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27531 - 	CGI_10028328	superfamily	241574	61	188	1.32E-55	175.49	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27532 - 	CGI_10028329	superfamily	241574	11	146	6.03E-47	150.837	cl00053	PTPc superfamily	 - 	 - 	"Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active."
Q#27533 - 	CGI_10028330	superfamily	221887	16	115	4.89E-21	85.2586	cl15229	ING superfamily	 - 	 - 	"Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterized C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail."
Q#27534 - 	CGI_10028331	superfamily	206050	241	331	0.000566768	38.024	cl16449	KIAA1430 superfamily	 - 	 - 	KIAA1430 homologue; This is a family of KIAA1430 homologues. The function is not known.
Q#27535 - 	CGI_10028332	superfamily	241597	13	57	0.000231838	39.9742	cl00082	HMG-box superfamily	C	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#27536 - 	CGI_10028333	superfamily	147490	470	526	1.49E-09	57.2172	cl09572	DUF719 superfamily	NC	 - 	Protein of unknown function (DUF719); This family consists of several eukaryotic proteins of unknown function.
Q#27537 - 	CGI_10028334	superfamily	197732	81	112	2.23E-08	47.6323	cl18195	ZnF_U1 superfamily	 - 	 - 	"U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins."
Q#27538 - 	CGI_10028335	superfamily	241874	190	622	2.04E-179	524.436	cl00456	SLC5-6-like_sbd superfamily	N	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#27538 - 	CGI_10028335	superfamily	241874	25	60	7.05E-18	86.079	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#27538 - 	CGI_10028335	superfamily	241874	132	176	1.25E-15	78.7602	cl00456	SLC5-6-like_sbd superfamily	C	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#27539 - 	CGI_10028336	superfamily	241563	17	51	1.75E-07	48.2444	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27540 - 	CGI_10028337	superfamily	241874	4	571	0	852.241	cl00456	SLC5-6-like_sbd superfamily	 - 	 - 	"Solute carrier families 5 and 6-like; solute binding domain; This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT."
Q#27540 - 	CGI_10028337	superfamily	241822	663	713	5.09E-14	67.8848	cl00373	Ribosomal_S18 superfamily	 - 	 - 	Ribosomal protein S18; Ribosomal protein S18.  
Q#27542 - 	CGI_10028339	superfamily	247724	220	466	1.40E-68	225.429	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27542 - 	CGI_10028339	superfamily	243185	477	585	4.47E-52	177.344	cl02787	Translation_Factor_II_like superfamily	 - 	 - 	"Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought  to be involved in binding of E.coli IF-2 to 30S subunits."
Q#27542 - 	CGI_10028339	superfamily	221359	582	688	1.70E-17	79.7975	cl13429	IF-2 superfamily	 - 	 - 	"Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes, Bacteria and Archaea). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyzes the hydrolysis of GTP following initiation-complex formation."
Q#27543 - 	CGI_10028340	superfamily	147416	108	216	1.36E-12	61.6408	cl04988	Sprouty superfamily	 - 	 - 	"Sprouty protein (Spry); This family consists of eukaryotic Sprouty protein homologues. Sprouty proteins have been revealed as inhibitors of the Ras/mitogen-activated protein kinase (MAPK) cascade, a pathway crucial for developmental processes initiated by activation of various receptor tyrosine kinases. The sprouty gene has found to be expressed in the the brain, cochlea, nasal organs, teeth, salivary gland, lungs, digestive tract, kidneys and limb buds in mice."
Q#27546 - 	CGI_10028343	superfamily	241782	6	363	0	585.027	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27547 - 	CGI_10028344	superfamily	247856	84	143	5.87E-09	48.6981	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27547 - 	CGI_10028344	superfamily	247856	26	73	0.0070834	32.1345	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27548 - 	CGI_10028345	superfamily	215754	146	233	1.24E-26	101.561	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27548 - 	CGI_10028345	superfamily	215754	50	143	6.76E-23	91.1608	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27548 - 	CGI_10028345	superfamily	215754	252	335	5.32E-21	85.768	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27550 - 	CGI_10028347	superfamily	243035	25	66	3.36E-06	42.7302	cl02432	CLECT superfamily	NC	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27551 - 	CGI_10028348	superfamily	247916	533	583	7.20E-07	48.1479	cl17362	Transglut_core superfamily	N	 - 	"Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease."
Q#27552 - 	CGI_10028349	superfamily	215647	39	136	0.000494966	38.7437	cl18338	7tm_2 superfamily	C	 - 	"7 transmembrane receptor (Secretin family); This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling."
Q#27558 - 	CGI_10028355	superfamily	243050	21	75	2.53E-34	122.068	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#27558 - 	CGI_10028355	superfamily	243050	83	137	3.19E-31	113.683	cl02475	LIM superfamily	 - 	 - 	"LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid)."
Q#27558 - 	CGI_10028355	superfamily	241599	216	273	7.43E-16	71.5056	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#27563 - 	CGI_10028361	superfamily	217293	29	237	1.64E-60	198.626	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#27563 - 	CGI_10028361	superfamily	202474	245	448	3.71E-07	49.5745	cl08379	Neur_chan_memb superfamily	 - 	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#27566 - 	CGI_10028365	superfamily	241573	149	379	1.56E-11	66.581	cl00051	CysPc superfamily	C	 - 	"Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction."
Q#27566 - 	CGI_10028365	superfamily	241749	1133	1218	5.48E-08	53.5437	cl00280	globin_like superfamily	N	 - 	superfamily containing globins and truncated hemoglobins
Q#27566 - 	CGI_10028365	superfamily	241749	1337	1378	0.00148389	39.232	cl00280	globin_like superfamily	C	 - 	superfamily containing globins and truncated hemoglobins
Q#27569 - 	CGI_10028368	superfamily	247723	237	319	1.35E-40	142.415	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27569 - 	CGI_10028368	superfamily	247723	158	234	1.23E-38	136.921	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27569 - 	CGI_10028368	superfamily	247723	333	404	3.16E-35	127.741	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27570 - 	CGI_10028369	superfamily	222269	52	271	1.01E-48	166.73	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#27571 - 	CGI_10028370	superfamily	217533	30	177	6.15E-71	221.258	cl04048	Ist1 superfamily	 - 	 - 	"Regulator of Vps4 activity in the MVB pathway; ESCRT-I, -II, and -III are endosomal sorting complexes required for transporting proteins and carry out cargo sorting and vesicle formation in the multivesicular bodies, MVBs, pathway. These complexes are transiently recruited from the cytoplasm to the endosomal membrane where they bind transmembrane proteins previously marked for degradation by mono-ubiquitination. Assembly of ESCRT-III, a complex composed of at least four subunits (Vps2, Vps24, Vps20, Snf7), is intimately linked with MVB vesicle formation, its disassembly being an essential step in the MVB vesicle formation, a reaction that is carried out by Vps4, an AAA-type ATPase. The family Ist1 is a regulator of Vps4 activity; by interacting with Did2 and Vps4, Ist1 appears to regulate the recruitment and oligomerisation of Vps4. Together Ist1, Did2, and Vta1 form a network of interconnected regulatory proteins that modulate Vps4 activity, thereby regulating the flow of cargo through the MVB pathway."
Q#27576 - 	CGI_10028375	superfamily	217293	1	150	1.44E-29	113.497	cl03788	Neur_chan_LBD superfamily	N	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#27576 - 	CGI_10028375	superfamily	202474	175	263	0.000222105	40.7149	cl08379	Neur_chan_memb superfamily	C	 - 	Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.
Q#27578 - 	CGI_10028377	superfamily	217293	72	246	1.74E-36	133.912	cl03788	Neur_chan_LBD superfamily	 - 	 - 	Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
Q#27580 - 	CGI_10028379	superfamily	247101	20	171	2.31E-15	71.4425	cl15849	Palm_thioest superfamily	N	 - 	Palmitoyl protein thioesterase; Palmitoyl protein thioesterase.  
Q#27585 - 	CGI_10028384	superfamily	243519	27	502	0	641.479	cl03757	phosphohexomutase superfamily	 - 	 - 	"The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model."
Q#27586 - 	CGI_10028385	superfamily	248458	52	252	5.28E-07	49.6197	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27588 - 	CGI_10028387	superfamily	243061	396	496	2.23E-37	134.007	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27588 - 	CGI_10028387	superfamily	243061	260	361	3.58E-37	133.236	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27588 - 	CGI_10028387	superfamily	243061	122	222	4.54E-36	130.155	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27588 - 	CGI_10028387	superfamily	243061	12	113	2.57E-34	125.532	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27590 - 	CGI_10028389	superfamily	245208	10	636	0	659.791	cl09933	ACAD superfamily	 - 	 - 	"Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH),  glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase.  The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC)"
Q#27591 - 	CGI_10028390	superfamily	241867	19	176	2.93E-23	93.387	cl00446	Lactamase_B superfamily	 - 	 - 	Metallo-beta-lactamase superfamily; Metallo-beta-lactamase superfamily.  
Q#27595 - 	CGI_10028394	superfamily	243066	24	122	1.53E-11	61.8645	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27595 - 	CGI_10028394	superfamily	222150	623	648	0.00917018	34.6749	cl16282	zf-H2C2_2 superfamily	 - 	 - 	Zinc-finger double domain; Zinc-finger double domain.  
Q#27596 - 	CGI_10028395	superfamily	241782	20	388	1.37E-81	267.285	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27596 - 	CGI_10028395	superfamily	241782	386	766	4.93E-66	224.528	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27597 - 	CGI_10028396	superfamily	247723	13	85	1.20E-42	140.833	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27598 - 	CGI_10028397	superfamily	245206	18	230	4.20E-81	245.282	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#27599 - 	CGI_10028398	superfamily	248054	6	220	1.79E-18	80.4243	cl17500	NAD_binding_8 superfamily	 - 	 - 	NAD(P)-binding Rossmann-like domain; NAD(P)-binding Rossmann-like domain.  
Q#27601 - 	CGI_10028401	superfamily	191182	290	391	2.81E-29	110.854	cl04917	Nsp1_C superfamily	 - 	 - 	Nsp1-like C-terminal region; This family probably forms a coiled-coil. This important region of Nsp1 is involved in binding Nup82.
Q#27601 - 	CGI_10028401	superfamily	222274	36	111	4.64E-07	47.866	cl18658	Nucleoporin_FG superfamily	N	 - 	"Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145."
Q#27603 - 	CGI_10028403	superfamily	247792	8	54	3.01E-07	46.67	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27605 - 	CGI_10028405	superfamily	191243	1	24	2.68E-05	38.1923	cl05016	zf-U11-48K superfamily	 - 	 - 	U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Q#27609 - 	CGI_10028409	superfamily	221442	473	543	3.18E-07	48.6994	cl18607	Hydrolase_4 superfamily	 - 	 - 	"Putative lysophospholipase; This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins."
Q#27611 - 	CGI_10028411	superfamily	244539	1549	1730	2.77E-48	173.645	cl06868	FNR_like superfamily	 - 	 - 	"Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H)."
Q#27611 - 	CGI_10028411	superfamily	247856	1120	1180	1.93E-07	50.6241	cl17302	EFh superfamily	 - 	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27611 - 	CGI_10028411	superfamily	246664	583	923	2.71E-110	363.928	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#27611 - 	CGI_10028411	superfamily	109874	63	189	1.89E-17	81.957	cl02980	Stathmin superfamily	 - 	 - 	Stathmin family; The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton. They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerisation of tubulin heterodimers.
Q#27611 - 	CGI_10028411	superfamily	109874	196	269	4.15E-08	53.4522	cl02980	Stathmin superfamily	N	 - 	Stathmin family; The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton. They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerisation of tubulin heterodimers.
Q#27611 - 	CGI_10028411	superfamily	242267	1375	1508	0.000130861	42.2772	cl01043	Ferric_reduct superfamily	 - 	 - 	"Ferric reductase like transmembrane component; This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease."
Q#27612 - 	CGI_10028412	superfamily	219153	117	282	9.72E-59	199.504	cl15854	DEAD_2 superfamily	 - 	 - 	"DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast."
Q#27612 - 	CGI_10028412	superfamily	248014	558	716	1.29E-49	173.907	cl17460	Csf4_U superfamily	 - 	 - 	CRISPR/Cas system-associated DinG family helicase Csf4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
Q#27613 - 	CGI_10028413	superfamily	246723	108	611	0	648.855	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27616 - 	CGI_10028416	superfamily	199166	308	420	1.02E-07	51.9444	cl15308	AMN1 superfamily	N	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#27616 - 	CGI_10028416	superfamily	199166	432	500	0.00570795	37.3068	cl15308	AMN1 superfamily	C	 - 	"Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model."
Q#27620 - 	CGI_10012549	superfamily	248305	63	207	4.46E-13	69.6888	cl17751	Glyco_transf_22 superfamily	C	 - 	Alg9-like mannosyltransferase family; Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Q#27621 - 	CGI_10012550	superfamily	241832	89	274	8.55E-74	229.546	cl00388	Thioredoxin_like superfamily	 - 	 - 	"Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others."
Q#27623 - 	CGI_10012552	superfamily	241567	36	120	3.09E-22	90.7606	cl00042	CASc superfamily	C	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#27623 - 	CGI_10012552	superfamily	241567	128	197	2.27E-21	88.4263	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#27624 - 	CGI_10012553	superfamily	241567	286	417	2.50E-34	128.487	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#27624 - 	CGI_10012553	superfamily	246680	1	89	3.38E-12	62.4436	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#27626 - 	CGI_10012555	superfamily	242880	5	232	1.98E-101	297.18	cl02098	14-3-3 superfamily	 - 	 - 	"14-3-3 domain; 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 14-3-3 proteins play important roles in many biological processes that are regulated by phosphorylation, including cell cycle regulation, cell proliferation, protein trafficking, metabolic regulation and apoptosis.  More than 300 binding partners of the 14-3-3 domain have been identified in all subcellular compartments and include transcription factors, signaling molecules, tumor suppressors, biosynthetic enzymes, cytoskeletal proteins and apoptosis factors. 14-3-3 binding can alter the conformation, localization, stability, phosphorylation state, activity as well as molecular interactions of a target protein. They function only as dimers, some preferring strictly homodimeric interaction, while others form heterodimers. Binding of the 14-3-3 domain to its target occurs in a phosphospecific manner where it binds to one of two consensus sequences of their target proteins; RSXpSXP (mode-1) and RXXXpSXP (mode-2). In some instances, 14-3-3 domain containing proteins are involved in regulation and signaling of a number of cellular processes in phosphorylation-independent manner. Many organisms express multiple isoforms: there are seven mammalian 14-3-3 family members (beta, gamma, eta, theta, epsilon, sigma, zeta), each encoded by a distinct gene, while plants contain up to 13 isoforms. The flexible C-terminal segment of 14-3-3 isoforms shows the highest sequence variability and may significantly contribute to individual isoform uniqueness by playing an important regulatory role by occupying the ligand binding groove and blocking the binding of inappropriate ligands in a distinct manner. Elevated amounts of 14-3-3 proteins are found in the cerebrospinal fluid of patients with Creutzfeldt-Jakob disease. In protozoa, like Plasmodium or Cryptosporidium parvum 14-3-3 proteins play an important role in key steps of parasite development."
Q#27627 - 	CGI_10012556	superfamily	242880	5	232	7.55E-103	301.032	cl02098	14-3-3 superfamily	 - 	 - 	"14-3-3 domain; 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 14-3-3 proteins play important roles in many biological processes that are regulated by phosphorylation, including cell cycle regulation, cell proliferation, protein trafficking, metabolic regulation and apoptosis.  More than 300 binding partners of the 14-3-3 domain have been identified in all subcellular compartments and include transcription factors, signaling molecules, tumor suppressors, biosynthetic enzymes, cytoskeletal proteins and apoptosis factors. 14-3-3 binding can alter the conformation, localization, stability, phosphorylation state, activity as well as molecular interactions of a target protein. They function only as dimers, some preferring strictly homodimeric interaction, while others form heterodimers. Binding of the 14-3-3 domain to its target occurs in a phosphospecific manner where it binds to one of two consensus sequences of their target proteins; RSXpSXP (mode-1) and RXXXpSXP (mode-2). In some instances, 14-3-3 domain containing proteins are involved in regulation and signaling of a number of cellular processes in phosphorylation-independent manner. Many organisms express multiple isoforms: there are seven mammalian 14-3-3 family members (beta, gamma, eta, theta, epsilon, sigma, zeta), each encoded by a distinct gene, while plants contain up to 13 isoforms. The flexible C-terminal segment of 14-3-3 isoforms shows the highest sequence variability and may significantly contribute to individual isoform uniqueness by playing an important regulatory role by occupying the ligand binding groove and blocking the binding of inappropriate ligands in a distinct manner. Elevated amounts of 14-3-3 proteins are found in the cerebrospinal fluid of patients with Creutzfeldt-Jakob disease. In protozoa, like Plasmodium or Cryptosporidium parvum 14-3-3 proteins play an important role in key steps of parasite development."
Q#27628 - 	CGI_10012557	superfamily	247724	319	593	2.81E-83	271.811	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27629 - 	CGI_10012558	superfamily	220393	4	197	1.89E-48	161.004	cl10751	Tmem26 superfamily	C	 - 	"Transmembrane protein 26; The function of this family of transmembrane proteins has not, as yet, been determined."
Q#27630 - 	CGI_10012559	superfamily	241613	39	73	1.75E-06	41.0382	cl00104	LDLa superfamily	 - 	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#27630 - 	CGI_10012559	superfamily	246918	1	34	0.000117844	36.0255	cl15278	TSP_1 superfamily	N	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27631 - 	CGI_10012560	superfamily	215754	203	291	3.49E-18	77.2936	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27631 - 	CGI_10012560	superfamily	215754	15	87	6.94E-13	63.0412	cl02813	Mito_carr superfamily	N	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27631 - 	CGI_10012560	superfamily	215754	98	197	5.36E-10	54.952	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27633 - 	CGI_10012562	superfamily	243061	173	274	7.47E-46	154.807	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27633 - 	CGI_10012562	superfamily	243061	65	165	2.84E-38	134.777	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27633 - 	CGI_10012562	superfamily	243061	279	379	1.26E-37	132.851	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27634 - 	CGI_10012563	superfamily	241554	2	123	1.03E-22	92.7187	cl00019	Macro superfamily	N	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#27634 - 	CGI_10012563	superfamily	241554	203	318	1.42E-08	51.456	cl00019	Macro superfamily	 - 	 - 	"Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes."
Q#27635 - 	CGI_10010099	superfamily	242406	185	287	1.12E-10	57.9865	cl01271	DUF1768 superfamily	N	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#27637 - 	CGI_10010101	superfamily	248012	2	91	4.97E-06	40.3844	cl17458	TIR_2 superfamily	N	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27638 - 	CGI_10010102	superfamily	150859	52	92	2.96E-12	56.2993	cl10937	PRCC_Cterm superfamily	 - 	 - 	Mitotic checkpoint protein PRCC_Cterm; This is the highly conserved C-terminal domain of the renal papillary carcinoma protein PRCC. The function of this domain is not known.
Q#27639 - 	CGI_10010103	superfamily	244535	27	300	1.17E-08	54.2792	cl06858	DUF1704 superfamily	N	 - 	Domain of unknown function (DUF1704); This family contains many hypothetical proteins.
Q#27640 - 	CGI_10010104	superfamily	246597	69	174	3.18E-51	170.593	cl13995	MPP_superfamily superfamily	C	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#27640 - 	CGI_10010104	superfamily	246597	249	333	7.37E-16	73.9079	cl13995	MPP_superfamily superfamily	N	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#27641 - 	CGI_10010105	superfamily	247905	295	403	2.71E-10	59.5589	cl17351	HELICc superfamily	N	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#27641 - 	CGI_10010105	superfamily	243778	455	547	3.21E-17	79.1903	cl04503	HA2 superfamily	 - 	 - 	"Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding."
Q#27641 - 	CGI_10010105	superfamily	219532	583	681	0.000183027	41.531	cl06657	OB_NTP_bind superfamily	 - 	 - 	"Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself - . The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins."
Q#27642 - 	CGI_10010106	superfamily	243129	227	338	6.81E-26	100.021	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#27642 - 	CGI_10010106	superfamily	243129	67	172	9.79E-20	83.0629	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#27644 - 	CGI_10010108	superfamily	118272	634	740	6.49E-31	118.308	cl10724	DUF2043 superfamily	 - 	 - 	Uncharacterized conserved protein (DUF2043); This is a 100 residue conserved region of a family of proteins found from fungi to humans. This region contains three conserved Cysteines and a motif of {CP}{y/l}{HG}.
Q#27647 - 	CGI_10010111	superfamily	110440	322	348	0.0025886	35.4613	cl03211	NHL superfamily	 - 	 - 	"NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in bovine PAM (peptidyl-glycine alpha-amidating monooxygenase), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. Human E3 ubiquitin-protein ligase TRIM32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats."
Q#27649 - 	CGI_10010113	superfamily	217410	15	81	0.000194322	38.104	cl18409	DDE_1 superfamily	N	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere."
Q#27651 - 	CGI_10010115	superfamily	245201	26	277	1.62E-130	386.799	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27651 - 	CGI_10010115	superfamily	201217	472	521	1.04E-14	69.4768	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#27651 - 	CGI_10010115	superfamily	201217	419	469	3.61E-12	62.158	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#27651 - 	CGI_10010115	superfamily	201217	366	416	9.25E-09	52.528	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#27651 - 	CGI_10010115	superfamily	201217	524	587	0.000958453	37.5052	cl08266	RCC1 superfamily	 - 	 - 	Regulator of chromosome condensation (RCC1) repeat; Regulator of chromosome condensation (RCC1) repeat.  
Q#27653 - 	CGI_10017787	superfamily	241600	4	85	5.27E-29	104.245	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#27655 - 	CGI_10017789	superfamily	241958	43	448	4.59E-68	225.087	cl00573	SDF superfamily	 - 	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#27657 - 	CGI_10017791	superfamily	241958	3	93	3.37E-08	50.977	cl00573	SDF superfamily	C	 - 	Sodium:dicarboxylate symporter family; Sodium:dicarboxylate symporter family.  
Q#27658 - 	CGI_10017792	superfamily	243142	84	204	2.43E-10	60.3327	cl02689	RUN superfamily	 - 	 - 	"RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases."
Q#27659 - 	CGI_10017793	superfamily	243066	26	127	2.41E-18	80.0424	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27659 - 	CGI_10017793	superfamily	198867	138	245	5.91E-10	56.1956	cl06652	BACK superfamily	 - 	 - 	"BTB And C-terminal Kelch; This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation)."
Q#27660 - 	CGI_10017794	superfamily	246597	129	424	1.21E-102	313.441	cl13995	MPP_superfamily superfamily	 - 	 - 	"metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases).  The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination."
Q#27661 - 	CGI_10017795	superfamily	238012	427	466	0.0058094	35.4078	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#27662 - 	CGI_10017796	superfamily	221258	131	280	1.61E-33	121.329	cl13308	DUF3361 superfamily	 - 	 - 	Domain of unknown function (DUF3361); This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 154 to 168 amino acids in length.
Q#27663 - 	CGI_10017797	superfamily	247725	277	406	2.33E-38	136.282	cl17171	PH-like superfamily	 - 	 - 	"Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins."
Q#27663 - 	CGI_10017797	superfamily	218231	35	210	1.20E-37	135.869	cl04708	ELMO_CED12 superfamily	 - 	 - 	"ELMO/CED-12 family; This family represents a conserved domain which is found in a number of eukaryotic proteins including CED-12, ELMO I and ELMO II. ELMO1 is a component of signalling pathways that regulate phagocytosis and cell migration and is the mammalian orthologue of the C. elegans gene, ced-12. CED-12 is required for the engulfment of dying cells and cell migration. In mammalian cells, ELMO1 interacts with Dock180 as part of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. ELMO1 is ubiquitously expressed, although its expression is highest in the spleen, an organ rich in immune cells. ELMO1 has a PH domain and a polyproline sequence motif at its C terminus which are not present in this alignment."
Q#27666 - 	CGI_10017800	superfamily	241600	2	170	6.97E-76	228.279	cl00085	FReD superfamily	N	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#27669 - 	CGI_10017803	superfamily	245814	380	448	0.000354523	39.0095	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#27670 - 	CGI_10017804	superfamily	247065	4	96	8.31E-16	69.2958	cl15777	GGCT_like superfamily	 - 	 - 	"GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC)."
Q#27671 - 	CGI_10017805	superfamily	247724	13	174	1.12E-100	290.867	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27672 - 	CGI_10017806	superfamily	220867	111	412	6.11E-37	145.7	cl11338	Med1 superfamily	 - 	 - 	"Mediator of RNA polymerase II transcription subunit 1; Mediator complexes are basic necessities for linking transcriptional regulators to RNA polymerase II. This domain, Med1, is conserved from plants to fungi to humans and forms part of the Med9 submodule of the Srb/Med complex. it is one of three subunits essential for viability of the whole organism via its role in environmentally-directed cell-fate decisions. Med1 is part of the tail region of the Mediator complex."
Q#27673 - 	CGI_10017807	superfamily	247724	9	172	1.31E-95	277.752	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27674 - 	CGI_10017809	superfamily	241596	61	118	1.07E-17	74.1727	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#27675 - 	CGI_10017810	superfamily	241596	50	110	3.02E-17	72.6319	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#27676 - 	CGI_10017811	superfamily	247792	22	69	1.07E-06	46.67	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27676 - 	CGI_10017811	superfamily	241563	97	132	0.00287416	36.5463	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27677 - 	CGI_10017812	superfamily	217473	249	397	1.23E-27	113.614	cl03978	Mab-21 superfamily	N	 - 	Mab-21 protein; This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development.
Q#27677 - 	CGI_10017812	superfamily	243034	709	742	0.00358486	36.2416	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#27678 - 	CGI_10017813	superfamily	241563	78	119	1.63E-05	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27678 - 	CGI_10017813	superfamily	241563	38	69	0.00752424	34.7624	cl00034	BBOX superfamily	N	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27679 - 	CGI_10017814	superfamily	242274	13	126	5.79E-05	40.1873	cl01053	SGNH_hydrolase superfamily	N	 - 	"SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid."
Q#27680 - 	CGI_10017815	superfamily	216101	27	480	1.02E-134	404.753	cl08288	Carn_acyltransf superfamily	 - 	 - 	Choline/Carnitine o-acyltransferase; Choline/Carnitine o-acyltransferase.  
Q#27682 - 	CGI_10017817	superfamily	216167	9	115	1.21E-32	121.925	cl02999	DNA_photolyase superfamily	C	 - 	DNA photolyase; This domain binds a light harvesting cofactor.
Q#27687 - 	CGI_10015570	superfamily	247683	296	353	3.20E-30	111.568	cl17036	SH3 superfamily	 - 	 - 	"Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction."
Q#27687 - 	CGI_10015570	superfamily	217886	128	277	2.49E-40	142.754	cl04393	Peroxin-13_N superfamily	 - 	 - 	"Peroxin 13, N-terminal region; Both termini of the Peroxin-13 are oriented to the cytosol. Peroxin-13 is required for peroxisomal association of peroxin-14."
Q#27688 - 	CGI_10015571	superfamily	243066	126	225	1.24E-42	145.388	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27689 - 	CGI_10015572	superfamily	219619	179	209	2.38E-08	51.4395	cl18518	Ion_trans_2 superfamily	NC	 - 	Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
Q#27690 - 	CGI_10015573	superfamily	247742	5	413	0	741.081	cl17188	enolase_like superfamily	 - 	 - 	"Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase."
Q#27693 - 	CGI_10015576	superfamily	241645	108	172	0.00887516	34.3797	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#27694 - 	CGI_10015577	superfamily	245622	477	612	2.44E-22	94.2134	cl11446	Rhomboid superfamily	 - 	 - 	"Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite."
Q#27695 - 	CGI_10015578	superfamily	112128	253	458	7.27E-108	321.742	cl03992	TF_AP-2 superfamily	 - 	 - 	Transcription factor AP-2; Transcription factor AP-2.  
Q#27697 - 	CGI_10015580	superfamily	248458	56	459	4.83E-32	124.734	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27700 - 	CGI_10015583	superfamily	241603	242	459	4.81E-21	94.3501	cl00089	NUC superfamily	 - 	 - 	DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.  They exists as monomers and homodimers.
Q#27700 - 	CGI_10015583	superfamily	241603	1739	1944	1.12E-18	87.0313	cl00089	NUC superfamily	 - 	 - 	DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.  They exists as monomers and homodimers.
Q#27700 - 	CGI_10015583	superfamily	241603	944	1104	5.74E-12	66.2305	cl00089	NUC superfamily	C	 - 	DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.  They exists as monomers and homodimers.
Q#27700 - 	CGI_10015583	superfamily	241603	1120	1226	1.24E-10	61.9933	cl00089	NUC superfamily	N	 - 	DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.  They exists as monomers and homodimers.
Q#27700 - 	CGI_10015583	superfamily	131388	504	749	6.86E-10	62.2245	cl17985	hydr_PhnA superfamily	C	 - 	"phosphonoacetate hydrolase; This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile that the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for pther specific phosphonatases."
Q#27700 - 	CGI_10015583	superfamily	131388	1270	1345	1.61E-06	51.4389	cl17985	hydr_PhnA superfamily	C	 - 	"phosphonoacetate hydrolase; This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile that the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for pther specific phosphonatases."
Q#27700 - 	CGI_10015583	superfamily	248017	1407	1481	0.0056047	40.0848	cl17463	iPGM_N superfamily	N	 - 	"BPG-independent PGAM N-terminus (iPGM_N); This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (EC:5.4.2.1). The family is found in conjunction with pfam01676 (located in the C-terminal region of the protein)."
Q#27701 - 	CGI_10015584	superfamily	220692	53	364	3.41E-11	62.6069	cl18570	7TM_GPCR_Srw superfamily	 - 	 - 	Serpentine type 7TM GPCR chemoreceptor Srw; Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Q#27702 - 	CGI_10015585	superfamily	243092	3	121	4.14E-20	82.768	cl02567	WD40 superfamily	NC	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#27703 - 	CGI_10015586	superfamily	216152	128	403	9.88E-69	226.811	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#27704 - 	CGI_10015587	superfamily	216152	13	369	1.71E-78	249.923	cl02988	Glyco_transf_10 superfamily	 - 	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#27705 - 	CGI_10015588	superfamily	216152	3	148	1.09E-36	132.823	cl02988	Glyco_transf_10 superfamily	N	 - 	"Glycosyltransferase family 10 (fucosyltransferase); This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10."
Q#27710 - 	CGI_10015593	superfamily	245622	568	692	3.81E-26	105.384	cl11446	Rhomboid superfamily	 - 	 - 	"Rhomboid family; This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite."
Q#27712 - 	CGI_10009312	superfamily	245213	862	895	0.000287525	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27712 - 	CGI_10009312	superfamily	245213	945	979	0.0019243	37.6162	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27712 - 	CGI_10009312	superfamily	245213	693	726	0.00369225	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27712 - 	CGI_10009312	superfamily	245213	482	522	0.00437357	36.8458	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27712 - 	CGI_10009312	superfamily	245213	523	564	0.00928812	35.6902	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27712 - 	CGI_10009312	superfamily	241578	646	690	8.22E-06	46.9944	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27712 - 	CGI_10009312	superfamily	241578	556	597	3.00E-05	45.4536	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27712 - 	CGI_10009312	superfamily	241578	730	772	0.00032146	42.372	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27712 - 	CGI_10009312	superfamily	241578	388	436	0.000763781	41.2164	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27712 - 	CGI_10009312	superfamily	241578	311	354	0.00141931	40.446	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27712 - 	CGI_10009312	superfamily	243060	1112	1170	0.00371301	37.3584	cl02507	SEA superfamily	N	 - 	"SEA domain; Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain."
Q#27712 - 	CGI_10009312	superfamily	241578	899	940	0.00900837	37.7496	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27714 - 	CGI_10009314	superfamily	241900	96	337	1.71E-83	256.116	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#27717 - 	CGI_10020075	superfamily	241782	1	141	2.47E-21	88.1672	cl00321	AAT_I superfamily	NC	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27718 - 	CGI_10020076	superfamily	241782	37	294	2.53E-40	144.791	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27719 - 	CGI_10020077	superfamily	241782	4	96	8.87E-13	65.8256	cl00321	AAT_I superfamily	N	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27720 - 	CGI_10020078	superfamily	245206	25	293	3.10E-95	285.272	cl09931	NADB_Rossmann superfamily	 - 	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#27724 - 	CGI_10020082	superfamily	243110	131	321	1.02E-19	87.0997	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#27725 - 	CGI_10020083	superfamily	246925	2	55	7.09E-05	38.1054	cl15309	LRR_RI superfamily	NC	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27727 - 	CGI_10020085	superfamily	243110	89	273	2.19E-19	87.0997	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#27728 - 	CGI_10020086	superfamily	243110	127	342	1.18E-19	87.8701	cl02616	MACPF superfamily	 - 	 - 	"MAC/Perforin domain; The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold."
Q#27731 - 	CGI_10020089	superfamily	241571	29	138	8.29E-19	78.223	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#27734 - 	CGI_10020092	superfamily	241900	285	558	5.33E-55	188.376	cl00490	EEP superfamily	 - 	 - 	"Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins."
Q#27737 - 	CGI_10020095	superfamily	202894	87	150	1.72E-13	61.853	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#27738 - 	CGI_10020096	superfamily	202894	93	156	1.30E-14	65.705	cl04406	Mpv17_PMP22 superfamily	 - 	 - 	"Mpv17 / PMP22 family; The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance."
Q#27739 - 	CGI_10020097	superfamily	217007	56	349	3.24E-116	350.747	cl11995	Syja_N superfamily	 - 	 - 	SacI homology domain; This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
Q#27740 - 	CGI_10020098	superfamily	241599	179	238	8.78E-14	66.498	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#27742 - 	CGI_10018163	superfamily	246664	163	537	2.60E-140	413.509	cl14561	An_peroxidase_like superfamily	 - 	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#27742 - 	CGI_10018163	superfamily	246664	59	101	1.80E-06	48.8458	cl14561	An_peroxidase_like superfamily	C	 - 	"Animal heme peroxidases and related proteins; A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well."
Q#27744 - 	CGI_10018165	superfamily	243066	23	123	1.95E-13	66.8721	cl02518	BTB superfamily	 - 	 - 	"BTB/POZ domain; The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN."
Q#27745 - 	CGI_10018166	superfamily	241644	6	148	1.42E-56	177.009	cl00154	UBCc superfamily	 - 	 - 	"Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3.  This pathway regulates many fundamental cellular processes.  There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD."
Q#27748 - 	CGI_10018169	superfamily	245201	4	264	0	533.431	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27749 - 	CGI_10018170	superfamily	245847	105	232	1.86E-12	61.3643	cl12042	FA58C superfamily	 - 	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#27751 - 	CGI_10018172	superfamily	246723	1145	1709	0	993.225	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27751 - 	CGI_10018172	superfamily	246723	1734	2299	0	983.21	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27751 - 	CGI_10018172	superfamily	246723	2325	2889	0	944.305	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27751 - 	CGI_10018172	superfamily	246723	556	1119	0	921.578	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27751 - 	CGI_10018172	superfamily	246723	2912	3494	0	834.908	cl14813	GluZincin superfamily	 - 	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27751 - 	CGI_10018172	superfamily	246723	35	485	0	679.288	cl14813	GluZincin superfamily	C	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27751 - 	CGI_10018172	superfamily	246723	480	525	4.38E-16	83.3839	cl14813	GluZincin superfamily	N	 - 	"Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as the M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), and contain HEXXH and EXXXD motifs as part of their active site. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H).  APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The peptidase M3 or neurolysin-like family, includes M3, M2 and M32 metallopeptidases.  The M3 peptidases have two subfamilies: M3A, includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; M3B contains oligopeptidase F. M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key part of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M32 family includes two eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, making them attractive targets for drug development. The M4 family includes secreted protease  thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, neutral protease as well as fungalysin and bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. Peptidase M36 (fungamysin) family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers."
Q#27758 - 	CGI_10018180	superfamily	243134	36	128	1.79E-20	83.4676	cl02663	Fasciclin superfamily	C	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#27758 - 	CGI_10018180	superfamily	243134	125	197	9.15E-15	67.2892	cl02663	Fasciclin superfamily	C	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#27759 - 	CGI_10018181	superfamily	243134	37	136	1.25E-31	111.202	cl02663	Fasciclin superfamily	 - 	 - 	"Fasciclin domain; This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria."
Q#27760 - 	CGI_10018182	superfamily	238191	28	536	1.02E-119	365.502	cl18907	Esterase_lipase superfamily	 - 	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#27762 - 	CGI_10018184	superfamily	243072	1	118	2.93E-18	79.3498	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27762 - 	CGI_10018184	superfamily	243072	66	185	1.25E-17	77.809	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27762 - 	CGI_10018184	superfamily	243072	131	252	1.01E-16	75.1126	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27762 - 	CGI_10018184	superfamily	243072	196	325	1.74E-12	63.1714	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27766 - 	CGI_10014441	superfamily	248264	45	188	2.60E-05	42.6094	cl17710	DDE_4 superfamily	 - 	 - 	"DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction."
Q#27767 - 	CGI_10014442	superfamily	243061	1	101	5.53E-44	140.17	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#27768 - 	CGI_10014443	superfamily	241594	950	1238	5.01E-76	256.338	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#27768 - 	CGI_10014443	superfamily	207685	839	900	4.11E-24	98.1242	cl02642	PABP superfamily	 - 	 - 	"Poly-adenylate binding protein, unique domain; The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family."
Q#27769 - 	CGI_10014444	superfamily	151983	178	228	1.31E-22	94.6757	cl13062	E3_UbLigase_EDD superfamily	 - 	 - 	"E3 ubiquitin ligase EDD; EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins."
Q#27770 - 	CGI_10014445	superfamily	241607	586	638	2.82E-19	83.1225	cl00097	KAZAL_FS superfamily	 - 	 - 	"Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the  Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD."
Q#27770 - 	CGI_10014445	superfamily	248458	199	406	9.37E-13	69.2649	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27771 - 	CGI_10014446	superfamily	243084	256	354	9.64E-47	164.864	cl02556	Bromodomain superfamily	 - 	 - 	Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Q#27771 - 	CGI_10014446	superfamily	243083	375	455	3.12E-33	125.594	cl02554	PWWP superfamily	 - 	 - 	"The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids.  The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation.  Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.  The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes.  Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors."
Q#27771 - 	CGI_10014446	superfamily	247999	195	235	8.61E-08	50.952	cl17445	PHD superfamily	 - 	 - 	PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
Q#27771 - 	CGI_10014446	superfamily	203213	1412	1452	4.23E-06	45.957	cl04999	HTH_psq superfamily	 - 	 - 	"helix-turn-helix, Psq domain; This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence."
Q#27772 - 	CGI_10014447	superfamily	243166	85	284	3.29E-31	117.377	cl02759	TRAM_LAG1_CLN8 superfamily	 - 	 - 	TLC domain; TLC domain.  
Q#27772 - 	CGI_10014447	superfamily	203928	15	83	2.44E-16	72.2143	cl07130	TRAM1 superfamily	 - 	 - 	"TRAM1-like protein; This family comprises sequences that are similar to human TRAM1. This is a transmembrane protein of the endoplasmic reticulum, thought to be involved in the membrane transfer of secretory proteins. The region featured in this family is found N-terminal to the longevity-assurance protein region (pfam03798)."
Q#27773 - 	CGI_10014448	superfamily	198738	226	311	2.19E-39	137.785	cl02599	Ets superfamily	 - 	 - 	Ets-domain; Ets-domain.  
Q#27773 - 	CGI_10014448	superfamily	247057	9	74	9.75E-26	99.3849	cl15755	SAM_superfamily superfamily	 - 	 - 	"SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases."
Q#27775 - 	CGI_10014450	superfamily	217414	345	764	3.73E-82	270.74	cl03927	Otopetrin superfamily	 - 	 - 	"Protein of unknown function, DUF270; Protein of unknown function, DUF270.  "
Q#27778 - 	CGI_10028709	superfamily	189857	4	123	2.69E-41	135.841	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27779 - 	CGI_10028710	superfamily	189857	8	126	1.88E-40	133.915	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27780 - 	CGI_10028711	superfamily	189857	6	128	6.37E-39	130.063	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27781 - 	CGI_10028712	superfamily	189857	83	211	4.73E-53	169.353	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27782 - 	CGI_10028713	superfamily	189857	15	124	4.09E-30	106.951	cl07832	Caveolin superfamily	N	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27783 - 	CGI_10028714	superfamily	189857	2	132	2.82E-39	130.833	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27784 - 	CGI_10028715	superfamily	189857	1	127	3.90E-46	148.552	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27785 - 	CGI_10028716	superfamily	189857	1	123	4.75E-40	132.374	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27786 - 	CGI_10028717	superfamily	245864	24	427	1.42E-52	189.026	cl12078	p450 superfamily	 - 	 - 	"Cytochrome P450; Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures."
Q#27786 - 	CGI_10028717	superfamily	189857	609	736	2.25E-46	162.034	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27786 - 	CGI_10028717	superfamily	189857	490	597	1.13E-36	135.07	cl07832	Caveolin superfamily	 - 	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27786 - 	CGI_10028717	superfamily	189857	3	23	0.000563231	39.5406	cl07832	Caveolin superfamily	C	 - 	"Caveolin; All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression."
Q#27787 - 	CGI_10028718	superfamily	248458	37	176	0.000425494	41.1453	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27787 - 	CGI_10028718	superfamily	248458	294	469	0.000714694	40.3749	cl17904	MFS superfamily	N	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27788 - 	CGI_10028719	superfamily	246908	6	75	3.32E-18	74.0555	cl15255	SH2 superfamily	N	 - 	"Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1),  Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others."
Q#27789 - 	CGI_10028720	superfamily	247905	188	304	3.22E-15	70.7296	cl17351	HELICc superfamily	 - 	 - 	"Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process"
Q#27789 - 	CGI_10028720	superfamily	247805	1	146	1.02E-08	52.3396	cl17251	DEXDc superfamily	 - 	 - 	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Q#27791 - 	CGI_10028722	superfamily	244819	9	64	0.000242416	37.7642	cl07874	zf-AD superfamily	C	 - 	"Zinc-finger associated domain (zf-AD); The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA."
Q#27792 - 	CGI_10028723	superfamily	247743	89	180	4.18E-07	48.6815	cl17189	AAA superfamily	 - 	 - 	"The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases."
Q#27792 - 	CGI_10028723	superfamily	247912	358	565	2.31E-18	84.8604	cl17358	Beta-lactamase superfamily	N	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#27792 - 	CGI_10028723	superfamily	204202	254	313	9.82E-16	72.288	cl07827	Vps4_C superfamily	 - 	 - 	Vps4 C terminal oligomerisation domain; This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Q#27793 - 	CGI_10028724	superfamily	247912	37	333	4.06E-23	99.1128	cl17358	Beta-lactamase superfamily	 - 	 - 	Beta-lactamase; This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.
Q#27794 - 	CGI_10028725	superfamily	247724	10	167	1.05E-41	139.583	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27798 - 	CGI_10028729	superfamily	243058	209	303	4.69E-10	57.3243	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#27798 - 	CGI_10028729	superfamily	248012	337	436	7.66E-20	85.322	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27800 - 	CGI_10028731	superfamily	216897	177	241	5.34E-12	59.2321	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#27801 - 	CGI_10028732	superfamily	243212	242	380	8.91E-19	82.7769	cl02844	Arrestin_C superfamily	 - 	 - 	"Arrestin (or S-antigen), C-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain."
Q#27801 - 	CGI_10028732	superfamily	215866	110	219	5.95E-18	80.4471	cl18349	Arrestin_N superfamily	N	 - 	"Arrestin (or S-antigen), N-terminal domain; Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain."
Q#27802 - 	CGI_10028733	superfamily	243161	5	63	1.51E-14	66.6489	cl02739	THAP superfamily	C	 - 	"THAP domain; The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes."
Q#27805 - 	CGI_10028737	superfamily	241596	44	100	1.21E-12	63.0019	cl00081	HLH superfamily	 - 	 - 	"Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins."
Q#27808 - 	CGI_10028740	superfamily	245847	68	145	1.66E-12	60.6481	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#27808 - 	CGI_10028740	superfamily	245847	4	63	0.00995383	33.6842	cl12042	FA58C superfamily	N	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#27810 - 	CGI_10028742	superfamily	218390	1	310	1.11E-152	438.673	cl04895	PARG_cat superfamily	 - 	 - 	"Poly (ADP-ribose) glycohydrolase (PARG); Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death."
Q#27811 - 	CGI_10028743	superfamily	245213	529	565	1.00E-05	43.3942	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27811 - 	CGI_10028743	superfamily	245213	418	452	9.63E-05	40.3126	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27811 - 	CGI_10028743	superfamily	245213	305	341	0.000136776	39.9274	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27811 - 	CGI_10028743	superfamily	245213	491	527	0.00105706	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27811 - 	CGI_10028743	superfamily	245213	46	77	0.00112919	37.231	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27811 - 	CGI_10028743	superfamily	245213	118	153	0.00224924	36.4606	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27811 - 	CGI_10028743	superfamily	245213	568	604	0.00624363	35.305	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27811 - 	CGI_10028743	superfamily	245213	380	415	0.00838311	34.9198	cl09941	EGF_CA superfamily	 - 	 - 	"Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements."
Q#27812 - 	CGI_10028744	superfamily	159801	18	357	3.41E-42	154.426	cl12141	Tweety_N superfamily	 - 	 - 	"N-terminal domain of the protein encoded by the Drosophila tweety gene and related proteins, a family of chloride ion channels; The protein product of the Drosophila tweety (tty) gene is thought to form a trans-membrane protein with five membrane-spanning regions and a cytoplasmic C-terminus. This N-terminal domain contains the putative transmembrane spanning regions. Tweety has been suggested as a candidate for a large conductance chloride channel, both in vertebrate and insect cells. Three human homologs have been identified and designated TTYH1-3. TTYH2 has been associated with the progression of cancer, and Drosophila melanogaster tweety has been assumed to play a role in development. TTYH2, and TTYH3 bind to and are ubiquinated by Nedd4-2, a HECT type E3 ubiquitin ligase, which most likely plays a role in controlling the cellular levels of tweety family proteins."
Q#27813 - 	CGI_10028745	superfamily	245201	74	351	0	509.273	cl09925	PKc_like superfamily	 - 	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27815 - 	CGI_10028747	superfamily	248318	40	93	1.63E-19	82.0985	cl17764	FYVE superfamily	 - 	 - 	"FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;"
Q#27815 - 	CGI_10028747	superfamily	243058	130	263	0.000861293	37.6792	cl02500	ARM superfamily	 - 	 - 	"Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model."
Q#27817 - 	CGI_10028749	superfamily	248030	100	467	2.17E-48	174.869	cl17476	Glyco_transf_7C superfamily	N	 - 	"N-terminal domain of galactosyltransferase; This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalyzed reaction."
Q#27818 - 	CGI_10028750	superfamily	247038	295	397	4.72E-53	182.904	cl15674	IPT superfamily	 - 	 - 	"Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers."
Q#27818 - 	CGI_10028750	superfamily	243072	779	910	8.10E-29	114.018	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27818 - 	CGI_10028750	superfamily	243072	1064	1187	1.05E-27	110.936	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27818 - 	CGI_10028750	superfamily	243072	855	991	1.07E-23	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27818 - 	CGI_10028750	superfamily	243072	1132	1268	1.07E-23	99.3802	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27818 - 	CGI_10028750	superfamily	243072	717	838	2.05E-19	87.0538	cl02529	ANK superfamily	 - 	 - 	"ankyrin repeats;  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats."
Q#27818 - 	CGI_10028750	superfamily	246680	1341	1415	1.12E-16	77.2904	cl14633	DD_superfamily superfamily	 - 	 - 	"The Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer."
Q#27818 - 	CGI_10028750	superfamily	208843	97	288	1.26E-73	245.08	cl08275	RHD-n superfamily	 - 	 - 	"N-terminal sub-domain of the Rel homology domain (RHD); Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal sub-domain, which may be distantly related to the DNA-binding domain found in P53. The C-terminal sub-domain has an immunoglobulin-like fold and serves as a dimerization module that also binds DNA (see cd00102). The RHD is found in NF-kappa B, nuclear factor of activated T-cells (NFAT), the tonicity-responsive enhancer binding protein (TonEBP), and the arthropod proteins Dorsal and Relish (Rel)."
Q#27820 - 	CGI_10028752	superfamily	241971	4	264	1.33E-92	276.715	cl00599	Extradiol_Dioxygenase_3B_like superfamily	 - 	 - 	"Subunit B of Class III Extradiol ring-cleavage dioxygenases; Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be further divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two-domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B. This model represents the catalytic subunit B of extradiol dioxygenase class III enzymes. Enzymes belonging to this family include Protocatechuate 4,5-dioxygenase (LigAB), 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB), 4,5-DOPA Dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase, and 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD). There are also some family members that do not show the typical dioxygenase activity."
Q#27822 - 	CGI_10028754	superfamily	207690	570	593	5.73E-07	46.9273	cl02656	zf-RanBP superfamily	 - 	 - 	Zn-finger in Ran binding protein and others; Zn-finger in Ran binding protein and others.  
Q#27829 - 	CGI_10028761	superfamily	150162	43	112	7.37E-20	79.4949	cl09646	FOP_dimer superfamily	 - 	 - 	FOP N terminal dimerisation domain; Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to subcellular structures. This domain includes a Lis-homology motif. It forms an alpha helical bundle and is involved in dimerisation.
Q#27830 - 	CGI_10028762	superfamily	215754	9	102	5.77E-19	79.2196	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27830 - 	CGI_10028762	superfamily	215754	102	192	1.05E-14	67.2784	cl02813	Mito_carr superfamily	 - 	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27830 - 	CGI_10028762	superfamily	215754	196	255	6.04E-09	51.4852	cl02813	Mito_carr superfamily	C	 - 	Mitochondrial carrier protein; Mitochondrial carrier protein.  
Q#27832 - 	CGI_10028764	superfamily	241797	37	284	2.56E-80	248.313	cl00337	UbiA superfamily	 - 	 - 	4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]
Q#27833 - 	CGI_10028766	superfamily	247724	26	225	6.06E-68	209.695	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27834 - 	CGI_10028767	superfamily	247724	27	226	2.42E-70	215.858	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27835 - 	CGI_10028768	superfamily	247724	27	229	2.50E-70	215.858	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27837 - 	CGI_10028770	superfamily	241641	276	335	6.46E-15	68.6445	cl00150	TY superfamily	 - 	 - 	Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
Q#27837 - 	CGI_10028770	superfamily	238155	159	276	2.49E-18	78.9558	cl08547	SPARC_EC superfamily	 - 	 - 	"SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate cell-matrix interactions; binds to such proteins as collagen and vitronectin and binds to endothelial cells thus inhibiting cellular proliferation. The EC domain interacts with a follistatin-like (FS) domain which appears to stabilize Ca2+ binding. The two EF-hands interact canonically but their conserved disulfide bonds confer a tight association between the EF-hand pair and an acid/amphiphilic N-terminal helix. Proposed active form involves a Ca2+ dependent symmetric homodimerization of EC-FS modules."
Q#27839 - 	CGI_10028772	superfamily	241591	300	378	2.08E-07	48.3863	cl00073	H15 superfamily	 - 	 - 	"linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber"
Q#27841 - 	CGI_10028774	superfamily	247723	1453	1532	6.98E-32	121.712	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27842 - 	CGI_10028775	superfamily	241677	27	166	2.79E-81	240.237	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#27843 - 	CGI_10028776	superfamily	247058	40	173	1.03E-39	140.774	cl15762	crotonase-like superfamily	C	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#27843 - 	CGI_10028776	superfamily	247058	177	312	5.39E-38	136.151	cl15762	crotonase-like superfamily	N	 - 	"Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole."
Q#27844 - 	CGI_10028777	superfamily	243035	134	246	4.31E-15	71.1117	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27845 - 	CGI_10028778	superfamily	244265	270	479	3.10E-107	320.365	cl05973	FAM20_C_like superfamily	 - 	 - 	"C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins; Drosophila Fj is a Golgi kinase that phosphorylates Ser or Thr residues within extracellular cadherin domains of a transmembrane receptor Fat and its ligand, Dachsous (Ds). The Fat signaling pathway regulates growth, gene expression, and planar cell polarity (PCP). Defects from mutation in the Drosophila fj gene include loss of the intermediate leg joint, and a PCP defect in the eye. Fjx1, the murine homologue of Fj, has been shown to be involved in both the Fat and Hippo signaling pathways, these two pathways intersect at multiple points. The Hippo pathway is important in organ size control and in cancer. FAM20B is a xylose kinase that may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. This domain has homology to a kinase-active site, mutation of three conserved Asp residues at the Drosophila Fj putative active site abolished its ability to phosphorylate Ft and Ds cadherin domains. FAM20A may participate in enamel development and gingival homeostasis, FAM20B in proteoglycan production, and FAM20C in bone development. FAM20C, also called Dentin Matrix Protein 4, is abundant in the dentin matrix, and may participate in the differentiation of mesenchymal precursor cells into functional odontoblast-like cells. Mutations in FAM20C are associated with lethal Osteosclerotic Bone Dysplasia (Raine Syndrome), and mutations in FAM20A with Amelogenesis imperfecta (AI) and Gingival Hyperplasia Syndrome. This model includes the FAM20_C domain family, previously known as DUF1193; FAM20_C appears to be homologous to the catalytic domain of the phosphoinositide 3-kinase (PI3K)-like family."
Q#27847 - 	CGI_10028780	superfamily	221663	878	1069	2.25E-38	143.206	cl14612	TFCD_C superfamily	 - 	 - 	"Tubulin folding cofactor D C terminal; This domain family is found in eukaryotes, and is typically between 182 and 199 amino acids in length. The family is found in association with pfam02985. There is a single completely conserved residue R that may be functionally important. Tubulin folding cofactor D does not co-polymerise with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alphabeta-heterodimers in microtubules."
Q#27848 - 	CGI_10028781	superfamily	247724	5	171	3.83E-88	273.444	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27848 - 	CGI_10028781	superfamily	247724	416	582	1.26E-61	204.015	cl17170	Ras_like_GTPase superfamily	 - 	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27848 - 	CGI_10028781	superfamily	192013	220	302	5.37E-37	132.689	cl07101	EF_assoc_2 superfamily	 - 	 - 	EF hand associated; This region predominantly appears near EF-hands (pfam00036) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Q#27848 - 	CGI_10028781	superfamily	192012	342	414	1.26E-30	115.032	cl07100	EF_assoc_1 superfamily	 - 	 - 	"EF hand associated; This region typically appears on the C-terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis). The EF hand associated region is found in yeast, vertebrates and plants."
Q#27849 - 	CGI_10028782	superfamily	243092	43	335	5.35E-25	101.643	cl02567	WD40 superfamily	 - 	 - 	"WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment."
Q#27852 - 	CGI_10028785	superfamily	199575	3	88	8.10E-40	138.897	cl15439	BTG superfamily	N	 - 	BTG family; BTG family.  
Q#27853 - 	CGI_10028786	superfamily	245836	518	736	2.84E-148	439.684	cl12015	Adenylation_DNA_ligase_like superfamily	 - 	 - 	"Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity."
Q#27853 - 	CGI_10028786	superfamily	244947	741	886	4.99E-89	281.288	cl08424	OBF_DNA_ligase_family superfamily	 - 	 - 	"The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain."
Q#27853 - 	CGI_10028786	superfamily	193687	303	371	2.00E-24	98.8039	cl00160	LbetaH superfamily	 - 	 - 	"Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms."
Q#27853 - 	CGI_10028786	superfamily	245596	4	159	1.54E-40	149.346	cl11394	Glyco_tranf_GTA_type superfamily	N	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#27854 - 	CGI_10028787	superfamily	242575	8	78	0.000806803	34.905	cl01548	YccV-like superfamily	N	 - 	Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.
Q#27855 - 	CGI_10028788	superfamily	245201	918	1005	1.40E-18	86.8216	cl09925	PKc_like superfamily	C	 - 	"Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins."
Q#27856 - 	CGI_10028789	superfamily	241782	5	72	0.00549735	34.6301	cl00321	AAT_I superfamily	C	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27857 - 	CGI_10028790	superfamily	241563	97	138	1.57E-05	42.8516	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27859 - 	CGI_10028792	superfamily	241563	65	106	4.99E-05	41.3108	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27861 - 	CGI_10028795	superfamily	241567	16	93	1.05E-05	43.7432	cl00042	CASc superfamily	NC	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#27862 - 	CGI_10028796	superfamily	241567	358	488	3.79E-08	52.9879	cl00042	CASc superfamily	N	 - 	"Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs."
Q#27863 - 	CGI_10028797	superfamily	216712	20	222	1.26E-74	233.296	cl03360	LIM_bind superfamily	 - 	 - 	"LIM-domain binding protein; The LIM-domain binding protein, binds to the LIM domain pfam00412 of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development. The Drosophila protein Chip is required for segmentation and activity of a remote wing margin enhancer. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions."
Q#27864 - 	CGI_10028799	superfamily	218497	15	120	1.02E-19	87.2819	cl04984	COMPASS-Shg1 superfamily	 - 	 - 	"COMPASS (Complex proteins associated with Set1p) component shg1; The Shg1 subunit is one of the eight subunits of the COMPASS complex, complex associated with SET1, conserved in yeasts and in other eukaryotes up to humans. It is associated with the region of the Set1 protein that is N-terminal to the C-terminus, ie Set1-560-900. The function of Shg1 seems to be to slightly inhibit histone 3 lysine 4 (H3K4) di- and tri-methylation, and it is a pioneer protein. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for silencing of genes close to the telomeres of chromosomes."
Q#27865 - 	CGI_10028800	superfamily	243077	7	59	3.36E-14	67.5705	cl02542	DnaJ superfamily	 - 	 - 	"DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification."
Q#27865 - 	CGI_10028800	superfamily	243034	183	260	1.35E-12	64.3236	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#27865 - 	CGI_10028800	superfamily	247723	353	420	1.05E-08	52.3073	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27867 - 	CGI_10028802	superfamily	241599	139	197	2.36E-20	82.6764	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#27870 - 	CGI_10028805	superfamily	247727	81	178	6.44E-06	42.8023	cl17173	AdoMet_MTases superfamily	 - 	 - 	"S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I;  AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.)."
Q#27871 - 	CGI_10028806	superfamily	203013	590	617	1.06E-07	49.1614	cl04519	zf-HIT superfamily	 - 	 - 	HIT zinc finger; This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) that specifically interacts with the ligand binding domain of the thyroid receptor.
Q#27871 - 	CGI_10028806	superfamily	241638	218	293	0.000536806	39.2504	cl00147	TNF superfamily	C	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#27872 - 	CGI_10028807	superfamily	241638	136	279	0.00038333	38.48	cl00147	TNF superfamily	 - 	 - 	"Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding."
Q#27873 - 	CGI_10028808	superfamily	238191	221	334	9.74E-09	56.1864	cl18907	Esterase_lipase superfamily	C	 - 	"Esterases and lipases (includes fungal lipases, cholinesterases, etc.)  These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate."
Q#27873 - 	CGI_10028808	superfamily	242244	77	169	0.00646632	37.4033	cl01002	DUF808 superfamily	NC	 - 	Protein of unknown function (DUF808); This family consists of several bacterial proteins of unknown function.
Q#27874 - 	CGI_10028809	superfamily	248458	27	203	8.16E-07	49.2345	cl17904	MFS superfamily	C	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#27875 - 	CGI_10028810	superfamily	241599	118	176	7.94E-25	95.388	cl00084	homeodomain superfamily	 - 	 - 	"Homeodomain;  DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner."
Q#27876 - 	CGI_10028811	superfamily	246925	339	531	9.30E-17	81.2477	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27876 - 	CGI_10028811	superfamily	246925	589	734	1.21E-10	62.7582	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27876 - 	CGI_10028811	superfamily	247723	871	933	0.000357013	39.9422	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#27877 - 	CGI_10028812	superfamily	241810	981	1031	2.37E-12	64.073	cl00354	KOW superfamily	 - 	 - 	"KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues."
Q#27879 - 	CGI_10028814	superfamily	219852	61	547	1.05E-06	51.237	cl15656	Sfi1 superfamily	 - 	 - 	Sfi1 spindle body protein; This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organising centres.
Q#27880 - 	CGI_10028815	superfamily	222269	7	237	3.73E-41	149.781	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#27881 - 	CGI_10028816	superfamily	247856	8	57	0.000160562	36.7569	cl17302	EFh superfamily	N	 - 	"EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers."
Q#27883 - 	CGI_10028818	superfamily	241597	185	250	3.99E-20	85.7483	cl00082	HMG-box superfamily	 - 	 - 	"High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions."
Q#27883 - 	CGI_10028818	superfamily	248469	464	574	3.22E-09	55.4539	cl17915	HAD_like superfamily	 - 	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#27883 - 	CGI_10028818	superfamily	248469	617	682	2.53E-08	52.7575	cl17915	HAD_like superfamily	N	 - 	"Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases."
Q#27884 - 	CGI_10028819	superfamily	243836	3	128	5.24E-51	160.539	cl04661	Polysacc_synt_4 superfamily	 - 	 - 	Polysaccharide biosynthesis; This family of proteins plays a role in xylan biosynthesis in plant cell walls. Its precise role in xylan biosynthesis is unknown. Its function in other organisms is unknown.
Q#27885 - 	CGI_10028820	superfamily	243129	308	419	2.98E-26	101.947	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#27885 - 	CGI_10028820	superfamily	243129	148	253	7.42E-20	84.6037	cl02653	MA3 superfamily	 - 	 - 	"MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains."
Q#27887 - 	CGI_10021135	superfamily	242915	13	254	3.56E-58	187.192	cl02164	Utp11 superfamily	 - 	 - 	"Utp11 protein; This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome."
Q#27888 - 	CGI_10021136	superfamily	248012	85	197	6.75E-17	75.692	cl17458	TIR_2 superfamily	 - 	 - 	TIR domain; This is a family of bacterial Toll-like receptors.
Q#27889 - 	CGI_10021137	superfamily	243035	39	148	7.96E-26	95.7645	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27893 - 	CGI_10021141	superfamily	222313	78	118	1.69E-11	60.2834	cl18662	Methyltransf_32 superfamily	N	 - 	Methyltransferase domain; This family appears to be a methyltransferase domain.
Q#27894 - 	CGI_10021142	superfamily	247724	3	156	1.04E-47	158.853	cl17170	Ras_like_GTPase superfamily	N	 - 	"Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions."
Q#27895 - 	CGI_10021143	superfamily	241571	601	704	1.01E-07	51.6443	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#27895 - 	CGI_10021143	superfamily	238012	525	574	2.36E-07	49.6602	cl11390	EGF_Lam superfamily	 - 	 - 	"Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies"
Q#27895 - 	CGI_10021143	superfamily	243146	790	838	1.29E-06	47.2839	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27895 - 	CGI_10021143	superfamily	205157	383	421	1.34E-05	44.0655	cl18264	EGF_3 superfamily	 - 	 - 	EGF domain; This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein.
Q#27895 - 	CGI_10021143	superfamily	243146	845	896	0.00795086	36.1131	cl02701	Kelch_3 superfamily	 - 	 - 	"Galactose oxidase, central domain; Galactose oxidase, central domain.  "
Q#27896 - 	CGI_10021144	superfamily	241600	1	44	0.00315069	36.0643	cl00085	FReD superfamily	C	 - 	"Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation."
Q#27897 - 	CGI_10021145	superfamily	217311	47	518	9.90E-101	317.741	cl18402	DUF229 superfamily	 - 	 - 	Protein of unknown function (DUF229); Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Q#27898 - 	CGI_10021146	superfamily	247858	276	403	6.77E-17	78.1986	cl17304	2OG-FeII_Oxy_3 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#27898 - 	CGI_10021146	superfamily	247858	22	102	8.14E-05	40.8469	cl17304	2OG-FeII_Oxy_3 superfamily	 - 	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#27902 - 	CGI_10021150	superfamily	243035	78	148	2.24E-11	57.2445	cl02432	CLECT superfamily	C	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#27904 - 	CGI_10021152	superfamily	214531	612	652	6.47E-06	44.1297	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#27904 - 	CGI_10021152	superfamily	214531	566	609	7.33E-06	44.1297	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#27905 - 	CGI_10021153	superfamily	241568	676	712	0.00217836	37.0572	cl00043	CCP superfamily	N	 - 	"Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function."
Q#27905 - 	CGI_10021153	superfamily	241578	38	72	5.04E-05	44.298	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27905 - 	CGI_10021153	superfamily	214531	506	557	0.0017937	37.1961	cl18310	LY superfamily	 - 	 - 	Low-density lipoprotein-receptor YWTD domain; Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Q#27906 - 	CGI_10021154	superfamily	241643	341	371	0.000209272	38.9795	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#27906 - 	CGI_10021154	superfamily	241645	4	59	0.000106898	40.3715	cl00155	UBQ superfamily	 - 	 - 	"Ubiquitin-like proteins; Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate."
Q#27906 - 	CGI_10021154	superfamily	241643	390	426	0.000208411	38.9707	cl00153	UBA superfamily	 - 	 - 	"Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins."
Q#27907 - 	CGI_10010600	superfamily	241563	86	120	0.00379263	35.7759	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27908 - 	CGI_10010601	superfamily	215724	31	343	1.86E-147	421.257	cl14706	wnt superfamily	 - 	 - 	"wnt family; Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families."
Q#27912 - 	CGI_10010606	superfamily	207662	41	113	9.44E-31	114.196	cl02596	NR_DBD_like superfamily	 - 	 - 	"DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).  Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers."
Q#27912 - 	CGI_10010606	superfamily	245599	363	521	1.05E-13	68.7887	cl11397	NR_LBD superfamily	 - 	 - 	"The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR):  Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD)."
Q#27913 - 	CGI_10010607	superfamily	243034	391	490	1.40E-11	61.242	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#27913 - 	CGI_10010607	superfamily	222269	128	327	1.07E-15	75.823	cl18657	Cupin_8 superfamily	 - 	 - 	Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
Q#27915 - 	CGI_10010609	superfamily	243069	191	329	3.51E-05	42.74	cl02525	Band_7 superfamily	 - 	 - 	"The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podicin gene give rise to autosomal recessive steroid resistant nephritic syndrome"
Q#27916 - 	CGI_10010610	superfamily	245206	15	105	1.80E-29	106.553	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#27917 - 	CGI_10010611	superfamily	245206	46	136	2.99E-32	115.027	cl09931	NADB_Rossmann superfamily	N	 - 	"Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the  first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction."
Q#27918 - 	CGI_10005619	superfamily	219977	38	123	1.01E-19	85.4144	cl18539	Vps51 superfamily	 - 	 - 	"Vps51/Vps67; This family includes a presumed domain found in a number of components of vesicular transport. The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1. Cog1_N is the N-terminus of the Cog1 subunit of the eight-unit Conserved Oligomeric Golgi (COG) complex that participates in retrograde vesicular transport and is required to maintain normal Golgi structure and function. The subunits are located in two lobes and Cog1 serves to bind the two lobes together probably via the highly conserved N-terminal domain of approximately 85 residues."
Q#27919 - 	CGI_10005620	superfamily	241563	61	100	0.000153652	40.5404	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27921 - 	CGI_10009423	superfamily	116688	428	654	6.89E-141	421.448	cl06910	PROCN superfamily	C	 - 	PROCN (NUC071) domain; The PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family.
Q#27921 - 	CGI_10009423	superfamily	149261	113	264	6.24E-81	255.706	cl06909	PRO8NT superfamily	 - 	 - 	"PRO8NT (NUC069), PrP8 N-terminal domain; The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region."
Q#27922 - 	CGI_10009424	superfamily	111042	76	253	3.46E-19	85.895	cl17928	Ocular_alb superfamily	C	 - 	Ocular albinism type 1 protein; Ocular albinism type 1 protein.  
Q#27923 - 	CGI_10009425	superfamily	193607	457	589	5.74E-67	215.899	cl15237	Deltex_C superfamily	 - 	 - 	"Domain found at the C-terminus of deltex-like; The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures.  Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage."
Q#27923 - 	CGI_10009425	superfamily	247792	411	450	0.000196558	39.7364	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27923 - 	CGI_10009425	superfamily	207713	7	77	9.68E-13	64.2629	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#27923 - 	CGI_10009425	superfamily	207713	83	160	1.12E-09	55.4033	cl02729	WWE superfamily	 - 	 - 	WWE domain; The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Q#27925 - 	CGI_10009427	superfamily	247684	1	334	1.97E-68	228.33	cl17037	NBD_sugar-kinase_HSP70_actin superfamily	 - 	 - 	"Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; This superfamily includes the actin family, the HSP70 family of molecular chaperones and nucleotide exchange factors, the ROK (repressor, ORF, kinase) family, the hexokinase family, the FGGY family (which includes glycerol kinase and similar carbohydrate kinases such as rhamnulokinase and xylulokinase), the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase/nucleoside triphosphate diphosphohydrolase family, propionate kinase/acetate kinase family, glycerol dehydratase reactivase, 2-hydroxyglutaryl-CoA dehydratase component A, N-acetylglucosamine kinase, butyrate kinase 2, Escherichia coli YeaZ and similar glycoproteases, the cell shape-determining protein MreB, the plasmid DNA segregation factor ParM, cell cycle proteins FtsA, Pili assembly protein PilM, ethanolamine utilization protein EutJ, and similar proteins. The nucleotide-binding site residues are conserved; the nucleotide sits in a deep cleft formed between the two lobes of the nucleotide-binding domain (NBD). Substrate binding to superfamily members is associated with closure of this catalytic site cleft. The functional activities of several members of the superfamily, including hexokinases, actin, and HSP70s, are modulated by allosteric effectors, which may act on the cleft closure."
Q#27928 - 	CGI_10009430	superfamily	150838	44	204	1.85E-50	164.945	cl10913	DUF2216 superfamily	 - 	 - 	"Uncharacterized conserved proteins (DUF2216); This is the conserved N-terminal half of a proteins which are found from worms to humans. some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed."
Q#27929 - 	CGI_10009431	superfamily	241563	26	62	3.69E-06	44.3924	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27930 - 	CGI_10009432	superfamily	247858	131	228	9.32E-10	55.0866	cl17304	2OG-FeII_Oxy_3 superfamily	N	 - 	2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Q#27931 - 	CGI_10009433	superfamily	217920	55	446	7.92E-154	443.675	cl09557	ERO1 superfamily	 - 	 - 	Endoplasmic Reticulum Oxidoreductin 1 (ERO1); Members of this family are required for the formation of disulphide bonds in the ER.
Q#27932 - 	CGI_10009434	superfamily	240521	314	434	1.82E-16	81.1992	cl18940	Syo1_like superfamily	NC	 - 	"Fungal symportin 1 (syo1) and similar proteins; This family of eukaryotic proteins includes Saccharomyces cerevisiae Ydl063c and Chaetomium thermophilum Syo1, which mediate the co-import of two ribosomal proteins, Rpl5 and Rpl11 (which both interact with 5S rRNA) into the nucleus. Import precedes their association with rRNA and subsequent ribosome assembly in the nucleolus. The primary structure of syo1 is a mixture of Armadillo- (ARM, N-terminal part of syo1) and HEAT-repeats (C-terminal part of syo1)."
Q#27932 - 	CGI_10009434	superfamily	218373	486	517	0.00936493	34.6885	cl04882	SGS superfamily	C	 - 	"SGS domain; This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins."
Q#27933 - 	CGI_10009435	superfamily	219316	25	187	1.85E-78	234.423	cl06268	B9-C2 superfamily	 - 	 - 	"Ciliary basal body-associated, B9 protein; The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains. There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease. All the three distinct types of B9-C2 proteins cooperatively localise to the basal body or centrosome of cilia."
Q#27934 - 	CGI_10009436	superfamily	246902	208	400	1.29E-107	319.626	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#27934 - 	CGI_10009436	superfamily	246902	17	186	3.67E-77	240.668	cl15239	PLDc_SF superfamily	 - 	 - 	"Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group."
Q#27935 - 	CGI_10009438	superfamily	241754	6	730	0	662.424	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#27935 - 	CGI_10009438	superfamily	245596	1473	1754	2.03E-76	256.466	cl11394	Glyco_tranf_GTA_type superfamily	 - 	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#27935 - 	CGI_10009438	superfamily	245596	1396	1452	8.30E-10	60.3992	cl11394	Glyco_tranf_GTA_type superfamily	C	 - 	"Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein.  Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold.  This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities."
Q#27935 - 	CGI_10009438	superfamily	245166	1841	1905	0.00315337	39.881	cl09823	Trep_Strep superfamily	C	 - 	"Hypothetical bacterial integral membrane protein (Trep_Strep); This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. It is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6."
Q#27936 - 	CGI_10026753	superfamily	241594	314	545	4.63E-07	50.3815	cl00077	HECTc superfamily	 - 	 - 	"HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains."
Q#27938 - 	CGI_10026755	superfamily	242406	2	145	1.48E-21	86.4913	cl01271	DUF1768 superfamily	 - 	 - 	Domain of unknown function (DUF1768); This is a domain of unknown function. It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.
Q#27940 - 	CGI_10026757	superfamily	246925	80	220	0.00170199	39.261	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27940 - 	CGI_10026757	superfamily	214507	446	495	0.00240584	36.254	cl15307	LRRCT superfamily	 - 	 - 	Leucine rich repeat C-terminal domain; Leucine rich repeat C-terminal domain.  
Q#27943 - 	CGI_10026760	superfamily	241578	844	983	9.54E-13	67.3166	cl00057	vWFA superfamily	 - 	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27943 - 	CGI_10026760	superfamily	242197	9	117	9.22E-45	158.094	cl00928	dsDNA_bind superfamily	 - 	 - 	Double-stranded DNA-binding domain; This domain is believed to bind double-stranded DNA of 20 bases length.
Q#27943 - 	CGI_10026760	superfamily	152683	522	624	4.17E-07	49.2085	cl13656	Methyltransf_FA superfamily	 - 	 - 	"Farnesoic acid 0-methyl transferase; This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH)."
Q#27943 - 	CGI_10026760	superfamily	241578	688	824	5.48E-06	46.6125	cl00057	vWFA superfamily	N	 - 	"Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains."
Q#27943 - 	CGI_10026760	superfamily	246918	434	479	5.83E-05	42.1887	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27943 - 	CGI_10026760	superfamily	216897	367	430	9.97E-05	41.8981	cl03463	Gal_Lectin superfamily	 - 	 - 	Galactose binding lectin domain; Galactose binding lectin domain.  
Q#27944 - 	CGI_10026761	superfamily	241571	299	403	3.39E-17	77.4526	cl00049	CUB superfamily	 - 	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#27944 - 	CGI_10026761	superfamily	245847	50	125	0.00216275	36.7116	cl12042	FA58C superfamily	C	 - 	"Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes."
Q#27945 - 	CGI_10026762	superfamily	245303	2	142	3.41E-70	217.427	cl10447	GH18_chitinase-like superfamily	C	 - 	"The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods.  Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.  The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins.  The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model."
Q#27948 - 	CGI_10026765	superfamily	148067	95	196	2.22E-27	101.194	cl05643	DUF1011 superfamily	 - 	 - 	Protein of unknown function (DUF1011); Family of uncharacterized eukaryotic proteins.
Q#27950 - 	CGI_10026767	superfamily	246918	53	106	2.61E-09	51.0483	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27950 - 	CGI_10026767	superfamily	246918	1	47	7.92E-05	38.7219	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#27951 - 	CGI_10026768	superfamily	241547	3	231	6.28E-40	139.725	cl00012	alpha_CA superfamily	N	 - 	"Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer."
Q#27952 - 	CGI_10026769	superfamily	248097	294	417	8.75E-28	106.195	cl17543	C1q superfamily	 - 	 - 	C1q domain; C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
Q#27954 - 	CGI_10026771	superfamily	241564	12	80	1.48E-25	97.3363	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#27954 - 	CGI_10026771	superfamily	247792	258	296	0.000242833	38.1956	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27955 - 	CGI_10026772	superfamily	241564	150	218	5.36E-25	95.0251	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#27955 - 	CGI_10026772	superfamily	241564	6	71	5.83E-18	75.3799	cl00035	BIR superfamily	 - 	 - 	"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger."
Q#27956 - 	CGI_10026773	superfamily	241802	1	296	7.38E-51	176.909	cl00342	Trp-synth-beta_II superfamily	 - 	 - 	"Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine  to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine."
Q#27962 - 	CGI_10026779	superfamily	241563	68	109	2.94E-05	42.0812	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27962 - 	CGI_10026779	superfamily	241717	121	213	0.00121363	38.9795	cl00240	RRF superfamily	N	 - 	"Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation.  Thus ribosomes are "recycled" and ready for another round of protein synthesis.  RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear.  RRF is essential for bacterial growth.  It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species."
Q#27964 - 	CGI_10026781	superfamily	241563	76	117	5.14E-06	43.622	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27965 - 	CGI_10026782	superfamily	246669	682	836	5.36E-71	232.583	cl14603	C2 superfamily	 - 	 - 	"C2 domain; The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins.  Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1.  However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain.  C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions."
Q#27965 - 	CGI_10026782	superfamily	128928	520	576	1.99E-15	72.7172	cl02734	DM14 superfamily	 - 	 - 	"Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.  "
Q#27965 - 	CGI_10026782	superfamily	128928	368	422	2.24E-15	72.332	cl02734	DM14 superfamily	 - 	 - 	"Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.  "
Q#27965 - 	CGI_10026782	superfamily	128928	269	324	6.73E-13	65.3984	cl02734	DM14 superfamily	 - 	 - 	"Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.  "
Q#27965 - 	CGI_10026782	superfamily	128928	137	193	1.00E-10	59.2352	cl02734	DM14 superfamily	 - 	 - 	"Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.  "
Q#27966 - 	CGI_10026783	superfamily	247792	263	306	4.57E-08	51.6776	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27966 - 	CGI_10026783	superfamily	149746	4	76	2.34E-24	99.2258	cl07884	DWNN superfamily	 - 	 - 	DWNN domain; DWNN is a ubiquitin like domain found at the N terminus of the RBBP6 family of splicing-associated proteins. The DWNN domain is independently expressed in higher vertebrates so it may function as a novel ubiquitin-like modifier of other proteins.
Q#27967 - 	CGI_10026784	superfamily	241754	13	348	8.15E-171	517.601	cl00286	Motor_domain superfamily	 - 	 - 	Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Q#27967 - 	CGI_10026784	superfamily	247746	343	436	0.00535037	37.7463	cl17192	ATP-synt_B superfamily	N	 - 	"ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006"
Q#27968 - 	CGI_10026785	superfamily	243106	2030	2149	4.28E-54	187.224	cl02608	BAH superfamily	 - 	 - 	"BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions."
Q#27970 - 	CGI_10026787	superfamily	215733	23	61	8.30E-06	47.1747	cl02811	E1-E2_ATPase superfamily	C	 - 	E1-E2 ATPase; E1-E2 ATPase.  
Q#27970 - 	CGI_10026787	superfamily	218499	1045	1131	0.00859504	38.5601	cl04986	ALG3 superfamily	NC	 - 	"ALG3 protein; The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl pyrophosphate. Whereas early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9GlcNAc2-PP-Dol on the lumenal side use Dol-P-Man. ALG3 gene encodes the Dol-P-Man:Man5GlcNAc2-PP-Dol mannosyltransferase."
Q#27971 - 	CGI_10026788	superfamily	246925	263	389	1.60E-08	55.0542	cl15309	LRR_RI superfamily	N	 - 	"Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1)."
Q#27972 - 	CGI_10026789	superfamily	241774	64	224	2.85E-34	121.505	cl00313	Ribosomal_S7 superfamily	 - 	 - 	Ribosomal protein S7p/S5e; This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.
Q#27974 - 	CGI_10026791	superfamily	241813	49	110	3.41E-11	55.5966	cl00359	Ribosomal_L27 superfamily	 - 	 - 	Ribosomal L27 protein; Ribosomal L27 protein.  
Q#27976 - 	CGI_10026793	superfamily	241563	62	103	3.24E-05	41.696	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#27980 - 	CGI_10026797	superfamily	248281	72	144	7.81E-11	57.6655	cl17727	GT1 superfamily	 - 	 - 	"GT1, myb-like, SANT family; GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcrtiption pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resemble the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins."
Q#27980 - 	CGI_10026797	superfamily	241750	231	360	4.85E-07	49.1091	cl00281	metallo-dependent_hydrolases superfamily	C	 - 	"Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase  dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others."
Q#27988 - 	CGI_10007779	superfamily	149667	41	140	1.93E-08	50.0615	cl07343	GON superfamily	N	 - 	GON domain; The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues.
Q#27990 - 	CGI_10007781	superfamily	247794	14	248	3.82E-37	134.186	cl17240	FDH_GDH_like superfamily	 - 	 - 	"Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases."
Q#27991 - 	CGI_10008930	superfamily	241782	70	539	6.08E-106	326.352	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27992 - 	CGI_10008931	superfamily	241782	79	460	1.80E-77	253.448	cl00321	AAT_I superfamily	 - 	 - 	"Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of  the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V)."
Q#27993 - 	CGI_10008932	superfamily	247792	24	72	0.0070601	35.4992	cl17238	RING superfamily	 - 	 - 	"RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)"
Q#27994 - 	CGI_10008933	superfamily	219941	1042	1208	5.59E-78	254.44	cl07298	TIP120 superfamily	 - 	 - 	TATA-binding protein interacting (TIP20); TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription.
Q#27999 - 	CGI_10008938	superfamily	241563	65	103	0.00197564	36.3032	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#28001 - 	CGI_10008940	superfamily	243035	47	171	1.07E-15	75.7341	cl02432	CLECT superfamily	 - 	 - 	"C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins.  This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs.  Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice.  Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis;  P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration.  CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose.  Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors.  C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces.  Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model.  In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer.  A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome.  Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model."
Q#28001 - 	CGI_10008940	superfamily	241613	184	204	1.71E-05	44.1198	cl00104	LDLa superfamily	C	 - 	"Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure"
Q#28001 - 	CGI_10008940	superfamily	241571	227	261	0.00197434	38.5252	cl00049	CUB superfamily	C	 - 	"CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast."
Q#28002 - 	CGI_10008941	superfamily	245010	14	118	9.20E-13	59.9391	cl09111	Prefoldin superfamily	 - 	 - 	"Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly.  The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils."
Q#28003 - 	CGI_10008942	superfamily	247799	61	177	1.05E-45	153.554	cl17245	KH-I superfamily	 - 	 - 	"K homology RNA-binding domain, type I.  KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension."
Q#28004 - 	CGI_10013873	superfamily	243034	214	295	3.81E-09	53.1528	cl02429	TPR superfamily	 - 	 - 	"Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here"
Q#28004 - 	CGI_10013873	superfamily	215821	97	184	1.91E-18	79.2066	cl18346	FKBP_C superfamily	 - 	 - 	FKBP-type peptidyl-prolyl cis-trans isomerase; FKBP-type peptidyl-prolyl cis-trans isomerase.  
Q#28005 - 	CGI_10013874	superfamily	247723	34	126	3.91E-48	168.976	cl17169	RRM_SF superfamily	 - 	 - 	"RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs)."
Q#28005 - 	CGI_10013874	superfamily	243061	724	825	2.13E-29	115.517	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	409	508	8.50E-18	82.0046	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	1520	1616	1.46E-17	81.2342	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	1625	1728	3.07E-17	80.4638	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	521	610	2.09E-16	77.7674	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	992	1094	2.17E-16	77.7674	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	309	400	2.25E-14	71.9894	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	1097	1196	2.98E-13	68.5226	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	189	291	3.39E-11	62.7446	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	1731	1828	4.24E-11	62.3594	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	1417	1507	1.27E-09	57.8618	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	627	717	1.74E-09	57.4766	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	1225	1301	6.17E-07	49.7726	cl02509	SRCR superfamily	N	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28005 - 	CGI_10013874	superfamily	243061	893	963	0.00444146	37.7066	cl02509	SRCR superfamily	 - 	 - 	Scavenger receptor cysteine-rich domain; These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Q#28006 - 	CGI_10013875	superfamily	192073	5	80	2.21E-29	101.161	cl07254	Yos1 superfamily	 - 	 - 	"Yos1-like; In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Yos1 appears to be conserved in eukaryotes."
Q#28007 - 	CGI_10013876	superfamily	241563	71	104	0.00806234	34.7624	cl00034	BBOX superfamily	 - 	 - 	"B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction."
Q#28009 - 	CGI_10013878	superfamily	241672	37	469	6.57E-110	335.525	cl00192	ribokinase_pfkB_like superfamily	 - 	 - 	"ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric  (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase)."
Q#28010 - 	CGI_10013879	superfamily	248458	69	439	1.94E-23	100.081	cl17904	MFS superfamily	 - 	 - 	"The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated."
Q#28011 - 	CGI_10013880	superfamily	241677	28	191	2.38E-87	257.185	cl00197	cyclophilin superfamily	 - 	 - 	"cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA).  Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin.   PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system;  human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing."
Q#28012 - 	CGI_10013881	superfamily	241583	226	434	1.95E-91	295.302	cl00064	ZnMc superfamily	 - 	 - 	"Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease."
Q#28012 - 	CGI_10013881	superfamily	216572	22	166	3.35E-28	112.368	cl03265	Pep_M12B_propep superfamily	 - 	 - 	Reprolysin family propeptide; This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Q#28012 - 	CGI_10013881	superfamily	246918	530	582	1.67E-15	73.3899	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#28012 - 	CGI_10013881	superfamily	246918	1340	1390	8.24E-07	48.3519	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#28012 - 	CGI_10013881	superfamily	246918	981	1028	8.64E-05	42.1887	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#28012 - 	CGI_10013881	superfamily	246918	1289	1334	0.00244309	37.7702	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#28012 - 	CGI_10013881	superfamily	246918	1228	1285	0.00790784	36.4107	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#28013 - 	CGI_10013882	superfamily	242392	11	169	7.74E-64	196.232	cl01251	OHCU_decarbox superfamily	 - 	 - 	OHCU decarboxylase; The proteins in this family are OHCU decarboxylase - enzymes of the purine catabolism that catalyze the conversion of OHCU into S(+)-allantoin. This is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalyzed by urate oxidase (pfam01014) and step two is catalyzed by HIUases (pfam00576).
Q#28014 - 	CGI_10013883	superfamily	245814	29	101	1.38E-05	42.0911	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#28014 - 	CGI_10013883	superfamily	245814	154	227	2.49E-05	41.2137	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#28017 - 	CGI_10013886	superfamily	245814	93	167	0.000647225	36.3131	cl11960	Ig superfamily	 - 	 - 	"Immunoglobulin domain; Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond."
Q#28018 - 	CGI_10013887	superfamily	217685	77	185	8.07E-26	98.9456	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#28018 - 	CGI_10013887	superfamily	216290	15	53	7.33E-13	62.3058	cl03089	Cu2_monooxygen superfamily	N	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#28019 - 	CGI_10013888	superfamily	216290	27	55	0.00134609	32.6454	cl03089	Cu2_monooxygen superfamily	NC	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#28020 - 	CGI_10013889	superfamily	217685	87	232	7.71E-49	161.733	cl04225	Cu2_monoox_C superfamily	 - 	 - 	"Copper type II ascorbate-dependent monooxygenase, C-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#28020 - 	CGI_10013889	superfamily	216290	11	61	2.70E-17	75.7877	cl03089	Cu2_monooxygen superfamily	N	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#28021 - 	CGI_10013890	superfamily	216290	73	122	3.74E-09	49.9794	cl03089	Cu2_monooxygen superfamily	C	 - 	"Copper type II ascorbate-dependent monooxygenase, N-terminal domain; The N and C-terminal domains of members of this family adopt the same PNGase F-like fold."
Q#28024 - 	CGI_10013893	superfamily	247692	196	546	3.15E-45	163.616	cl17068	AFD_class_I superfamily	 - 	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#28024 - 	CGI_10013893	superfamily	247692	49	221	1.08E-09	59.4827	cl17068	AFD_class_I superfamily	C	 - 	"Adenylate forming domain, Class I; This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain."
Q#28026 - 	CGI_10003117	superfamily	245225	1	202	1.80E-25	101.234	cl10011	Periplasmic_Binding_Protein_Type_1 superfamily	C	 - 	"Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has  six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold."
Q#28027 - 	CGI_10003118	superfamily	246918	4	55	2.04E-10	52.5891	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.  
Q#28027 - 	CGI_10003118	superfamily	246918	60	111	2.04E-10	52.5891	cl15278	TSP_1 superfamily	 - 	 - 	Thrombospondin type 1 domain; Thrombospondin type 1 domain.